Daily Papers

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.

While Large Language Models (LLMs) have shown strong performance on clinical text understanding, they struggle with longitudinal prediction tasks such as dementia prognosis, which require reasoning over complex, non-monotonic symptom trajectories across multiple visits. Standard supervised training lacks explicit annotations for symptom evolution, while direct Reinforcement Learning (RL) is hindered by sparse binary rewards. To address this challenge, we introduce Dementia-R1, an RL-based framework for longitudinal dementia prognosis from unstructured clinical notes. Our approach adopts a Cold-Start RL strategy that pre-trains the model to predict verifiable clinical indices extracted from patient histories, enhancing the capability to reason about disease progression before determining the final clinical status. Extensive experiments demonstrate that Dementia-R1 achieves an F1 score of 77.03% on real-world unstructured clinical datasets. Notably, on the ADNI benchmark, our 7B model rivals GPT-4o, effectively capturing fluctuating cognitive trajectories. Code is available at https://anonymous.4open.science/r/dementiar1-CDB5

Accurate Vehicle Trajectory Prediction is critical for automated vehicles and advanced driver assistance systems. Vehicle trajectory prediction consists of two essential tasks, i.e., longitudinal position prediction and lateral position prediction. There is a significant correlation between driving intentions and vehicle motion. In existing work, the three tasks are often conducted separately without considering the relationships between the longitudinal position, lateral position, and driving intention. In this paper, we propose a novel Temporal Multi-Gate Mixture-of-Experts (TMMOE) model for simultaneously predicting the vehicle trajectory and driving intention. The proposed model consists of three layers: a shared layer, an expert layer, and a fully connected layer. In the model, the shared layer utilizes Temporal Convolutional Networks (TCN) to extract temporal features. Then the expert layer is built to identify different information according to the three tasks. Moreover, the fully connected layer is used to integrate and export prediction results. To achieve better performance, uncertainty algorithm is used to construct the multi-task loss function. Finally, the publicly available CitySim dataset validates the TMMOE model, demonstrating superior performance compared to the LSTM model, achieving the highest classification and regression results. Keywords: Vehicle trajectory prediction, driving intentions Classification, Multi-task

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

Decisions about managing patients on the heart transplant waitlist are currently made by committees of doctors who consider multiple factors, but the process remains largely ad-hoc. With the growing volume of longitudinal patient, donor, and organ data collected by the United Network for Organ Sharing (UNOS) since 2018, there is increasing interest in analytical approaches to support clinical decision-making at the time of organ availability. In this study, we benchmark machine learning models that leverage longitudinal waitlist history data for time-dependent, time-to-event modeling of waitlist mortality. We train on 23,807 patient records with 77 variables and evaluate both survival prediction and discrimination at a 1-year horizon. Our best model achieves a C-Index of 0.94 and AUROC of 0.89, significantly outperforming previous models. Key predictors align with known risk factors while also revealing novel associations. Our findings can support urgency assessment and policy refinement in heart transplant decision making.

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.

Accurate estimation of brain infarction (i.e., irreversibly damaged tissue) is critical for guiding treatment decisions in acute ischemic stroke. Reliable infarct prediction informs key clinical interventions, including the need for patient transfer to comprehensive stroke centers, the potential benefit of additional reperfusion attempts during mechanical thrombectomy, decisions regarding secondary neuroprotective treatments, and ultimately, prognosis of clinical outcomes. This work introduces the Ischemic Stroke Lesion Segmentation (ISLES) 2024 challenge, which focuses on the prediction of final infarct volumes from pre-interventional acute stroke imaging and clinical data. ISLES24 provides a comprehensive, multimodal setting where participants can leverage all clinically and practically available data, including full acute CT imaging, sub-acute follow-up MRI, and structured clinical information, across a train set of 150 cases. On the hidden test set of 98 cases, the top-performing model, a multimodal nnU-Net-based architecture, achieved a Dice score of 0.285 (+/- 0.213) and an absolute volume difference of 21.2 (+/- 37.2) mL, underlining the significant challenges posed by this task and the need for further advances in multimodal learning. This work makes two primary contributions: first, we establish a standardized, clinically realistic benchmark for post-treatment infarct prediction, enabling systematic evaluation of multimodal algorithmic strategies on a longitudinal stroke dataset; second, we analyze current methodological limitations and outline key research directions to guide the development of next-generation infarct prediction models.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

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.

