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Oct 16

Dynamics around non-spherical symmetric bodies - III. The case of a spherical body with a crater

Motivated by the peculiar features of the trans-Neptunian object (TNO) Máni and the discovery of ring systems around Centaurs and trans-Neptunian bodies, we investigate the stability of particles around a small irregular body hosting a deep equatorial crater. This study is the third contribution in a sequence devoted to the dynamics around non-spherically symmetric bodies. Using Máni as a reference model, whose crater depth exceeds 10% of its radius, we map the system stability through complementary methods: Poincaré surfaces of section (PSS), survival maps, and the finite-time Lyapunov exponent (FTLE). In the nominal case, the 1!:!1, 2!:!1, 3!:!1, and 4!:!1 spin-orbit resonances (SORs) are consistently identified by all techniques. The prominent 3!:!1 SOR exhibits a bifurcated structure at high eccentricities, matching structural transitions observed at lower Jacobi constant values in the PSSs. Increasing the rotation rate (λ) and crater mass ratio (μ) enlarges resonance widths and promotes overlap, making the 2!:!1 and 4!:!1 SORs progressively dominant. Lower rotation rates allow stable trajectories to persist at higher eccentricities, whereas the 1!:!1 SOR is highly sensitive to stronger perturbations and disappears in the most extreme cases. In contrast to mass-anomaly models, which can clear the region interior to the 2!:!1 SOR, the crater configuration considered here preserves stable regions in this vicinity, suggesting alternative scenarios for the formation and maintenance of debris structures around irregular minor bodies.

  • 5 authors
·
Oct 4

ProtoPathway: Biologically Structured Prototype-Pathway Fusion for Multimodal Cancer Survival Prediction

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

  • 5 authors
·
May 19

A Flexible Parametric Modelling Framework for Survival Analysis

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

  • 3 authors
·
Jan 10, 2019

DeepSurv: Personalized Treatment Recommender System Using A Cox Proportional Hazards Deep Neural Network

Medical practitioners use survival models to explore and understand the relationships between patients' covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems. We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient's covariates and treatment effectiveness in order to provide personalized treatment recommendations. We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient's covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient's features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it's personalized treatment recommendations would increase the survival time of a set of patients. The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient's characteristics on their risk of failure.

  • 6 authors
·
Aug 8, 2017

Multimodal Optimal Transport-based Co-Attention Transformer with Global Structure Consistency for Survival Prediction

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

  • 2 authors
·
Jun 14, 2023

SurvHTE-Bench: A Benchmark for Heterogeneous Treatment Effect Estimation in Survival Analysis

Estimating heterogeneous treatment effects (HTEs) from right-censored survival data is critical in high-stakes applications such as precision medicine and individualized policy-making. Yet, the survival analysis setting poses unique challenges for HTE estimation due to censoring, unobserved counterfactuals, and complex identification assumptions. Despite recent advances, from Causal Survival Forests to survival meta-learners and outcome imputation approaches, evaluation practices remain fragmented and inconsistent. We introduce SurvHTE-Bench, the first comprehensive benchmark for HTE estimation with censored outcomes. The benchmark spans (i) a modular suite of synthetic datasets with known ground truth, systematically varying causal assumptions and survival dynamics, (ii) semi-synthetic datasets that pair real-world covariates with simulated treatments and outcomes, and (iii) real-world datasets from a twin study (with known ground truth) and from an HIV clinical trial. Across synthetic, semi-synthetic, and real-world settings, we provide the first rigorous comparison of survival HTE methods under diverse conditions and realistic assumption violations. SurvHTE-Bench establishes a foundation for fair, reproducible, and extensible evaluation of causal survival methods. The data and code of our benchmark are available at: https://github.com/Shahriarnz14/SurvHTE-Bench .

