Daily Papers

Deep learning models achieve state-of-the art results in predicting blood glucose trajectories, with a wide range of architectures being proposed. However, the adaptation of such models in clinical practice is slow, largely due to the lack of uncertainty quantification of provided predictions. In this work, we propose to model the future glucose trajectory conditioned on the past as an infinite mixture of basis distributions (i.e., Gaussian, Laplace, etc.). This change allows us to learn the uncertainty and predict more accurately in the cases when the trajectory has a heterogeneous or multi-modal distribution. To estimate the parameters of the predictive distribution, we utilize the Transformer architecture. We empirically demonstrate the superiority of our method over existing state-of-the-art techniques both in terms of accuracy and uncertainty on the synthetic and benchmark glucose data sets.

Postprandial hyperglycemia, marked by the blood glucose level exceeding the normal range after meals, is a critical indicator of progression toward type 2 diabetes in prediabetic and healthy individuals. A key metric for understanding blood glucose dynamics after eating is the postprandial area under the curve (PAUC). Predicting PAUC in advance based on a person's diet and activity level and explaining what affects postprandial blood glucose could allow an individual to adjust their lifestyle accordingly to maintain normal glucose levels. In this paper, we propose GlucoLens, an explainable machine learning approach to predict PAUC and hyperglycemia from diet, activity, and recent glucose patterns. We conducted a five-week user study with 10 full-time working individuals to develop and evaluate the computational model. Our machine learning model takes multimodal data including fasting glucose, recent glucose, recent activity, and macronutrient amounts, and provides an interpretable prediction of the postprandial glucose pattern. Our extensive analyses of the collected data revealed that the trained model achieves a normalized root mean squared error (NRMSE) of 0.123. On average, GlucoLense with a Random Forest backbone provides a 16% better result than the baseline models. Additionally, GlucoLens predicts hyperglycemia with an accuracy of 74% and recommends different options to help avoid hyperglycemia through diverse counterfactual explanations. Code available: https://github.com/ab9mamun/GlucoLens.

Precise glucose level monitoring is critical for people with diabetes to avoid serious complications. While there are several methods for continuous glucose level monitoring, research on maintenance devices is limited. To mitigate the gap, we provide a novel neural control system for continuous glucose monitoring and management that uses differential predictive control. Our approach, led by a sophisticated neural policy and differentiable modeling, constantly adjusts insulin supply in real-time, thereby improving glucose level optimization in the body. This end-to-end method maximizes efficiency, providing personalized care and improved health outcomes, as confirmed by empirical evidence.

Objective digital data is scarce yet needed in many domains to enable research that can transform the standard of healthcare. While data from consumer-grade wearables and smartphones is more accessible, there is critical need for similar data from clinical-grade devices used by patients with a diagnosed condition. The prevalence of wearable medical devices in the diabetes domain sets the stage for unique research and development within this field and beyond. However, the scarcity of open-source datasets presents a major barrier to progress. To facilitate broader research on diabetes-relevant problems and accelerate development of robust computational solutions, we provide the DiaTrend dataset. The DiaTrend dataset is composed of intensive longitudinal data from wearable medical devices, including a total of 27,561 days of continuous glucose monitor data and 8,220 days of insulin pump data from 54 patients with diabetes. This dataset is useful for developing novel analytic solutions that can reduce the disease burden for people living with diabetes and increase knowledge on chronic condition management in outpatient settings.

Cell tracking is a subject of active research gathering great interest in medicine and biology. Positron emission tomography (PET) is well suited for tracking radio-labeled cells in vivo due to its exceptional sensitivity and whole-body capability. For validation, ground-truth data are desirable that realistically mimic the flow of cells in a clinical situation. This study develops a workflow (CeFloPS) for simulating moving radio-labeled cells in a human phantom. From the XCAT phantom, the blood vessels are reduced to nodal networks along which cells can move and distribute to organs and tissues. The movement is directed by the blood flow, which is calculated in each node using the Hagen-Pooiseuille equation and Kirchhoff's laws assuming laminar flow. Organs are voxelized and movement of cells from artery entry to vein exit is generated via a biased 3D random walk. The probabilities of cells moving or remaining in tissues are derived from rate constants of tracer kinetic-based compartment modeling. PET listmode data is generated using the Monte-Carlo simulation framework GATE based on the definition of a large-body PET scanner with cell paths as moving radioactive sources and the XCAT phantom providing attenuation data. From the flow simulation of 100,000 cells, 100 sample cells were further processed by GATE and listmode data was reconstructed into images for comparison. As demonstrated by comparisons of simulated and reconstructed cell distributions, CeFloPS is capable of simulating cell behavior in whole-body PET. It achieves this simulation in a way that is anatomically and physiologically reasonable, thereby providing valuable data for the development and validation of cell tracking algorithms.

When humans read or listen, they make implicit commonsense inferences that frame their understanding of what happened and why. As a step toward AI systems that can build similar mental models, we introduce GLUCOSE, a large-scale dataset of implicit commonsense causal knowledge, encoded as causal mini-theories about the world, each grounded in a narrative context. To construct GLUCOSE, we drew on cognitive psychology to identify ten dimensions of causal explanation, focusing on events, states, motivations, and emotions. Each GLUCOSE entry includes a story-specific causal statement paired with an inference rule generalized from the statement. This paper details two concrete contributions. First, we present our platform for effectively crowdsourcing GLUCOSE data at scale, which uses semi-structured templates to elicit causal explanations. Using this platform, we collected a total of ~670K specific statements and general rules that capture implicit commonsense knowledge about everyday situations. Second, we show that existing knowledge resources and pretrained language models do not include or readily predict GLUCOSE's rich inferential content. However, when state-of-the-art neural models are trained on this knowledge, they can start to make commonsense inferences on unseen stories that match humans' mental models.

Accurate nutrition estimation helps people make informed dietary choices and is essential in the prevention of serious health complications. We present NutriBench, the first publicly available natural language meal description nutrition benchmark. NutriBench consists of 11,857 meal descriptions generated from real-world global dietary intake data. The data is human-verified and annotated with macro-nutrient labels, including carbohydrates, proteins, fats, and calories. We conduct an extensive evaluation of NutriBench on the task of carbohydrate estimation, testing twelve leading Large Language Models (LLMs), including GPT-4o, Llama3.1, Qwen2, Gemma2, and OpenBioLLM models, using standard, Chain-of-Thought and Retrieval-Augmented Generation strategies. Additionally, we present a study involving professional nutritionists, finding that LLMs can provide more accurate and faster estimates. Finally, we perform a real-world risk assessment by simulating the effect of carbohydrate predictions on the blood glucose levels of individuals with diabetes. Our work highlights the opportunities and challenges of using LLMs for nutrition estimation, demonstrating their potential to aid professionals and laypersons and improve health outcomes. Our benchmark is publicly available at: https://mehak126.github.io/nutribench.html

User profiling and region analysis are two tasks of significant commercial value. However, in practical applications, modeling different features typically involves four main steps: data preparation, data processing, model establishment, evaluation, and optimization. This process is time-consuming and labor-intensive. Repeating this workflow for each feature results in abundant development time for tasks and a reduced overall volume of task development. Indeed, human mobility data contains a wealth of information. Several successful cases suggest that conducting in-depth analysis of population movement data could potentially yield meaningful profiles about users and areas. Nonetheless, most related works have not thoroughly utilized the semantic information within human mobility data and trained on a fixed number of the regions. To tap into the rich information within population movement, based on the perspective that Regions Are Who walk them, we propose a large spatiotemporal model based on trajectories (RAW). It possesses the following characteristics: 1) Tailored for trajectory data, introducing a GPT-like structure with a parameter count of up to 1B; 2) Introducing a spatiotemporal fine-tuning module, interpreting trajectories as collection of users to derive arbitrary region embedding. This framework allows rapid task development based on the large spatiotemporal model. We conducted extensive experiments to validate the effectiveness of our proposed large spatiotemporal model. It's evident that our proposed method, relying solely on human mobility data without additional features, exhibits a certain level of relevance in user profiling and region analysis. Moreover, our model showcases promising predictive capabilities in trajectory generation tasks based on the current state, offering the potential for further innovative work utilizing this large spatiotemporal model.

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

A significant number of traffic crashes are secondary crashes that occur because of an earlier incident on the road. Thus, early detection of traffic incidents is crucial for road users from safety perspectives with a potential to reduce the risk of secondary crashes. The wide availability of GPS devices now-a-days gives an opportunity of tracking and recording vehicle trajectories. The objective of this study is to use vehicle trajectory data for advance real-time detection of traffic incidents on highways using machine learning-based algorithms. The study uses three days of unevenly sequenced vehicle trajectory data and traffic incident data on I-10, one of the most crash-prone highways in Louisiana. Vehicle trajectories are converted to trajectories based on virtual detector locations to maintain spatial uniformity as well as to generate historical traffic data for machine learning algorithms. Trips matched with traffic incidents on the way are separated and along with other trips with similar spatial attributes are used to build a database for modeling. Multiple machine learning algorithms such as Logistic Regression, Random Forest, Extreme Gradient Boost, and Artificial Neural Network models are used to detect a trajectory that is likely to face an incident in the downstream road section. Results suggest that the Random Forest model achieves the best performance for predicting an incident with reasonable recall value and discrimination capability.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

Rapid growth of high-dimensional datasets in fields such as single-cell RNA sequencing and spatial genomics has led to unprecedented opportunities for scientific discovery, but it also presents unique computational and statistical challenges. Traditional methods struggle with geometry-aware data generation, interpolation along meaningful trajectories, and transporting populations via feasible paths. To address these issues, we introduce Geometry-Aware Generative Autoencoder (GAGA), a novel framework that combines extensible manifold learning with generative modeling. GAGA constructs a neural network embedding space that respects the intrinsic geometries discovered by manifold learning and learns a novel warped Riemannian metric on the data space. This warped metric is derived from both the points on the data manifold and negative samples off the manifold, allowing it to characterize a meaningful geometry across the entire latent space. Using this metric, GAGA can uniformly sample points on the manifold, generate points along geodesics, and interpolate between populations across the learned manifold using geodesic-guided flows. GAGA shows competitive performance in simulated and real-world datasets, including a 30% improvement over the state-of-the-art methods in single-cell population-level trajectory inference.