The 2024 US presidential election is the first major contest to occur in the US since the popularization of large language models (LLMs). Building on lessons from earlier shifts in media (most notably social media's well studied role in targeted messaging and political polarization) this moment raises urgent questions about how LLMs may shape the information ecosystem and influence political discourse. While platforms have announced some election safeguards, how well they work in practice remains unclear. Against this backdrop, we conduct a large-scale, longitudinal study of 12 models, queried using a structured survey with over 12,000 questions on a near-daily cadence from July through November 2024. Our design systematically varies content and format, resulting in a rich dataset that enables analyses of the models' behavior over time (e.g., across model updates), sensitivity to steering, responsiveness to instructions, and election-related knowledge and "beliefs." In the latter half of our work, we perform four analyses of the dataset that (i) study the longitudinal variation of model behavior during election season, (ii) illustrate the sensitivity of election-related responses to demographic steering, (iii) interrogate the models' beliefs about candidates' attributes, and (iv) reveal the models' implicit predictions of the election outcome. To facilitate future evaluations of LLMs in electoral contexts, we detail our methodology, from question generation to the querying pipeline and third-party tooling. We also publicly release our dataset at https://huggingface.co/datasets/sarahcen/llm-election-data-2024

Modeling empathy is a complex endeavor that is rooted in interpersonal and experiential dimensions of human interaction, and remains an open problem within AI. Existing empathy datasets fall short in capturing the richness of empathy responses, often being confined to in-lab or acted scenarios, lacking longitudinal data, and missing self-reported labels. We introduce a new multimodal dataset for empathy during personal experience sharing: the EmpathicStories++ dataset (https://mitmedialab.github.io/empathic-stories-multimodal/) containing 53 hours of video, audio, and text data of 41 participants sharing vulnerable experiences and reading empathically resonant stories with an AI agent. EmpathicStories++ is the first longitudinal dataset on empathy, collected over a month-long deployment of social robots in participants' homes, as participants engage in natural, empathic storytelling interactions with AI agents. We then introduce a novel task of predicting individuals' empathy toward others' stories based on their personal experiences, evaluated in two contexts: participants' own personal shared story context and their reflections on stories they read. We benchmark this task using state-of-the-art models to pave the way for future improvements in contextualized and longitudinal empathy modeling. Our work provides a valuable resource for further research in developing empathetic AI systems and understanding the intricacies of human empathy within genuine, real-world settings.

Misinformation and disinformation demand fact checking that goes beyond simple evidence-based reasoning. Existing benchmarks fall short: they are largely single modality (text-only), span short time horizons, use shallow evidence, cover domains unevenly, and often omit full articles -- obscuring models' real-world capability. We present MMM-Fact, a large-scale benchmark of 125,449 fact-checked statements (1995--2025) across multiple domains, each paired with the full fact-check article and multimodal evidence (text, images, videos, tables) from four fact-checking sites and one news outlet. To reflect verification effort, each statement is tagged with a retrieval-difficulty tier -- Basic (1--5 sources), Intermediate (6--10), and Advanced (>10) -- supporting fairness-aware evaluation for multi-step, cross-modal reasoning. The dataset adopts a three-class veracity scheme (true/false/not enough information) and enables tasks in veracity prediction, explainable fact-checking, complex evidence aggregation, and longitudinal analysis. Baselines with mainstream LLMs show MMM-Fact is markedly harder than prior resources, with performance degrading as evidence complexity rises. MMM-Fact offers a realistic, scalable benchmark for transparent, reliable, multimodal fact-checking.

Diagnosing and treating skin diseases require advanced visual skills across domains and the ability to synthesize information from multiple imaging modalities. While current deep learning models excel at specific tasks like skin cancer diagnosis from dermoscopic images, they struggle to meet the complex, multimodal requirements of clinical practice. Here, we introduce PanDerm, a multimodal dermatology foundation model pretrained through self-supervised learning on over 2 million real-world skin disease images from 11 clinical institutions across 4 imaging modalities. We evaluated PanDerm on 28 diverse benchmarks, including skin cancer screening, risk stratification, differential diagnosis of common and rare skin conditions, lesion segmentation, longitudinal monitoring, and metastasis prediction and prognosis. PanDerm achieved state-of-the-art performance across all evaluated tasks, often outperforming existing models when using only 10% of labeled data. We conducted three reader studies to assess PanDerm's potential clinical utility. PanDerm outperformed clinicians by 10.2% in early-stage melanoma detection through longitudinal analysis, improved clinicians' skin cancer diagnostic accuracy by 11% on dermoscopy images, and enhanced non-dermatologist healthcare providers' differential diagnosis by 16.5% across 128 skin conditions on clinical photographs. These results demonstrate PanDerm's potential to improve patient care across diverse clinical scenarios and serve as a model for developing multimodal foundation models in other medical specialties, potentially accelerating the integration of AI support in healthcare. The code can be found at https://github.com/SiyuanYan1/PanDerm.

End-to-end driving systems have recently made rapid progress, in particular on CARLA. Independent of their major contribution, they introduce changes to minor system components. Consequently, the source of improvements is unclear. We identify two biases that recur in nearly all state-of-the-art methods and are critical for the observed progress on CARLA: (1) lateral recovery via a strong inductive bias towards target point following, and (2) longitudinal averaging of multimodal waypoint predictions for slowing down. We investigate the drawbacks of these biases and identify principled alternatives. By incorporating our insights, we develop TF++, a simple end-to-end method that ranks first on the Longest6 and LAV benchmarks, gaining 14 driving score over the best prior work on Longest6.