CACSurv: Concordance-Aligned Comparative Learning with Large Language Models for Cancer Survival Prediction

Cancer survival prediction supports treatment planning, risk stratification, and follow-up management. Existing methods use structured clinical variables, whole-slide images, genomic profiles, or multimodal inputs, while patient reports remain underexplored. We study report-centric survival prediction using reports that organize pathological, clinical, and molecular evidence. Large language models (LLMs) can reason over such reports, but case-wise time regression introduces two mismatches. First, a formulation mismatch arises because survival evaluation depends on ordering comparable patients, whereas independent time predictions do not enforce ranking consistency. Second, a supervision mismatch arises because a censored patient's observed time indicates survival beyond that point and cannot serve as an exact regression target, although it still implies orderings relative to patients who died earlier. To address these mismatches, we propose CACSurv, a Concordance-Aligned Comparative framework for report-centric survival prediction. CACSurv reformulates survival modeling as mini-cohort comparative reasoning, where an LLM predicts relative prognostic orderings. We introduce concordance-aligned rewards derived from comparable relations under right censoring, enabling censored outcomes to provide ranking supervision without exact event-time targets. At inference, Monte Carlo Reference Aggregation compares each patient with sampled references and aggregates positions into a cohort-level ranking. We establish TCGA-SurvReport, a benchmark covering six TCGA cancer cohorts. CACSurv achieves the highest C-index on all six cohorts and an average C-index of 0.722, outperforming the strongest published survival model by 6.5 percentage points and the strongest LLM time-regression baseline by 4.2 percentage points. Our code, models, and dataset will be available at https://github.com/xmed-lab/CACSurv.

  • 5 authors
·
Aug 16

Delay-of-Gratification as a Multi-Agent Survival Micro-benchmark for Long-Horizon LLMs: Social Exposure, Personas, and Tool Use Budgets

Large language models (LLMs) are increasingly deployed as multi-turn agents that must sustain goals, use tools, and adapt to other agents over extended interactions. However, existing research lacks auditable, multi-turn, multi-factorial experiments that quantify LLM behavior under explicit constraints, with time-resolved statistics that reveal how behavior unfolds over long horizons. To address this gap, we develop a multi-agent micro-benchmark inspired by the Stanford marshmallow experiment: ReAct agents operate minute-by-minute with a "raise a question" tool under a per-step budget, while we factorially manipulate social context (broadcast vs. isolated), personas (age, hedonic drive), and metacognitive policy (mandatory vs. optional tool use). We analyze outcomes with Kaplan-Meier (KM) survival curves and discrete-time hazard models over a long risk horizon across 19,200 agent trajectories in 64 cells. Behavior shows a sharp early "eat" impulse, and only 75.9% of agents persist to the end. In a discrete-time hazard model, isolation reduces per-minute risk relative to broadcast, whereas a must-use self-questioning policy increases risk. On average, agents ask approx 7.12 questions and hit the per-step budget in approx 6% of minutes. Questioning declines faster under broadcast than isolation. Ablation experiments demonstrated that removing hedonic drive and/or persona age increases survival and completion, narrows the broadcast/isolated gap, but leaves the must vs. may ordering intact. The combined ablation (no hedonic + no persona age) yields the highest completion (approaching 1.0). These results establish delay-of-gratification as a compact, multi-turn interaction benchmark that captures social contagion and tool-use dynamics in LLM agents, providing a reproducible testbed and statistics for analyzing long-horizon, multi-agent behavior.

  • 3 authors
·
Aug 25

Do RUL explanations hold up? Faithfulness and stability of attributions on C-MAPSS