The field of trajectory forecasting has grown significantly in recent years, partially owing to the release of numerous large-scale, real-world human trajectory datasets for autonomous vehicles (AVs) and pedestrian motion tracking. While such datasets have been a boon for the community, they each use custom and unique data formats and APIs, making it cumbersome for researchers to train and evaluate methods across multiple datasets. To remedy this, we present trajdata: a unified interface to multiple human trajectory datasets. At its core, trajdata provides a simple, uniform, and efficient representation and API for trajectory and map data. As a demonstration of its capabilities, in this work we conduct a comprehensive empirical evaluation of existing trajectory datasets, providing users with a rich understanding of the data underpinning much of current pedestrian and AV motion forecasting research, and proposing suggestions for future datasets from these insights. trajdata is permissively licensed (Apache 2.0) and can be accessed online at https://github.com/NVlabs/trajdata

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

The prediction of ship trajectories is a growing field of study in artificial intelligence. Traditional methods rely on the use of LSTM, GRU networks, and even Transformer architectures for the prediction of spatio-temporal series. This study proposes a viable alternative for predicting these trajectories using only GNSS positions. It considers this spatio-temporal problem as a natural language processing problem. The latitude/longitude coordinates of AIS messages are transformed into cell identifiers using the H3 index. Thanks to the pseudo-octal representation, it becomes easier for language models to learn the spatial hierarchy of the H3 index. The method is compared with a classical Kalman filter, widely used in the maritime domain, and introduces the Fr\'echet distance as the main evaluation metric. We show that it is possible to predict ship trajectories quite precisely up to 8 hours with 30 minutes of context. We demonstrate that this alternative works well enough to predict trajectories worldwide.

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

Diabetes, resulting from inadequate insulin production or utilization, causes extensive harm to the body. Existing diagnostic methods are often invasive and come with drawbacks, such as cost constraints. Although there are machine learning models like Classwise k Nearest Neighbor (CkNN) and General Regression Neural Network (GRNN), they struggle with imbalanced data and result in under-performance. Leveraging advancements in sensor technology and machine learning, we propose a non-invasive diabetes diagnosis using a Back Propagation Neural Network (BPNN) with batch normalization, incorporating data re-sampling and normalization for class balancing. Our method addresses existing challenges such as limited performance associated with traditional machine learning. Experimental results on three datasets show significant improvements in overall accuracy, sensitivity, and specificity compared to traditional methods. Notably, we achieve accuracies of 89.81% in Pima diabetes dataset, 75.49% in CDC BRFSS2015 dataset, and 95.28% in Mesra Diabetes dataset. This underscores the potential of deep learning models for robust diabetes diagnosis. See project website https://steve-zeyu-zhang.github.io/DiabetesDiagnosis/

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

Diabetes is a chronic disease that poses a significant global health burden, and optimizing diabetes management requires multi-stakeholder collaboration. Large language models (LLMs) have shown promise in various healthcare scenarios, but their effectiveness across a diverse range of diabetes tasks remains unproven. In this study, we introduced a framework to train and validate diabetes-specific LLMs. We first developed a comprehensive data processing pipeline that includes data collection, filtering, augmentation and refinement. This approach contributes to creating a high-quality, diabetes-specific dataset, and several evaluation benchmarks entirely from scratch. Utilizing the collected training dataset, we fine-tuned a diabetes-specific LLM family that demonstrated state-of-the-art proficiency in understanding and processing various diabetes tasks compared to other LLMs. Furthermore, clinical studies showed the potential applications of our models in diabetes care, including providing personalized healthcare, assisting medical education, and streamlining clinical tasks. In conclusion, our study introduced a framework to develop and evaluate a diabetes-specific LLM family, and highlighted its potential to enhance clinical practice and provide personalized, data-driven support for diabetes support when facing different end users. The code is provided via GitHub at https://github.com/waltonfuture/Diabetica.

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA

Purpose: Magnetic resonance imaging (MRI) to visualize anatomical motion is becoming increasingly important when treating cancer patients with radiotherapy. Hybrid MRI-linear accelerator (MRI-linac) systems allow real-time motion management during irradiation. This paper presents a multi-institutional real-time MRI time series dataset from different MRI-linac vendors. The dataset is designed to support developing and evaluating real-time tumor localization (tracking) algorithms for MRI-guided radiotherapy within the TrackRAD2025 challenge (https://trackrad2025.grand-challenge.org/). Acquisition and validation methods: The dataset consists of sagittal 2D cine MRIs in 585 patients from six centers (3 Dutch, 1 German, 1 Australian, and 1 Chinese). Tumors in the thorax, abdomen, and pelvis acquired on two commercially available MRI-linacs (0.35 T and 1.5 T) were included. For 108 cases, irradiation targets or tracking surrogates were manually segmented on each temporal frame. The dataset was randomly split into a public training set of 527 cases (477 unlabeled and 50 labeled) and a private testing set of 58 cases (all labeled). Data Format and Usage Notes: The data is publicly available under the TrackRAD2025 collection: https://doi.org/10.57967/hf/4539. Both the images and segmentations for each patient are available in metadata format. Potential Applications: This novel clinical dataset will enable the development and evaluation of real-time tumor localization algorithms for MRI-guided radiotherapy. By enabling more accurate motion management and adaptive treatment strategies, this dataset has the potential to advance the field of radiotherapy significantly.

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.

Automated Vehicles (AVs) promise significant advances in transportation. Critical to these improvements is understanding AVs' longitudinal behavior, relying heavily on real-world trajectory data. Existing open-source trajectory datasets of AV, however, often fall short in refinement, reliability, and completeness, hindering effective performance metrics analysis and model development. This study addresses these challenges by creating a Unified Longitudinal TRAjectory dataset for AVs (Ultra-AV) to analyze their microscopic longitudinal driving behaviors. This dataset compiles data from 13 distinct sources, encompassing various AV types, test sites, and experiment scenarios. We established a three-step data processing: 1. extraction of longitudinal trajectory data, 2. general data cleaning, and 3. data-specific cleaning to obtain the longitudinal trajectory data and car-following trajectory data. The validity of the processed data is affirmed through performance evaluations across safety, mobility, stability, and sustainability, along with an analysis of the relationships between variables in car-following models. Our work not only furnishes researchers with standardized data and metrics for longitudinal AV behavior studies but also sets guidelines for data collection and model development.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static structures, neglecting the fact that physical systems are always dynamic in nature. In this work, we propose geometric trajectory diffusion models (GeoTDM), the first diffusion model for modeling the temporal distribution of 3D geometric trajectories. Modeling such distribution is challenging as it requires capturing both the complex spatial interactions with physical symmetries and temporal correspondence encapsulated in the dynamics. We theoretically justify that diffusion models with equivariant temporal kernels can lead to density with desired symmetry, and develop a novel transition kernel leveraging SE(3)-equivariant spatial convolution and temporal attention. Furthermore, to induce an expressive trajectory distribution for conditional generation, we introduce a generalized learnable geometric prior into the forward diffusion process to enhance temporal conditioning. We conduct extensive experiments on both unconditional and conditional generation in various scenarios, including physical simulation, molecular dynamics, and pedestrian motion. Empirical results on a wide suite of metrics demonstrate that GeoTDM can generate realistic geometric trajectories with significantly higher quality.

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty. Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7. We show that methylation profiles predicted by multi-mean GPs can be used to estimate other phenotypes, such as epigenetic age, and enable comparison to other health measures of interest. This approach encourages epigenetic studies to move towards longitudinal design for investigating epigenetic changes during development, ageing and disease progression.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

We present Vehicle Energy Dataset (VED), a novel large-scale dataset of fuel and energy data collected from 383 personal cars in Ann Arbor, Michigan, USA. This open dataset captures GPS trajectories of vehicles along with their time-series data of fuel, energy, speed, and auxiliary power usage. A diverse fleet consisting of 264 gasoline vehicles, 92 HEVs, and 27 PHEV/EVs drove in real-world from Nov, 2017 to Nov, 2018, where the data were collected through onboard OBD-II loggers. Driving scenarios range from highways to traffic-dense downtown area in various driving conditions and seasons. In total, VED accumulates approximately 374,000 miles. We discuss participant privacy protection and develop a method to de-identify personally identifiable information while preserving the quality of the data. After the de-identification, we conducted case studies on the dataset to investigate the impacts of factors known to affect fuel economy and identify energy-saving opportunities that hybrid-electric vehicles and eco-driving techniques can provide. The case studies are supplemented with a number of examples to demonstrate how VED can be utilized for vehicle energy and behavior studies. Potential research opportunities include data-driven vehicle energy consumption modeling, driver behavior modeling, machine and deep learning, calibration of traffic simulators, optimal route choice modeling, prediction of human driver behaviors, and decision making of self-driving cars. We believe that VED can be an instrumental asset to the development of future automotive technologies. The dataset can be accessed at https://github.com/gsoh/VED.

Gaussian processes (GPs) are popular nonparametric statistical models for learning unknown functions and quantifying the spatiotemporal uncertainty in data. Recent works have extended GPs to model scalar and vector quantities distributed over non-Euclidean domains, including smooth manifolds appearing in numerous fields such as computer vision, dynamical systems, and neuroscience. However, these approaches assume that the manifold underlying the data is known, limiting their practical utility. We introduce RVGP, a generalisation of GPs for learning vector signals over latent Riemannian manifolds. Our method uses positional encoding with eigenfunctions of the connection Laplacian, associated with the tangent bundle, readily derived from common graph-based approximation of data. We demonstrate that RVGP possesses global regularity over the manifold, which allows it to super-resolve and inpaint vector fields while preserving singularities. Furthermore, we use RVGP to reconstruct high-density neural dynamics derived from low-density EEG recordings in healthy individuals and Alzheimer's patients. We show that vector field singularities are important disease markers and that their reconstruction leads to a comparable classification accuracy of disease states to high-density recordings. Thus, our method overcomes a significant practical limitation in experimental and clinical applications.

Large language models (LLMs) have made remarkable strides in various natural language processing tasks, but their performance on complex reasoning problems remains hindered by a lack of explainability and trustworthiness. This issue, often manifesting as hallucinations or unattributable reasoning processes, limits their applicability in complex reasoning scenarios. To address this, we propose Knowledge Graph-constrained Trajectory Reasoning Attribution and Chain Explanation Supervision (KG-TRACES), a novel framework that enhances the reasoning ability of LLMs through explicit supervision over reasoning paths and processes. KG-TRACES jointly supervises the model to: (1) predict symbolic relation paths, (2) predict full triple-level reasoning paths, and (3) generate attribution-aware reasoning processes grounded in the reasoning paths. At inference phase, the model adapts to both KG-available and KG-unavailable scenarios, retrieving reasoning paths from a KG when possible or predicting plausible reasoning paths with only intrinsic knowledge when not. This design enables the model to reason in an explainable and source-attributable pattern. Through extensive experiments on complex reasoning tasks, we demonstrate that KG-TRACES significantly outperforms existing SOTA: it improves Hits@1 by 1.6% and F1 by 4.7% on WebQSP, and achieves improvements of 4.8% in Hits@1 and 2.1% in F1 on CWQ. Moreover, we show its transferability to specialized domains such as medicine. By visualizing the intermediate steps of reasoning processes, we further show that the explicit supervision introduced by KG-TRACES leads to more stable and goal-directed reasoning processes, aligning closely with correct answers. Code is available at https://github.com/Edaizi/KG-TRACES.