Floods cause extensive global damage annually, making effective monitoring essential. While satellite observations have proven invaluable for flood detection and tracking, comprehensive global flood datasets spanning extended time periods remain scarce. In this study, we introduce a novel deep learning flood detection model that leverages the cloud-penetrating capabilities of Sentinel-1 Synthetic Aperture Radar (SAR) satellite imagery, enabling consistent flood extent mapping in any weather condition. By applying this model to nearly 10 years of SAR data, we create a unique, longitudinal global flood extent dataset with predictions unaffected by cloud coverage, offering comprehensive and consistent insights into historically flood-prone areas over the past decade. We use our model predictions to identify historically flood-prone areas in Ethiopia and demonstrate real-time disaster response capabilities during the May 2024 floods in Kenya. Additionally, our longitudinal analysis reveals potential increasing trends in global flood extent over time, although further validation is required to explore links to climate change. To maximize impact, we provide public access to both our model predictions and a code repository, empowering researchers and practitioners worldwide to advance flood monitoring and enhance disaster response strategies.

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.

Predicting human mobility holds significant practical value, with applications ranging from enhancing disaster risk planning to simulating epidemic spread. In this paper, we present the GeoFormer, a decoder-only transformer model adapted from the GPT architecture to forecast human mobility. Our proposed model is rigorously tested in the context of the HuMob Challenge 2023 -- a competition designed to evaluate the performance of prediction models on standardized datasets to predict human mobility. The challenge leverages two datasets encompassing urban-scale data of 25,000 and 100,000 individuals over a longitudinal period of 75 days. GeoFormer stands out as a top performer in the competition, securing a place in the top-3 ranking. Its success is underscored by performing well on both performance metrics chosen for the competition -- the GEO-BLEU and the Dynamic Time Warping (DTW) measures. The performance of the GeoFormer on the HuMob Challenge 2023 underscores its potential to make substantial contributions to the field of human mobility prediction, with far-reaching implications for disaster preparedness, epidemic control, and beyond.

The maintenance risks of open source software (OSS) projects pose significant threats to the quality, security, and resilience of modern software supply chains. While prior research has proposed diverse approaches for predicting OSS maintenance risk -- leveraging signals ranging from surface features (e.g., stars, commits) to social network analyses and behavioral patterns -- existing methods often suffer from ambiguous operational definitions, limited interpretability, and datasets of insufficient scale or generalizability. In this work, we introduce ``maintenance cessation'', grounded in both explicit archival status and rigorous semantic analysis of project documentation. Building on this foundation, we curate a large-scale, longitudinal dataset of 115,466 GitHub repositories -- encompassing 57,733 confirmed cessation events -- complemented by comprehensive, timeline-based behavioral features. We propose an integrated, multi-perspective feature framework for predicting maintenance cessation, systematically combining user-centric features, maintainer-centric features and project evolution features. AFT survival analysis demonstrates a high C-index (0.846), substantially outperforming models relying only on surface features. Feature ablation and SHAP analysis further confirm the effectiveness and interpretability of our approach. Finally, we demonstrate real-world applicability by deploying a GBSA classifier in the openEuler ecosystem for proactive package risk screening. Our work establishes a scalable, interpretable foundation for maintenance-risk prediction, enabling reproducible risk management across large-scale open source ecosystems.

Bias assessment of news sources is paramount for professionals, organizations, and researchers who rely on truthful evidence for information gathering and reporting. While certain bias indicators are discernible from content analysis, descriptors like political bias and fake news pose greater challenges. In this paper, we propose an extension to a recently presented news media reliability estimation method that focuses on modeling outlets and their longitudinal web interactions. Concretely, we assess the classification performance of four reinforcement learning strategies on a large news media hyperlink graph. Our experiments, targeting two challenging bias descriptors, factual reporting and political bias, showed a significant performance improvement at the source media level. Additionally, we validate our methods on the CLEF 2023 CheckThat! Lab challenge, outperforming the reported results in both, F1-score and the official MAE metric. Furthermore, we contribute by releasing the largest annotated dataset of news source media, categorized with factual reporting and political bias labels. Our findings suggest that profiling news media sources based on their hyperlink interactions over time is feasible, offering a bird's-eye view of evolving media landscapes.

The COVID-19 pandemic has escalated mental health crises worldwide, with social isolation and economic instability contributing to a rise in suicidal behavior. Suicide can result from social factors such as shame, abuse, abandonment, and mental health conditions like depression, Post-Traumatic Stress Disorder (PTSD), Attention-Deficit/Hyperactivity Disorder (ADHD), anxiety disorders, and bipolar disorders. As these conditions develop, signs of suicidal ideation may manifest in social media interactions. Analyzing social media data using artificial intelligence (AI) techniques can help identify patterns of suicidal behavior, providing invaluable insights for suicide prevention agencies, professionals, and broader community awareness initiatives. Machine learning algorithms for this purpose require large volumes of accurately labeled data. Previous research has not fully explored the potential of incorporating explanations in analyzing and labeling longitudinal social media data. In this study, we employed a model explanation method, Layer Integrated Gradients, on top of a fine-tuned state-of-the-art language model, to assign each token from Reddit users' posts an attribution score for predicting suicidal ideation. By extracting and analyzing attributions of tokens from the data, we propose a methodology for preliminary screening of social media posts for suicidal ideation without using large language models during inference.