Deep remaining-useful-life (RUL) models on NASA C-MAPSS are now routine, and so are heatmaps that colour sensors and timesteps. A heatmap that looks mechanical is not the same as an explanation an engineer can act on. We train three standard architectures - a 1D CNN, an LSTM, and a small Transformer encoder - on the official FD001 and FD003 splits with the piecewise RUL cap of 125 cycles and the official PHM08 asymmetric score. We then attach three attribution maps (Integrated Gradients, occlusion, last-layer attention) and evaluate them with the checks the XAI-for-PdM literature still under-reports: deletion/insertion faithfulness, Spearman stability under sensor-scale noise, agreement across training seeds, and cosine consistency inside RUL bins. Prediction error is a prerequisite, not the claim. The headline is which explanation method moves the RUL output when its top cells are removed, and which map survives a 5% input perturbation. Integrated Gradients and occlusion are similarly faithful on the LSTM; Transformer attention is cheap and temporally smooth but weakly faithful. All three maps are almost unchanged under 5% input noise, yet IG/occlusion agree only moderately across two LSTM seeds - stability to sensor jitter is not the same as stability to retraining. A secondary tabular check on the AI4I 2020 failure dataset shows the same deletion pattern for tree importances. We recommend occlusion or IG for any C-MAPSS-style report that will be read by a maintenance engineer, and we treat raw attention weights as a visualisation only.

  • 8 authors
·
Oct 2

SurvBench: A Standardised Preprocessing Pipeline for Multi-Modal Electronic Health Record Survival Analysis

Deep-learning survival models for electronic health record (EHR) data are hard to compare across papers because the upstream preprocessing step, which includes cohort definition, time discretisation, missingness handling, and censoring rules, is typically undocumented and inconsistent. A reported difference in concordance between two mortality models can therefore reflect any of these choices rather than a modelling contribution. We present SurvBench, an open-source preprocessing pipeline that converts raw PhysioNet exports into model-ready tensors for survival analysis. SurvBench covers four critical-care databases (MIMIC-IV, eICU, MC-MED, HiRID) and four input modalities: time-series vitals and laboratory values, static demographics, International Classification of Diseases (ICD) codes, and radiology report embeddings. Every preprocessing decision is controlled through YAML configuration. Imputation, scaling, and feature filtering are fit on the training fold only. Missingness is recorded as a binary mask alongside each feature tensor. The pipeline handles single-risk endpoints (in-hospital and in-ICU mortality) and competing-risks endpoints (a three-way emergency-department admission pathway, with home discharge treated as administrative censoring). We also provide support for harmonised cross-dataset external validation between eICU and MIMIC-IV. SurvBench is publicly available at https://github.com/munibmesinovic/SurvBench, providing a robust platform that future deep-learning EHR survival work, especially nascent multi-modal approaches, can be measured against under matched preprocessing.

  • 2 authors
·
May 11

Evaluating Intelligence via Trial and Error

Intelligence is a crucial trait for species to find solutions within a limited number of trial-and-error attempts. Building on this idea, we introduce Survival Game as a framework to evaluate intelligence based on the number of failed attempts in a trial-and-error process. Fewer failures indicate higher intelligence. When the expectation and variance of failure counts are both finite, it signals the ability to consistently find solutions to new challenges, which we define as the Autonomous Level of intelligence. Using Survival Game, we comprehensively evaluate existing AI systems. Our results show that while AI systems achieve the Autonomous Level in simple tasks, they are still far from it in more complex tasks, such as vision, search, recommendation, and language. While scaling current AI technologies might help, this would come at an astronomical cost. Projections suggest that achieving the Autonomous Level for general tasks would require 10^{26} parameters. To put this into perspective, loading such a massive model requires so many H100 GPUs that their total value is 10^{7} times that of Apple Inc.'s market value. Even with Moore's Law, supporting such a parameter scale would take 70 years. This staggering cost highlights the complexity of human tasks and the inadequacies of current AI technologies. To further investigate this phenomenon, we conduct a theoretical analysis of Survival Game and its experimental results. Our findings suggest that human tasks possess a criticality property. As a result, Autonomous Level requires a deep understanding of the task's underlying mechanisms. Current AI systems, however, do not fully grasp these mechanisms and instead rely on superficial mimicry, making it difficult for them to reach an autonomous level. We believe Survival Game can not only guide the future development of AI but also offer profound insights into human intelligence.