Time series are the primary data type used to record dynamic system measurements and generated in great volume by both physical sensors and online processes (virtual sensors). Time series analytics is therefore crucial to unlocking the wealth of information implicit in available data. With the recent advancements in graph neural networks (GNNs), there has been a surge in GNN-based approaches for time series analysis. These approaches can explicitly model inter-temporal and inter-variable relationships, which traditional and other deep neural network-based methods struggle to do. In this survey, we provide a comprehensive review of graph neural networks for time series analysis (GNN4TS), encompassing four fundamental dimensions: forecasting, classification, anomaly detection, and imputation. Our aim is to guide designers and practitioners to understand, build applications, and advance research of GNN4TS. At first, we provide a comprehensive task-oriented taxonomy of GNN4TS. Then, we present and discuss representative research works and introduce mainstream applications of GNN4TS. A comprehensive discussion of potential future research directions completes the survey. This survey, for the first time, brings together a vast array of knowledge on GNN-based time series research, highlighting foundations, practical applications, and opportunities of graph neural networks for time series analysis.

Tool tracking in surgical videos is essential for advancing computer-assisted interventions, such as skill assessment, safety zone estimation, and human-machine collaboration. However, the lack of context-rich datasets limits AI applications in this field. Existing datasets rely on overly generic tracking formalizations that fail to capture surgical-specific dynamics, such as tools moving out of the camera's view or exiting the body. This results in less clinically relevant trajectories and a lack of flexibility for real-world surgical applications. Methods trained on these datasets often struggle with visual challenges such as smoke, reflection, and bleeding, further exposing the limitations of current approaches. We introduce CholecTrack20, a specialized dataset for multi-class, multi-tool tracking in surgical procedures. It redefines tracking formalization with three perspectives: (i) intraoperative, (ii) intracorporeal, and (iii) visibility, enabling adaptable and clinically meaningful tool trajectories. The dataset comprises 20 full-length surgical videos, annotated at 1 fps, yielding over 35K frames and 65K labeled tool instances. Annotations include spatial location, category, identity, operator, phase, and scene visual challenge. Benchmarking state-of-the-art methods on CholecTrack20 reveals significant performance gaps, with current approaches (< 45\% HOTA) failing to meet the accuracy required for clinical translation. These findings motivate the need for advanced and intuitive tracking algorithms and establish CholecTrack20 as a foundation for developing robust AI-driven surgical assistance systems.

We present a novel model for Tracking Any Point (TAP) that effectively tracks any queried point on any physical surface throughout a video sequence. Our approach employs two stages: (1) a matching stage, which independently locates a suitable candidate point match for the query point on every other frame, and (2) a refinement stage, which updates both the trajectory and query features based on local correlations. The resulting model surpasses all baseline methods by a significant margin on the TAP-Vid benchmark, as demonstrated by an approximate 20% absolute average Jaccard (AJ) improvement on DAVIS. Our model facilitates fast inference on long and high-resolution video sequences. On a modern GPU, our implementation has the capacity to track points faster than real-time, and can be flexibly extended to higher-resolution videos. Given the high-quality trajectories extracted from a large dataset, we demonstrate a proof-of-concept diffusion model which generates trajectories from static images, enabling plausible animations. Visualizations, source code, and pretrained models can be found on our project webpage.

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Counterfactual medical image generation enables clinicians to explore clinical hypotheses, such as predicting disease progression, facilitating their decision-making. While existing methods can generate visually plausible images from disease progression prompts, they produce silent predictions that lack interpretation to verify how the generation reflects the hypothesized progression -- a critical gap for medical applications that require traceable reasoning. In this paper, we propose Interpretable Counterfactual Generation (ICG), a novel task requiring the joint generation of counterfactual images that reflect the clinical hypothesis and interpretation texts that outline the visual changes induced by the hypothesis. To enable ICG, we present ICG-CXR, the first dataset pairing longitudinal medical images with hypothetical progression prompts and textual interpretations. We further introduce ProgEmu, an autoregressive model that unifies the generation of counterfactual images and textual interpretations. We demonstrate the superiority of ProgEmu in generating progression-aligned counterfactuals and interpretations, showing significant potential in enhancing clinical decision support and medical education. Project page: https://progemu.github.io.

Alzheimer's Disease (AD) is marked by significant inter-individual variability in its progression, complicating accurate prognosis and personalized care planning. This heterogeneity underscores the critical need for predictive models capable of forecasting patient-specific disease trajectories. Artificial Intelligence (AI) offers powerful tools to address this challenge by analyzing complex, multi-modal, and longitudinal patient data. This paper provides a comprehensive survey of AI methodologies applied to personalized AD progression prediction. We review key approaches including state-space models for capturing temporal dynamics, deep learning techniques like Recurrent Neural Networks for sequence modeling, Graph Neural Networks (GNNs) for leveraging network structures, and the emerging concept of AI-driven digital twins for individualized simulation. Recognizing that data limitations often impede progress, we examine common challenges such as high dimensionality, missing data, and dataset imbalance. We further discuss AI-driven mitigation strategies, with a specific focus on synthetic data generation using Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs) to augment and balance datasets. The survey synthesizes the strengths and limitations of current approaches, emphasizing the trend towards multimodal integration and the persistent need for model interpretability and generalizability. Finally, we identify critical open challenges, including robust external validation, clinical integration, and ethical considerations, and outline promising future research directions such as hybrid models, causal inference, and federated learning. This review aims to consolidate current knowledge and guide future efforts in developing clinically relevant AI tools for personalized AD prognostication.

Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative modeling. In these settings, we assume access to cross-sectional samples that are uncorrelated over time, rather than full trajectories of samples. In order to better understand the systems under observation, we would like to learn a model of the underlying process that allows us to propagate samples in time and thereby simulate entire individual trajectories. In this work, we propose Action Matching, a method for learning a rich family of dynamics using only independent samples from its time evolution. We derive a tractable training objective, which does not rely on explicit assumptions about the underlying dynamics and does not require back-propagation through differential equations or optimal transport solvers. Inspired by connections with optimal transport, we derive extensions of Action Matching to learn stochastic differential equations and dynamics involving creation and destruction of probability mass. Finally, we showcase applications of Action Matching by achieving competitive performance in a diverse set of experiments from biology, physics, and generative modeling.

Molecular dynamics (MD) simulations play a crucial role in scientific research. Yet their computational cost often limits the timescales and system sizes that can be explored. Most data-driven efforts have been focused on reducing the computational cost of accurate interatomic forces required for solving the equations of motion. Despite their success, however, these machine learning interatomic potentials (MLIPs) are still bound to small time-steps. In this work, we introduce TrajCast, a transferable and data-efficient framework based on autoregressive equivariant message passing networks that directly updates atomic positions and velocities lifting the constraints imposed by traditional numerical integration. We benchmark our framework across various systems, including a small molecule, crystalline material, and bulk liquid, demonstrating excellent agreement with reference MD simulations for structural, dynamical, and energetic properties. Depending on the system, TrajCast allows for forecast intervals up to 30times larger than traditional MD time-steps, generating over 15 ns of trajectory data per day for a solid with more than 4,000 atoms. By enabling efficient large-scale simulations over extended timescales, TrajCast can accelerate materials discovery and explore physical phenomena beyond the reach of traditional simulations and experiments. An open-source implementation of TrajCast is accessible under https://github.com/IBM/trajcast.

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

The ultimate goal of Dataset Distillation is to synthesize a small synthetic dataset such that a model trained on this synthetic set will perform equally well as a model trained on the full, real dataset. Until now, no method of Dataset Distillation has reached this completely lossless goal, in part due to the fact that previous methods only remain effective when the total number of synthetic samples is extremely small. Since only so much information can be contained in such a small number of samples, it seems that to achieve truly loss dataset distillation, we must develop a distillation method that remains effective as the size of the synthetic dataset grows. In this work, we present such an algorithm and elucidate why existing methods fail to generate larger, high-quality synthetic sets. Current state-of-the-art methods rely on trajectory-matching, or optimizing the synthetic data to induce similar long-term training dynamics as the real data. We empirically find that the training stage of the trajectories we choose to match (i.e., early or late) greatly affects the effectiveness of the distilled dataset. Specifically, early trajectories (where the teacher network learns easy patterns) work well for a low-cardinality synthetic set since there are fewer examples wherein to distribute the necessary information. Conversely, late trajectories (where the teacher network learns hard patterns) provide better signals for larger synthetic sets since there are now enough samples to represent the necessary complex patterns. Based on our findings, we propose to align the difficulty of the generated patterns with the size of the synthetic dataset. In doing so, we successfully scale trajectory matching-based methods to larger synthetic datasets, achieving lossless dataset distillation for the very first time. Code and distilled datasets are available at https://gzyaftermath.github.io/DATM.

Optimal Transport (OT) has fueled machine learning (ML) across many domains. When paired data measurements (mu, nu) are coupled to covariates, a challenging conditional distribution learning setting arises. Existing approaches for learning a global transport map parameterized through a potentially unseen context utilize Neural OT and largely rely on Brenier's theorem. Here, we propose a first-of-its-kind quantum computing formulation for amortized optimization of contextualized transportation plans. We exploit a direct link between doubly stochastic matrices and unitary operators thus unravelling a natural connection between OT and quantum computation. We verify our method (QontOT) on synthetic and real data by predicting variations in cell type distributions conditioned on drug dosage. Importantly we conduct a 24-qubit hardware experiment on a task challenging for classical computers and report a performance that cannot be matched with our classical neural OT approach. In sum, this is a first step toward learning to predict contextualized transportation plans through quantum computing.

Radiotherapy often involves a prolonged treatment period. During this time, patients may experience organ motion due to breathing and other physiological factors. Predicting and modeling this motion before treatment is crucial for ensuring precise radiation delivery. However, existing pre-treatment organ motion prediction methods primarily rely on deformation analysis using principal component analysis (PCA), which is highly dependent on registration quality and struggles to capture periodic temporal dynamics for motion modeling.In this paper, we observe that organ motion prediction closely resembles an autoregressive process, a technique widely used in natural language processing (NLP). Autoregressive models predict the next token based on previous inputs, naturally aligning with our objective of predicting future organ motion phases. Building on this insight, we reformulate organ motion prediction as an autoregressive process to better capture patient-specific motion patterns. Specifically, we acquire 4D CT scans for each patient before treatment, with each sequence comprising multiple 3D CT phases. These phases are fed into the autoregressive model to predict future phases based on prior phase motion patterns. We evaluate our method on a real-world test set of 4D CT scans from 50 patients who underwent radiotherapy at our institution and a public dataset containing 4D CT scans from 20 patients (some with multiple scans), totaling over 1,300 3D CT phases. The performance in predicting the motion of the lung and heart surpasses existing benchmarks, demonstrating its effectiveness in capturing motion dynamics from CT images. These results highlight the potential of our method to improve pre-treatment planning in radiotherapy, enabling more precise and adaptive radiation delivery.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

We introduce M2DGR: a novel large-scale dataset collected by a ground robot with a full sensor-suite including six fish-eye and one sky-pointing RGB cameras, an infrared camera, an event camera, a Visual-Inertial Sensor (VI-sensor), an inertial measurement unit (IMU), a LiDAR, a consumer-grade Global Navigation Satellite System (GNSS) receiver and a GNSS-IMU navigation system with real-time kinematic (RTK) signals. All those sensors were well-calibrated and synchronized, and their data were recorded simultaneously. The ground truth trajectories were obtained by the motion capture device, a laser 3D tracker, and an RTK receiver. The dataset comprises 36 sequences (about 1TB) captured in diverse scenarios including both indoor and outdoor environments. We evaluate state-of-the-art SLAM algorithms on M2DGR. Results show that existing solutions perform poorly in some scenarios. For the benefit of the research community, we make the dataset and tools public. The webpage of our project is https://github.com/SJTU-ViSYS/M2DGR.

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success in Natural Language Processing and Computer Vision domains. However, the development of PTMs on healthcare time-series data is lagging behind.This underscores the limitations of the existing transformer-based architectures, particularly their scalability to handle large-scale time series and ability to capture long-term temporal dependencies. In this study, we present Timely Generative Pre-trained Transformer (TimelyGPT). TimelyGPT employs an extrapolatable position (xPos) embedding to encode trend and periodic patterns into time-series representations. It also integrates recurrent attention and temporal convolution modules to effectively capture global-local temporal dependencies. We evaluated TimelyGPT on two large-scale healthcare time series datasets corresponding to continuous biosignals and irregularly-sampled time series, respectively. Our experiments show that during pre-training, TimelyGPT excels in learning time-series representations from continuously monitored biosignals and irregularly-sampled time series data commonly observed in longitudinal electronic health records (EHRs). In forecasting continuous biosignals, TimelyGPT achieves accurate extrapolation up to 6,000 timesteps of body temperature during the sleep stage transition, given a short look-up window (i.e., prompt) containing only 2,000 timesteps. For irregularly-sampled time series, TimelyGPT with a proposed time-specific inference demonstrates high top recall scores in predicting future diagnoses using early diagnostic records, effectively handling irregular intervals between clinical records. Together, we envision TimelyGPT to be useful in a broad spectrum of health domains, including long-term patient health state forecasting and patient risk trajectory prediction.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

A new research framework is proposed to incorporate machine learning techniques into the field of experimental chemistry to facilitate chromatographic enantioseparation. A documentary dataset of chiral molecular retention times (CMRT dataset) in high-performance liquid chromatography is established to handle the challenge of data acquisition. Based on the CMRT dataset, a quantile geometry-enhanced graph neural network is proposed to learn the molecular structure-retention time relationship, which shows a satisfactory predictive ability for enantiomers. The domain knowledge of chromatography is incorporated into the machine learning model to achieve multi-column prediction, which paves the way for chromatographic enantioseparation prediction by calculating the separation probability. Experiments confirm that the proposed research framework works well in retention time prediction and chromatographic enantioseparation facilitation, which sheds light on the application of machine learning techniques to the experimental scene and improves the efficiency of experimenters to speed up scientific discovery.

The growing availability of longitudinal Magnetic Resonance Imaging (MRI) datasets has facilitated Artificial Intelligence (AI)-driven modeling of disease progression, making it possible to predict future medical scans for individual patients. However, despite significant advancements in AI, current methods continue to face challenges including achieving patient-specific individualization, ensuring spatiotemporal consistency, efficiently utilizing longitudinal data, and managing the substantial memory demands of 3D scans. To address these challenges, we propose Brain Latent Progression (BrLP), a novel spatiotemporal model designed to predict individual-level disease progression in 3D brain MRIs. The key contributions in BrLP are fourfold: (i) it operates in a small latent space, mitigating the computational challenges posed by high-dimensional imaging data; (ii) it explicitly integrates subject metadata to enhance the individualization of predictions; (iii) it incorporates prior knowledge of disease dynamics through an auxiliary model, facilitating the integration of longitudinal data; and (iv) it introduces the Latent Average Stabilization (LAS) algorithm, which (a) enforces spatiotemporal consistency in the predicted progression at inference time and (b) allows us to derive a measure of the uncertainty for the prediction at the global and voxel level. We train and evaluate BrLP on 11,730 T1-weighted (T1w) brain MRIs from 2,805 subjects and validate its generalizability on an external test set comprising 2,257 MRIs from 962 subjects. Our experiments compare BrLP-generated MRI scans with real follow-up MRIs, demonstrating state-of-the-art accuracy compared to existing methods. The code is publicly available at: https://github.com/LemuelPuglisi/BrLP.

We present a novel approach for traffic forecasting in urban traffic scenarios using a combination of spectral graph analysis and deep learning. We predict both the low-level information (future trajectories) as well as the high-level information (road-agent behavior) from the extracted trajectory of each road-agent. Our formulation represents the proximity between the road agents using a weighted dynamic geometric graph (DGG). We use a two-stream graph-LSTM network to perform traffic forecasting using these weighted DGGs. The first stream predicts the spatial coordinates of road-agents, while the second stream predicts whether a road-agent is going to exhibit overspeeding, underspeeding, or neutral behavior by modeling spatial interactions between road-agents. Additionally, we propose a new regularization algorithm based on spectral clustering to reduce the error margin in long-term prediction (3-5 seconds) and improve the accuracy of the predicted trajectories. Moreover, we prove a theoretical upper bound on the regularized prediction error. We evaluate our approach on the Argoverse, Lyft, Apolloscape, and NGSIM datasets and highlight the benefits over prior trajectory prediction methods. In practice, our approach reduces the average prediction error by approximately 75% over prior algorithms and achieves a weighted average accuracy of 91.2% for behavior prediction. Additionally, our spectral regularization improves long-term prediction by up to 70%.

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

The recovery of time-varying graph signals is a fundamental problem with numerous applications in sensor networks and forecasting in time series. Effectively capturing the spatio-temporal information in these signals is essential for the downstream tasks. Previous studies have used the smoothness of the temporal differences of such graph signals as an initial assumption. Nevertheless, this smoothness assumption could result in a degradation of performance in the corresponding application when the prior does not hold. In this work, we relax the requirement of this hypothesis by including a learning module. We propose a Time Graph Neural Network (TimeGNN) for the recovery of time-varying graph signals. Our algorithm uses an encoder-decoder architecture with a specialized loss composed of a mean squared error function and a Sobolev smoothness operator.TimeGNN shows competitive performance against previous methods in real datasets.

Large language model (LLM)-based agents increasingly rely on tool use to complete real-world tasks. While existing works evaluate the LLMs' tool use capability, they largely focus on the final answers yet overlook the detailed tool usage trajectory, i.e., whether tools are selected, parameterized, and ordered correctly. We introduce TRAJECT-Bench, a trajectory-aware benchmark to comprehensively evaluate LLMs' tool use capability through diverse tasks with fine-grained evaluation metrics. TRAJECT-Bench pairs high-fidelity, executable tools across practical domains with tasks grounded in production-style APIs, and synthesizes trajectories that vary in breadth (parallel calls) and depth (interdependent chains). Besides final accuracy, TRAJECT-Bench also reports trajectory-level diagnostics, including tool selection and argument correctness, and dependency/order satisfaction. Analyses reveal failure modes such as similar tool confusion and parameter-blind selection, and scaling behavior with tool diversity and trajectory length where the bottleneck of transiting from short to mid-length trajectories is revealed, offering actionable guidance for LLMs' tool use.

Longitudinal multimodal data, including electronic health records (EHR) and sequential chest X-rays (CXRs), is critical for modeling disease progression, yet remains underutilized due to two key challenges: (1) redundancy in consecutive CXR sequences, where static anatomical regions dominate over clinically-meaningful dynamics, and (2) temporal misalignment between sparse, irregular imaging and continuous EHR data. We introduce DiPro, a novel framework that addresses these challenges through region-aware disentanglement and multi-timescale alignment. First, we disentangle static (anatomy) and dynamic (pathology progression) features in sequential CXRs, prioritizing disease-relevant changes. Second, we hierarchically align these static and dynamic CXR features with asynchronous EHR data via local (pairwise interval-level) and global (full-sequence) synchronization to model coherent progression pathways. Extensive experiments on the MIMIC dataset demonstrate that DiPro could effectively extract temporal clinical dynamics and achieve state-of-the-art performance on both disease progression identification and general ICU prediction tasks.

This paper reports on the second "Throughput" phase of the Tracking Machine Learning (TrackML) challenge on the Codalab platform. As in the first "Accuracy" phase, the participants had to solve a difficult experimental problem linked to tracking accurately the trajectory of particles as e.g. created at the Large Hadron Collider (LHC): given O(10^5) points, the participants had to connect them into O(10^4) individual groups that represent the particle trajectories which are approximated helical. While in the first phase only the accuracy mattered, the goal of this second phase was a compromise between the accuracy and the speed of inference. Both were measured on the Codalab platform where the participants had to upload their software. The best three participants had solutions with good accuracy and speed an order of magnitude faster than the state of the art when the challenge was designed. Although the core algorithms were less diverse than in the first phase, a diversity of techniques have been used and are described in this paper. The performance of the algorithms are analysed in depth and lessons derived.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

We introduce EMMA, an End-to-end Multimodal Model for Autonomous driving. Built on a multi-modal large language model foundation, EMMA directly maps raw camera sensor data into various driving-specific outputs, including planner trajectories, perception objects, and road graph elements. EMMA maximizes the utility of world knowledge from the pre-trained large language models, by representing all non-sensor inputs (e.g. navigation instructions and ego vehicle status) and outputs (e.g. trajectories and 3D locations) as natural language text. This approach allows EMMA to jointly process various driving tasks in a unified language space, and generate the outputs for each task using task-specific prompts. Empirically, we demonstrate EMMA's effectiveness by achieving state-of-the-art performance in motion planning on nuScenes as well as competitive results on the Waymo Open Motion Dataset (WOMD). EMMA also yields competitive results for camera-primary 3D object detection on the Waymo Open Dataset (WOD). We show that co-training EMMA with planner trajectories, object detection, and road graph tasks yields improvements across all three domains, highlighting EMMA's potential as a generalist model for autonomous driving applications. However, EMMA also exhibits certain limitations: it can process only a small amount of image frames, does not incorporate accurate 3D sensing modalities like LiDAR or radar and is computationally expensive. We hope that our results will inspire further research to mitigate these issues and to further evolve the state of the art in autonomous driving model architectures.

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular "graph convolutions", a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph---atoms, bonds, distances, etc.---which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

In this work, we introduce Brain Latent Progression (BrLP), a novel spatiotemporal disease progression model based on latent diffusion. BrLP is designed to predict the evolution of diseases at the individual level on 3D brain MRIs. Existing deep generative models developed for this task are primarily data-driven and face challenges in learning disease progressions. BrLP addresses these challenges by incorporating prior knowledge from disease models to enhance the accuracy of predictions. To implement this, we propose to integrate an auxiliary model that infers volumetric changes in various brain regions. Additionally, we introduce Latent Average Stabilization (LAS), a novel technique to improve spatiotemporal consistency of the predicted progression. BrLP is trained and evaluated on a large dataset comprising 11,730 T1-weighted brain MRIs from 2,805 subjects, collected from three publicly available, longitudinal Alzheimer's Disease (AD) studies. In our experiments, we compare the MRI scans generated by BrLP with the actual follow-up MRIs available from the subjects, in both cross-sectional and longitudinal settings. BrLP demonstrates significant improvements over existing methods, with an increase of 22% in volumetric accuracy across AD-related brain regions and 43% in image similarity to the ground-truth scans. The ability of BrLP to generate conditioned 3D scans at the subject level, along with the novelty of integrating prior knowledge to enhance accuracy, represents a significant advancement in disease progression modeling, opening new avenues for precision medicine. The code of BrLP is available at the following link: https://github.com/LemuelPuglisi/BrLP.

In this paper, we propose a third-order, i.e., white-noise-on-jerk, Gaussian Process (GP) Trajectory Representation (TR) framework for continuous-time (CT) motion estimation (ME) tasks. Our framework features a unified trajectory representation that encapsulates the kinematic models of both SO(3)timesR^3 and SE(3) pose representations. This encapsulation strategy allows users to use the same implementation of measurement-based factors for either choice of pose representation, which facilitates experimentation and comparison to achieve the best model for the ME task. In addition, unique to our framework, we derive the kinematic models with the closed-form temporal derivatives of the local variable of SO(3) and SE(3), which so far has only been approximated based on the Taylor expansion in the literature. Our experiments show that these kinematic models can improve the estimation accuracy in high-speed scenarios. All analytical Jacobians of the interpolated states with respect to the support states of the trajectory representation, as well as the motion prior factors, are also provided for accelerated Gauss-Newton (GN) optimization. Our experiments demonstrate the efficacy and efficiency of the framework in various motion estimation tasks such as localization, calibration, and odometry, facilitating fast prototyping for ME researchers. We release the source code for the benefit of the community. Our project is available at https://github.com/brytsknguyen/gptr.

Trajectory prediction in autonomous driving relies on accurate representation of all relevant contexts of the driving scene, including traffic participants, road topology, traffic signs, as well as their semantic relations to each other. Despite increased attention to this issue, most approaches in trajectory prediction do not consider all of these factors sufficiently. We present SemanticFormer, an approach for predicting multimodal trajectories by reasoning over a semantic traffic scene graph using a hybrid approach. It utilizes high-level information in the form of meta-paths, i.e. trajectories on which an agent is allowed to drive from a knowledge graph which is then processed by a novel pipeline based on multiple attention mechanisms to predict accurate trajectories. SemanticFormer comprises a hierarchical heterogeneous graph encoder to capture spatio-temporal and relational information across agents as well as between agents and road elements. Further, it includes a predictor to fuse different encodings and decode trajectories with probabilities. Finally, a refinement module assesses permitted meta-paths of trajectories and speed profiles to obtain final predicted trajectories. Evaluation of the nuScenes benchmark demonstrates improved performance compared to several SOTA methods. In addition, we demonstrate that our knowledge graph can be easily added to two graph-based existing SOTA methods, namely VectorNet and Laformer, replacing their original homogeneous graphs. The evaluation results suggest that by adding our knowledge graph the performance of the original methods is enhanced by 5% and 4%, respectively.

Autoregressive models (ARMs) have become the workhorse for sequence generation tasks, since many problems can be modeled as next-token prediction. While there appears to be a natural ordering for text (i.e., left-to-right), for many data types, such as graphs, the canonical ordering is less obvious. To address this problem, we introduce a variant of ARM that generates high-dimensional data using a probabilistic ordering that is sequentially inferred from data. This model incorporates a trainable probability distribution, referred to as an order-policy, that dynamically decides the autoregressive order in a state-dependent manner. To train the model, we introduce a variational lower bound on the exact log-likelihood, which we optimize with stochastic gradient estimation. We demonstrate experimentally that our method can learn meaningful autoregressive orderings in image and graph generation. On the challenging domain of molecular graph generation, we achieve state-of-the-art results on the QM9 and ZINC250k benchmarks, evaluated using the Fr\'{e}chet ChemNet Distance (FCD).

Next point-of-interest (POI) recommendation predicts a user's next destination from historical movements. Traditional models require intensive training, while LLMs offer flexible and generalizable zero-shot solutions but often generate generic or geographically irrelevant results due to missing trajectory and spatial context. To address these issues, we propose RALLM-POI, a framework that couples LLMs with retrieval-augmented generation and self-rectification. We first propose a Historical Trajectory Retriever (HTR) that retrieves relevant past trajectories to serve as contextual references, which are then reranked by a Geographical Distance Reranker (GDR) for prioritizing spatially relevant trajectories. Lastly, an Agentic LLM Rectifier (ALR) is designed to refine outputs through self-reflection. Without additional training, RALLM-POI achieves substantial accuracy gains across three real-world Foursquare datasets, outperforming both conventional and LLM-based baselines. Code is released at https://github.com/LKRcrocodile/RALLM-POI.

Natural agents can effectively learn from multiple data sources that differ in size, quality, and types of measurements. We study this heterogeneity in the context of offline reinforcement learning (RL) by introducing a new, practically motivated semi-supervised setting. Here, an agent has access to two sets of trajectories: labelled trajectories containing state, action and reward triplets at every timestep, along with unlabelled trajectories that contain only state and reward information. For this setting, we develop and study a simple meta-algorithmic pipeline that learns an inverse dynamics model on the labelled data to obtain proxy-labels for the unlabelled data, followed by the use of any offline RL algorithm on the true and proxy-labelled trajectories. Empirically, we find this simple pipeline to be highly successful -- on several D4RL benchmarks~fu2020d4rl, certain offline RL algorithms can match the performance of variants trained on a fully labelled dataset even when we label only 10\% of trajectories which are highly suboptimal. To strengthen our understanding, we perform a large-scale controlled empirical study investigating the interplay of data-centric properties of the labelled and unlabelled datasets, with algorithmic design choices (e.g., choice of inverse dynamics, offline RL algorithm) to identify general trends and best practices for training RL agents on semi-supervised offline datasets.

Drug-protein binding and dissociation dynamics are fundamental to understanding molecular interactions in biological systems. While many tools for drug-protein interaction studies have emerged, especially artificial intelligence (AI)-based generative models, predictive tools on binding/dissociation kinetics and dynamics are still limited. We propose a novel research paradigm that combines molecular dynamics (MD) simulations, enhanced sampling, and AI generative models to address this issue. We propose an enhanced sampling strategy to efficiently implement the drug-protein dissociation process in MD simulations and estimate the free energy surface (FES). We constructed a program pipeline of MD simulations based on this sampling strategy, thus generating a dataset including 26,612 drug-protein dissociation trajectories containing about 13 million frames. We named this dissociation dynamics dataset DD-13M and used it to train a deep equivariant generative model UnbindingFlow, which can generate collision-free dissociation trajectories. The DD-13M database and UnbindingFlow model represent a significant advancement in computational structural biology, and we anticipate its broad applicability in machine learning studies of drug-protein interactions. Our ongoing efforts focus on expanding this methodology to encompass a broader spectrum of drug-protein complexes and exploring novel applications in pathway prediction.

This work explores the problem of generating task graphs of real-world activities. Different from prior formulations, we consider a setting where text transcripts of instructional videos performing a real-world activity (e.g., making coffee) are provided and the goal is to identify the key steps relevant to the task as well as the dependency relationship between these key steps. We propose a novel task graph generation approach that combines the reasoning capabilities of instruction-tuned language models along with clustering and ranking components to generate accurate task graphs in a completely unsupervised manner. We show that the proposed approach generates more accurate task graphs compared to a supervised learning approach on tasks from the ProceL and CrossTask datasets.

Effective self-supervised learning (SSL) techniques have been key to unlocking large datasets for representation learning. While many promising methods have been developed using online corpora and captioned photographs, their application to scientific domains, where data encodes highly specialized knowledge, remains a challenge. Liquid Argon Time Projection Chambers (LArTPCs) provide high-resolution 3D imaging for fundamental physics, but analysis of their sparse, complex point cloud data often relies on supervised methods trained on large simulations, introducing potential biases. We introduce the Point-based Liquid Argon Masked Autoencoder (PoLAr-MAE), applying masked point modeling to unlabeled LArTPC images using domain-specific volumetric tokenization and energy prediction. We show this SSL approach learns physically meaningful trajectory representations directly from data. This yields remarkable data efficiency: fine-tuning on just 100 labeled events achieves track/shower semantic segmentation performance comparable to the state-of-the-art supervised baseline trained on >100,000 events. Furthermore, internal attention maps exhibit emergent instance segmentation of particle trajectories. While challenges remain, particularly for fine-grained features, we make concrete SSL's potential for building a foundation model for LArTPC image analysis capable of serving as a common base for all data reconstruction tasks. To facilitate further progress, we release PILArNet-M, a large dataset of 1M LArTPC events. Project site: https://youngsm.com/polarmae.

Trajectory planning is commonly used as part of a local planner in autonomous driving. This paper considers the problem of planning a continuous-curvature-rate trajectory between fixed start and goal states that minimizes a tunable trade-off between passenger comfort and travel time. The problem is an instance of infinite dimensional optimization over two continuous functions: a path, and a velocity profile. We propose a simplification of this problem that facilitates the discretization of both functions. This paper also proposes a method to quickly generate minimal-length paths between start and goal states based on a single tuning parameter: the second derivative of curvature. Furthermore, we discretize the set of velocity profiles along a given path into a selection of acceleration way-points along the path. Gradient-descent is then employed to minimize cost over feasible choices of the second derivative of curvature, and acceleration way-points, resulting in a method that repeatedly solves the path and velocity profiles in an iterative fashion. Numerical examples are provided to illustrate the benefits of the proposed methods.

Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots. While challenging, reconstructing their temporal evolution to decipher underlying dynamic properties is of major interest to scientific research. Existing approaches enable data transport along a temporal axis but are poorly scalable in high dimension and require restrictive assumptions to be met. To address these issues, we propose \textbf{Multi-Marginal temporal Schr\"odinger Bridge Matching} (MMtSBM) for video generation from unpaired data, extending the theoretical guarantees and empirical efficiency of Diffusion Schr\"odinger Bridge Matching (arXiv:archive/2303.16852) by deriving the Iterative Markovian Fitting algorithm to multiple marginals in a novel factorized fashion. Experiments show that MMtSBM retains theoretical properties on toy examples, achieves state-of-the-art performance on real world datasets such as transcriptomic trajectory inference in 100 dimensions, and for the first time recovers couplings and dynamics in very high dimensional image settings. Our work establishes multi-marginal Schr\"odinger bridges as a practical and principled approach for recovering hidden dynamics from static data.

Recent successful generative models are trained by fitting a neural network to an a-priori defined tractable probability density path taking noise to training examples. In this paper we investigate the space of Gaussian probability paths, which includes diffusion paths as an instance, and look for an optimal member in some useful sense. In particular, minimizing the Kinetic Energy (KE) of a path is known to make particles' trajectories simple, hence easier to sample, and empirically improve performance in terms of likelihood of unseen data and sample generation quality. We investigate Kinetic Optimal (KO) Gaussian paths and offer the following observations: (i) We show the KE takes a simplified form on the space of Gaussian paths, where the data is incorporated only through a single, one dimensional scalar function, called the data separation function. (ii) We characterize the KO solutions with a one dimensional ODE. (iii) We approximate data-dependent KO paths by approximating the data separation function and minimizing the KE. (iv) We prove that the data separation function converges to 1 in the general case of arbitrary normalized dataset consisting of n samples in d dimension as n/drightarrow 0. A consequence of this result is that the Conditional Optimal Transport (Cond-OT) path becomes kinetic optimal as n/drightarrow 0. We further support this theory with empirical experiments on ImageNet.

Human trajectory prediction is a practical task of predicting the future positions of pedestrians on the road, which typically covers all temporal ranges from short-term to long-term within a trajectory. However, existing works attempt to address the entire trajectory prediction with a singular, uniform training paradigm, neglecting the distinction between short-term and long-term dynamics in human trajectories. To overcome this limitation, we introduce a novel Progressive Pretext Task learning (PPT) framework, which progressively enhances the model's capacity of capturing short-term dynamics and long-term dependencies for the final entire trajectory prediction. Specifically, we elaborately design three stages of training tasks in the PPT framework. In the first stage, the model learns to comprehend the short-term dynamics through a stepwise next-position prediction task. In the second stage, the model is further enhanced to understand long-term dependencies through a destination prediction task. In the final stage, the model aims to address the entire future trajectory task by taking full advantage of the knowledge from previous stages. To alleviate the knowledge forgetting, we further apply a cross-task knowledge distillation. Additionally, we design a Transformer-based trajectory predictor, which is able to achieve highly efficient two-step reasoning by integrating a destination-driven prediction strategy and a group of learnable prompt embeddings. Extensive experiments on popular benchmarks have demonstrated that our proposed approach achieves state-of-the-art performance with high efficiency. Code is available at https://github.com/iSEE-Laboratory/PPT.

In trajectory forecasting tasks for traffic, future output trajectories can be computed by advancing the ego vehicle's state with predicted actions according to a kinematics model. By unrolling predicted trajectories via time integration and models of kinematic dynamics, predicted trajectories should not only be kinematically feasible but also relate uncertainty from one timestep to the next. While current works in probabilistic prediction do incorporate kinematic priors for mean trajectory prediction, variance is often left as a learnable parameter, despite uncertainty in one time step being inextricably tied to uncertainty in the previous time step. In this paper, we show simple and differentiable analytical approximations describing the relationship between variance at one timestep and that at the next with the kinematic bicycle model. These approximations can be easily incorporated with negligible additional overhead into any existing trajectory forecasting framework utilizing probabilistic predictions, whether it is autoregressive or one-shot prediction. In our results, we find that encoding the relationship between variance across timesteps works especially well in unoptimal settings, such as with small or noisy datasets. We observe up to a 50% performance boost in partial dataset settings and up to an 8% performance boost in large-scale learning compared to previous kinematic prediction methods on SOTA trajectory forecasting architectures out-of-the-box, with no fine-tuning. In this paper, we show four analytical formulations of probabilistic kinematic priors which can be used for any Gaussian Mixture Model (GMM)-based deep learning models, quantify the error bound on linear approximations applied during trajectory unrolling, and show results to evaluate each formulation in trajectory forecasting.

Carbon nanotubes (CNTs) are critical building blocks in nanotechnology, yet the characterization of their dynamic growth is limited by the experimental challenges in nanoscale motion measurement using scanning electron microscopy (SEM) imaging. Existing ex situ methods offer only static analysis, while in situ techniques often require manual initialization and lack continuous per-particle trajectory decomposition. We present Visual Feature Tracking (VFTrack) an in-situ real-time particle tracking framework that automatically detects and tracks individual CNT particles in SEM image sequences. VFTrack integrates handcrafted or deep feature detectors and matchers within a particle tracking framework to enable kinematic analysis of CNT micropillar growth. A systematic using 13,540 manually annotated trajectories identifies the ALIKED detector with LightGlue matcher as an optimal combination (F1-score of 0.78, alpha-score of 0.89). VFTrack motion vectors decomposed into axial growth, lateral drift, and oscillations, facilitate the calculation of heterogeneous regional growth rates and the reconstruction of evolving CNT pillar morphologies. This work enables advancement in automated nano-material characterization, bridging the gap between physics-based models and experimental observation to enable real-time optimization of CNT synthesis.

Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health scenarios. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data may be sparse. We demonstrate our approach to estimate the effect of environmental tobacco smoke on body mass index z-scores among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We give a general algorithm and supply SAS and Stan code that can be adopted to implement our computational approach in both time-fixed and longitudinal data.

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance.

Capturing high-dimensional social interactions and feasible futures is essential for predicting trajectories. To address this complex nature, several attempts have been devoted to reducing the dimensionality of the output variables via parametric curve fitting such as the B\'ezier curve and B-spline function. However, these functions, which originate in computer graphics fields, are not suitable to account for socially acceptable human dynamics. In this paper, we present EigenTrajectory (ET), a trajectory prediction approach that uses a novel trajectory descriptor to form a compact space, known here as ET space, in place of Euclidean space, for representing pedestrian movements. We first reduce the complexity of the trajectory descriptor via a low-rank approximation. We transform the pedestrians' history paths into our ET space represented by spatio-temporal principle components, and feed them into off-the-shelf trajectory forecasting models. The inputs and outputs of the models as well as social interactions are all gathered and aggregated in the corresponding ET space. Lastly, we propose a trajectory anchor-based refinement method to cover all possible futures in the proposed ET space. Extensive experiments demonstrate that our EigenTrajectory predictor can significantly improve both the prediction accuracy and reliability of existing trajectory forecasting models on public benchmarks, indicating that the proposed descriptor is suited to represent pedestrian behaviors. Code is publicly available at https://github.com/inhwanbae/EigenTrajectory .

In this work, we seek new insights into the underlying challenges of the Scene Graph Generation (SGG) task. Quantitative and qualitative analysis of the Visual Genome dataset implies -- 1) Ambiguity: even if inter-object relationship contains the same object (or predicate), they may not be visually or semantically similar, 2) Asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies, and 3) Higher-order contexts: leveraging the identities of certain graph elements can help to generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-Global Interaction Networks (LOGIN). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract & Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the Visual Genome benchmark (in SGG task).

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity of diseases (e.g., small pleural effusion). Since incorrect attributes will lead to imprecise radiology reports, strengthening the generation process with precise attribute modeling becomes necessary. Additionally, the temporal information contained in the historical records, which is crucial in evaluating a patient's current condition (e.g., heart size is unchanged), has also been largely disregarded. To address these issues, we propose RECAP, which generates precise and accurate radiology reports via dynamic disease progression reasoning. Specifically, RECAP first predicts the observations and progressions (i.e., spatiotemporal information) given two consecutive radiographs. It then combines the historical records, spatiotemporal information, and radiographs for report generation, where a disease progression graph and dynamic progression reasoning mechanism are devised to accurately select the attributes of each observation and progression. Extensive experiments on two publicly available datasets demonstrate the effectiveness of our model.

Over the past three decades, numerous controllers have been developed to regulate complex chemical processes, but they have certain limitations. Traditional PI/PID controllers often require customized tuning for various set-point scenarios. On the other hand, MPC frameworks involve resource-intensive steps, and the utilization of black-box machine learning (ML) models can lead to issues such as local minima and infeasibility. Thus, there is a need for an alternative controller paradigm that combines the simplicity of a PI controller with the grade-to-grade (G2G) transferability of an MPC approach. To this end, we developed a novel LSTM controller (LSTMc) as a model-free data-driven controller framework. The LSTMc considers an augmented input tensor that incorporates information on state evolution and error dynamics for the current and previous W time steps, to predict the manipulated input at the next step (u_{t+1}). To demonstrate LSTMc, batch crystallization of dextrose was taken as a representative case study. The desired output for set-point tracking was the mean crystal size (L), with the manipulated input being the jacket temperature (T_j). Extensive training data, encompassing 7000+ different operating conditions, was compiled to ensure comprehensive training of LSTMc across a wide state space region. For comparison, we also designed a PI controller and an LSTM-MPC for different set-point tracking cases. The results consistently showed that LSTMc achieved the lowest set-point deviation (<2\%), three times lower than the MPC. Remarkably, LSTMc maintained this superior performance across all set points, even when sensor measurements contained noise levels of 10\% to 15\%. In summary, by effectively leveraging process data and utilizing sequential ML models, LSTMc offers a superior controller design approach.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.

We focus on the utilisation of reactive trajectory imitation controllers for goal-directed mobile robot navigation. We propose a topological navigation graph (TNG) - an imitation-learning-based framework for navigating through environments with intersecting trajectories. The TNG framework represents the environment as a directed graph composed of deep neural networks. Each vertex of the graph corresponds to a trajectory and is represented by a trajectory identification classifier and a trajectory imitation controller. For trajectory following, we propose the novel use of neural object detection architectures. The edges of TNG correspond to intersections between trajectories and are all represented by a classifier. We provide empirical evaluation of the proposed navigation framework and its components in simulated and real-world environments, demonstrating that TNG allows us to utilise non-goal-directed, imitation-learning methods for goal-directed autonomous navigation.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

The Quantum-Inspired Stacked Integrated Concept Graph Model (QISICGM) is an innovative machine learning framework that harnesses quantum-inspired techniques to predict diabetes risk with exceptional accuracy and efficiency. Utilizing the PIMA Indians Diabetes dataset augmented with 2,000 synthetic samples to mitigate class imbalance (total: 2,768 samples, 1,949 positives), QISICGM integrates a self-improving concept graph with a stacked ensemble comprising Random Forests (RF), Extra Trees (ET), transformers, convolutional neural networks (CNNs), and feed-forward neural networks (FFNNs). This approach achieves an out-of-fold (OOF) F1 score of 0.8933 and an AUC of 0.8699, outperforming traditional methods. Quantum inspired elements, such as phase feature mapping and neighborhood sequence modeling, enrich feature representations, enabling CPU-efficient inference at 8.5 rows per second. This paper presents a detailed architecture, theoretical foundations, code insights, and performance evaluations, including visualizations from the outputs subfolder. The open-source implementation (v1.0.0) is available at https://github.com/keninayoung/QISICGM, positioning QISICGM as a potential benchmark for AI-assisted clinical triage in diabetes and beyond. Ultimately, this work emphasizes trustworthy AI through calibration, interpretability, and open-source reproducibility.

There is a recent surge in the development of spatio-temporal forecasting models in the transportation domain. Long-range traffic forecasting, however, remains a challenging task due to the intricate and extensive spatio-temporal correlations observed in traffic networks. Current works primarily rely on road networks with graph structures and learn representations using graph neural networks (GNNs), but this approach suffers from over-smoothing problem in deep architectures. To tackle this problem, recent methods introduced the combination of GNNs with residual connections or neural ordinary differential equations (ODE). However, current graph ODE models face two key limitations in feature extraction: (1) they lean towards global temporal patterns, overlooking local patterns that are important for unexpected events; and (2) they lack dynamic semantic edges in their architectural design. In this paper, we propose a novel architecture called Graph-based Multi-ODE Neural Networks (GRAM-ODE) which is designed with multiple connective ODE-GNN modules to learn better representations by capturing different views of complex local and global dynamic spatio-temporal dependencies. We also add some techniques like shared weights and divergence constraints into the intermediate layers of distinct ODE-GNN modules to further improve their communication towards the forecasting task. Our extensive set of experiments conducted on six real-world datasets demonstrate the superior performance of GRAM-ODE compared with state-of-the-art baselines as well as the contribution of different components to the overall performance. The code is available at https://github.com/zbliu98/GRAM-ODE

This paper is about the problem of learning a stochastic policy for generating an object (like a molecular graph) from a sequence of actions, such that the probability of generating an object is proportional to a given positive reward for that object. Whereas standard return maximization tends to converge to a single return-maximizing sequence, there are cases where we would like to sample a diverse set of high-return solutions. These arise, for example, in black-box function optimization when few rounds are possible, each with large batches of queries, where the batches should be diverse, e.g., in the design of new molecules. One can also see this as a problem of approximately converting an energy function to a generative distribution. While MCMC methods can achieve that, they are expensive and generally only perform local exploration. Instead, training a generative policy amortizes the cost of search during training and yields to fast generation. Using insights from Temporal Difference learning, we propose GFlowNet, based on a view of the generative process as a flow network, making it possible to handle the tricky case where different trajectories can yield the same final state, e.g., there are many ways to sequentially add atoms to generate some molecular graph. We cast the set of trajectories as a flow and convert the flow consistency equations into a learning objective, akin to the casting of the Bellman equations into Temporal Difference methods. We prove that any global minimum of the proposed objectives yields a policy which samples from the desired distribution, and demonstrate the improved performance and diversity of GFlowNet on a simple domain where there are many modes to the reward function, and on a molecule synthesis task.

Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance).

The success of automated medical image analysis depends on large-scale and expert-annotated training sets. Unsupervised domain adaptation (UDA) has been raised as a promising approach to alleviate the burden of labeled data collection. However, they generally operate under the closed-set adaptation setting assuming an identical label set between the source and target domains, which is over-restrictive in clinical practice where new classes commonly exist across datasets due to taxonomic inconsistency. While several methods have been presented to tackle both domain shifts and incoherent label sets, none of them take into account the common characteristics of the two issues and consider the learning dynamics along network training. In this work, we propose optimization trajectory distillation, a unified approach to address the two technical challenges from a new perspective. It exploits the low-rank nature of gradient space and devises a dual-stream distillation algorithm to regularize the learning dynamics of insufficiently annotated domain and classes with the external guidance obtained from reliable sources. Our approach resolves the issue of inadequate navigation along network optimization, which is the major obstacle in the taxonomy adaptive cross-domain adaptation scenario. We evaluate the proposed method extensively on several tasks towards various endpoints with clinical and open-world significance. The results demonstrate its effectiveness and improvements over previous methods.

As unmanned aerial systems (UASs) increasingly integrate into the US national airspace system, there is an increasing need to characterize how commercial and recreational UASs may encounter each other. To inform the development and evaluation of safety critical technologies, we demonstrate a methodology to analytically calculate all potential relative geometries between different UAS operations performing inspection missions. This method is based on a previously demonstrated technique that leverages open source geospatial information to generate representative unmanned aircraft trajectories. Using open source data and parallel processing techniques, we performed trillions of calculations to estimate the relative horizontal distance between geospatial points across sixteen locations.

The Automatic Identification System (AIS) enables data-driven maritime surveillance but suffers from reliability issues and irregular intervals. We address vessel destination estimation using global-scope AIS data by proposing a differentiated approach that recasts long port-to-port trajectories as a nested sequence structure. Using spatial grids, this method mitigates spatio-temporal bias while preserving detailed resolution. We introduce a novel deep learning architecture, WAY, designed to process these reformulated trajectories for long-term destination estimation days to weeks in advance. WAY comprises a trajectory representation layer and Channel-Aggregative Sequential Processing (CASP) blocks. The representation layer generates multi-channel vector sequences from kinematic and non-kinematic features. CASP blocks utilize multi-headed channel- and self-attention for aggregation and sequential information delivery. Additionally, we propose a task-specialized Gradient Dropout (GD) technique to enable many-to-many training on single labels, preventing biased feedback surges by stochastically blocking gradient flow based on sample length. Experiments on 5-year AIS data demonstrate WAY's superiority over conventional spatial grid-based approaches regardless of trajectory progression. Results further confirm that adopting GD leads to performance gains. Finally, we explore WAY's potential for real-world application through multitask learning for ETA estimation.

As hyperparameter tuning becomes increasingly costly at scale, efficient tuning methods are essential. Yet principles for guiding hyperparameter tuning remain limited. In this work, we seek to establish such principles by considering a broad range of hyperparameters, including batch size, learning rate, and weight decay. We identify a phenomenon we call trajectory invariance, where pre-training loss curves, gradient noise, and gradient norm exhibit invariance--closely overlapping--with respect to a quantity that combines learning rate and weight decay. This phenomenon effectively reduces the original two-dimensional hyperparameter space to one dimension, yielding an efficient tuning rule: follow the salient direction revealed by trajectory invariance. Furthermore, we refine previous scaling laws and challenge several existing viewpoints. Overall, our work proposes new principles for efficient tuning and inspires future research on scaling laws.

People with diabetes are at risk of developing an eye disease called diabetic retinopathy (DR). This disease occurs when high blood glucose levels cause damage to blood vessels in the retina. Computer-aided DR diagnosis is a promising tool for early detection of DR and severity grading, due to the great success of deep learning. However, most current DR diagnosis systems do not achieve satisfactory performance or interpretability for ophthalmologists, due to the lack of training data with consistent and fine-grained annotations. To address this problem, we construct a large fine-grained annotated DR dataset containing 2,842 images (FGADR). This dataset has 1,842 images with pixel-level DR-related lesion annotations, and 1,000 images with image-level labels graded by six board-certified ophthalmologists with intra-rater consistency. The proposed dataset will enable extensive studies on DR diagnosis. We set up three benchmark tasks for evaluation: 1. DR lesion segmentation; 2. DR grading by joint classification and segmentation; 3. Transfer learning for ocular multi-disease identification. Moreover, a novel inductive transfer learning method is introduced for the third task. Extensive experiments using different state-of-the-art methods are conducted on our FGADR dataset, which can serve as baselines for future research.

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton-Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity. We anticipate that our models will enable patient counseling, clinical trial design, and ultimately individualized clinical care.

We present a novel data-driven simulation environment for modeling traffic in metropolitan street intersections. Using real-world tracking data collected over an extended period of time, we train trajectory forecasting models to learn agent interactions and environmental constraints that are difficult to capture conventionally. Trajectories of new agents are first coarsely generated by sampling from the spatial and temporal generative distributions, then refined using state-of-the-art trajectory forecasting models. The simulation can run either autonomously, or under explicit human control conditioned on the generative distributions. We present the experiments for a variety of model configurations. Under an iterative prediction scheme, the way-point-supervised TrajNet++ model obtained 0.36 Final Displacement Error (FDE) in 20 FPS on an NVIDIA A100 GPU.

Predicting drug-target interactions (DTI) is an essential part of the drug discovery process, which is an expensive process in terms of time and cost. Therefore, reducing DTI cost could lead to reduced healthcare costs for a patient. In addition, a precisely learned molecule representation in a DTI model could contribute to developing personalized medicine, which will help many patient cohorts. In this paper, we propose a new molecule representation based on the self-attention mechanism, and a new DTI model using our molecule representation. The experiments show that our DTI model outperforms the state of the art by up to 4.9% points in terms of area under the precision-recall curve. Moreover, a study using the DrugBank database proves that our model effectively lists all known drugs targeting a specific cancer biomarker in the top-30 candidate list.

Computational quantum chemistry plays a critical role in drug discovery, chemical synthesis, and materials science. While first-principles methods, such as density functional theory (DFT), provide high accuracy in modeling electronic structures and predicting molecular properties, they are computationally expensive. Machine learning interatomic potentials (MLIPs) have emerged as promising surrogate models that aim to achieve DFT-level accuracy while enabling efficient large-scale atomistic simulations. The development of accurate and transferable MLIPs requires large-scale, high-quality datasets with both energy and force labels. Critically, MLIPs must generalize not only to stable geometries but also to intermediate, non-equilibrium conformations encountered during atomistic simulations. In this work, we introduce PubChemQCR, a large-scale dataset of molecular relaxation trajectories curated from the raw geometry optimization outputs of the PubChemQC project. PubChemQCR is the largest publicly available dataset of DFT-based relaxation trajectories for small organic molecules, comprising approximately 3.5 million trajectories and over 300 million molecular conformations computed at various levels of theory. Each conformation is labeled with both total energy and atomic forces, making the dataset suitable for training and evaluating MLIPs. To provide baselines for future developments, we benchmark nine representative MLIP models on the dataset. Our resources are publicly available at https://huggingface.co/divelab

Majorities of distillation methods on pre-trained diffusion models or on pre-trained rectified flow, focus on either the distillation outputs or the trajectories between random noises and clean images to speed up sample generations from pre-trained models. In those trajectory-based distillation methods, consistency distillation requires the self-consistent trajectory projection to regulate the trajectory, which might avoid the common ODE approximation error {while still be concerning about sampling efficiencies}. At the same time, rectified flow distillations enforce straight trajectory for fast sampling, although an ODE solver is still required. In this work, we propose a trajectory distillation method, \modelname, that enjoys the benefits of both and enables few-step generations. TraFlow adopts the settings of consistency trajectory models, and further enforces the properties of self-consistency and straightness throughout the entire trajectory. These two properties are pursued by reaching a balance with following three targets: (1) reconstruct the output from pre-trained models; (2) learn the amount of changes by pre-trained models; (3) satisfy the self-consistency over its trajectory. Extensive experimental results have shown the effectiveness of our proposed method.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on recent advances in the spatial modeling of the tumor microenvironment using graph neural networks, we present an explainable cell graph (xCG) approach for survival prediction. We validate our model on a public cohort of imaging mass cytometry (IMC) data for 416 cases of lung adenocarcinoma. We explain survival predictions in terms of known phenotypes on the cell level by computing risk attributions over cell graphs, for which we propose an efficient grid-based layer-wise relevance propagation (LRP) method. Our ablation studies highlight the importance of incorporating the cancer stage and model ensembling to improve the quality of risk estimates. Our xCG method, together with the IMC data, is made publicly available to support further research.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Recovering dense and long-range pixel motion in videos is a challenging problem. Part of the difficulty arises from the 3D-to-2D projection process, leading to occlusions and discontinuities in the 2D motion domain. While 2D motion can be intricate, we posit that the underlying 3D motion can often be simple and low-dimensional. In this work, we propose to estimate point trajectories in 3D space to mitigate the issues caused by image projection. Our method, named SpatialTracker, lifts 2D pixels to 3D using monocular depth estimators, represents the 3D content of each frame efficiently using a triplane representation, and performs iterative updates using a transformer to estimate 3D trajectories. Tracking in 3D allows us to leverage as-rigid-as-possible (ARAP) constraints while simultaneously learning a rigidity embedding that clusters pixels into different rigid parts. Extensive evaluation shows that our approach achieves state-of-the-art tracking performance both qualitatively and quantitatively, particularly in challenging scenarios such as out-of-plane rotation.

This paper introduces a structural equation formulation that gives rise to a new family of quasi-periodic Gaussian processes, useful to process a broad class of natural and physiological signals. The proposed formulation simplifies generation and forecasting, and provides hyperparameter estimates, which we exploit in a convergent and consistent iterative estimation algorithm. A bootstrap approach for standard error estimation and confidence intervals is also provided. We demonstrate the computational and scaling benefits of the proposed approach on a broad class of problems, including water level tidal analysis, CO_{2} emission data, and sunspot numbers data. By leveraging the structural equations, our method reduces the cost of likelihood evaluations and predictions from O(k^2 p^2) to O(p^2), significantly improving scalability.

Temporal motion modeling has always been a key component in multiple object tracking (MOT) which can ensure smooth trajectory movement and provide accurate positional information to enhance association precision. However, current motion models struggle to be both efficient and effective across different application scenarios. To this end, we propose TrackSSM inspired by the recently popular state space models (SSM), a unified encoder-decoder motion framework that uses data-dependent state space model to perform temporal motion of trajectories. Specifically, we propose Flow-SSM, a module that utilizes the position and motion information from historical trajectories to guide the temporal state transition of object bounding boxes. Based on Flow-SSM, we design a flow decoder. It is composed of a cascaded motion decoding module employing Flow-SSM, which can use the encoded flow information to complete the temporal position prediction of trajectories. Additionally, we propose a Step-by-Step Linear (S^2L) training strategy. By performing linear interpolation between the positions of the object in the previous frame and the current frame, we construct the pseudo labels of step-by-step linear training, ensuring that the trajectory flow information can better guide the object bounding box in completing temporal transitions. TrackSSM utilizes a simple Mamba-Block to build a motion encoder for historical trajectories, forming a temporal motion model with an encoder-decoder structure in conjunction with the flow decoder. TrackSSM is applicable to various tracking scenarios and achieves excellent tracking performance across multiple benchmarks, further extending the potential of SSM-like temporal motion models in multi-object tracking tasks. Code and models are publicly available at https://github.com/Xavier-Lin/TrackSSM.

This work presents an extended version of the Vehicle Energy Dataset (VED), which is a openly released large-scale dataset for vehicle energy consumption analysis. Compared with its original version, the extended VED (eVED) dataset is enhanced with accurate vehicle trip GPS coordinates, serving as a basis to associate the VED trip records with external information, e.g., road speed limit and intersections, from accessible map services to accumulate attributes that is essential in analyzing vehicle energy consumption. In particularly, we calibrate all the GPS trace records in the original VED data, upon which we associated the VED data with attributes extracted from the Geographic Information System (QGIS), the Overpass API, the Open Street Map API, and Google Maps API. The associated attributes include 12,609,170 records of road elevation, 12,203,044 of speed limit, 12,281,719 of speed limit with direction (in case the road is bi-directional), 584,551 of intersections, 429,638 of bus stop, 312,196 of crossings, 195,856 of traffic signals, 29,397 of stop signs, 5,848 of turning loops, 4,053 of railway crossings (level crossing), 3,554 of turning circles, and 2,938 of motorway junctions. With the accurate GPS coordinates and enriched features of the vehicle trip record, the obtained eVED dataset can provide a precise and abundant medium to feed a learning engine, especially a deep learning engine that is more demanding on data sufficiency and richness. Moreover, our software work for data calibration and enrichment can be reused to generate further vehicle trip datasets for specific user cases, contributing to deep insights into vehicle behaviors and traffic dynamics analyses. We anticipate that the eVED dataset and our data enrichment software can serve the academic and industrial automotive section as apparatus in developing future technologies.

Mental health disorders affect hundreds of millions globally, and the Web now serves as a primary medium for accessing support, information, and assessment. Large language models (LLMs) offer scalable and accessible assistance, yet their deployment in mental-health settings remains risky when their reasoning is incomplete, inconsistent, or ungrounded. Existing psychological LLMs emphasize emotional understanding or knowledge recall but overlook the step-wise, clinically aligned reasoning required for appraisal, diagnosis, intervention planning, abstraction, and verification. To address these issues, we introduce MentraSuite, a unified framework for advancing reliable mental-health reasoning. We propose MentraBench, a comprehensive benchmark spanning five core reasoning aspects, six tasks, and 13 datasets, evaluating both task performance and reasoning quality across five dimensions: conciseness, coherence, hallucination avoidance, task understanding, and internal consistency. We further present Mindora, a post-trained model optimized through a hybrid SFT-RL framework with an inconsistency-detection reward to enforce faithful and coherent reasoning. To support training, we construct high-quality trajectories using a novel reasoning trajectory generation strategy, that strategically filters difficult samples and applies a structured, consistency-oriented rewriting process to produce concise, readable, and well-balanced trajectories. Across 20 evaluated LLMs, Mindora achieves the highest average performance on MentraBench and shows remarkable performances in reasoning reliability, demonstrating its effectiveness for complex mental-health scenarios.

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

Recent advances in large language models (LLMs) have sparked growing interest in integrating language-driven techniques into trajectory prediction. By leveraging their semantic and reasoning capabilities, LLMs are reshaping how autonomous systems perceive, model, and predict trajectories. This survey provides a comprehensive overview of this emerging field, categorizing recent work into five directions: (1) Trajectory prediction via language modeling paradigms, (2) Direct trajectory prediction with pretrained language models, (3) Language-guided scene understanding for trajectory prediction, (4) Language-driven data generation for trajectory prediction, (5) Language-based reasoning and interpretability for trajectory prediction. For each, we analyze representative methods, highlight core design choices, and identify open challenges. This survey bridges natural language processing and trajectory prediction, offering a unified perspective on how language can enrich trajectory prediction.

PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise, time, and cost. Meanwhile, machine learning has transformed drug design and development. In this work, we present a strategy for curating open-source PROTAC data and an open-source deep learning tool for predicting the degradation activity of novel PROTAC molecules. The curated dataset incorporates important information such as pDC_{50}, D_{max}, E3 ligase type, POI amino acid sequence, and experimental cell type. Our model architecture leverages learned embeddings from pretrained machine learning models, in particular for encoding protein sequences and cell type information. We assessed the quality of the curated data and the generalization ability of our model architecture against new PROTACs and targets via three tailored studies, which we recommend other researchers to use in evaluating their degradation activity models. In each study, three models predict protein degradation in a majority vote setting, reaching a top test accuracy of 82.6% and 0.848 ROC AUC, and a test accuracy of 61% and 0.615 ROC AUC when generalizing to novel protein targets. Our results are not only comparable to state-of-the-art models for protein degradation prediction, but also part of an open-source implementation which is easily reproducible and less computationally complex than existing approaches.

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss (ODIL), where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation (PDE) model, which is adapted for complex cases.

Motivation: The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts through the graphical Cohort Builder, users (especially new ones) may struggle to find specific cohort descriptors across hundreds of possible fields and properties. However, users may be better able to describe their desired cohort in free-text natural language. Results: We introduce GDC Cohort Copilot, an open-source copilot tool for curating cohorts from the GDC. GDC Cohort Copilot automatically generates the GDC cohort filter corresponding to a user-input natural language description of their desired cohort, before exporting the cohort back to the GDC for further analysis. An interactive user interface allows users to further refine the generated cohort. We develop and evaluate multiple large language models (LLMs) for GDC Cohort Copilot and demonstrate that our locally-served, open-source GDC Cohort LLM achieves better results than GPT-4o prompting in generating GDC cohorts. Availability and implementation: The standalone docker image for GDC Cohort Copilot is available at https://quay.io/repository/cdis/gdc-cohort-copilot. Source code is available at https://github.com/uc-cdis/gdc-cohort-copilot. GDC Cohort LLM weights are available at https://huggingface.co/uc-ctds.