  • 10 authors
·
Feb 26, 2025 3

Golden Hour Divide: Trauma Care Accessibility and Resource Vulnerability in Sri Lanka

Timely intensive care dictates survival, yet emergency infrastructure remains unevenly distributed across Sri Lanka. While pre-hospital services have expanded, the transition to definitive care remains a critical bottleneck. This study evaluates national emergency resilience by quantifying the gap between clinical demand and the availability of specialized resources across all 25 districts. Using the latest national epidemiological data and terrain-aware H3 hexagonal modeling, we analyzed accessibility for seven critical conditions based on spatial gaps, clinical need-gaps, lethality, coverage, and resource availability. Based on these metrics, unsupervised K-Means clustering was applied to categorize districts into four policy-actionable archetypes: Critical Structural Exclusion, Institutional Mirages, Operational Capacity Strain, and High-Resilience Benchmarks. Our study suggests that severe service deficits exist in the Northern and Eastern provinces, where spatial gaps exceed 70%, rendering the Golden Hour operationally impossible. Notably, specialist scarcity drives systemic pressure more than bed capacity; underserved regions effectively function as institutional mirages. This study suggests that improving accessibility by 25% in high-priority clusters would reduce the national need-gap by 9.65%, providing a roadmap for the strategic redistribution of specialists to ensure healthcare equity.

  • 9 authors
·
Jul 5

Path Planning in Physically Viable World Models

Robots deployed in unstructured outdoor environments often plan from scene reconstructions collected before deployment because operators cannot remap large or remote sites before every mission. As a result, robots must make long-horizon planning decisions using stale maps that assume the terrain remains unchanged, even though physical changes to the environment may render previously feasible routes unsafe or unreachable at execution time. We present a physically viable world model for evaluating what-if queries for robot navigation under future terrain change. The system augments reconstructed 3D Gaussian splat scenes with physics-based simulation to generate physically modified versions of the same environment without recollecting sensor data or rebuilding the map. We then implement a terrain-aware planner that accounts for physical events, obstacles, and deformations that are simulated by the world model. This allows robots and human operators to evaluate whether planned routes remain feasible before committing to a planned route, particularly in constrained environments where retreat or recovery may become impossible once conditions change. We evaluate the system on a real outdoor field site in Central Texas using simulated flooding across multiple severity levels. We measure route and mission feasibility as terrain conditions deteriorate under physically simulated interventions. Our results show that physically viable world models expose long-horizon route failures and rerouting behavior that are not apparent when planning only on the original reconstructed environment, allowing robots to evaluate how future terrain changes may affect route feasibility before deployment.

  • 6 authors
·
Jun 30

SPRING: GPT-4 Out-performs RL Algorithms by Studying Papers and Reasoning

Open-world survival games pose significant challenges for AI algorithms due to their multi-tasking, deep exploration, and goal prioritization requirements. Despite reinforcement learning (RL) being popular for solving games, its high sample complexity limits its effectiveness in complex open-world games like Crafter or Minecraft. We propose a novel approach, SPRING, to read the game's original academic paper and use the knowledge learned to reason and play the game through a large language model (LLM). Prompted with the LaTeX source as game context and a description of the agent's current observation, our SPRING framework employs a directed acyclic graph (DAG) with game-related questions as nodes and dependencies as edges. We identify the optimal action to take in the environment by traversing the DAG and calculating LLM responses for each node in topological order, with the LLM's answer to final node directly translating to environment actions. In our experiments, we study the quality of in-context "reasoning" induced by different forms of prompts under the setting of the Crafter open-world environment. Our experiments suggest that LLMs, when prompted with consistent chain-of-thought, have great potential in completing sophisticated high-level trajectories. Quantitatively, SPRING with GPT-4 outperforms all state-of-the-art RL baselines, trained for 1M steps, without any training. Finally, we show the potential of games as a test bed for LLMs.

  • 8 authors
·
May 24, 2023

PathoHR: Breast Cancer Survival Prediction on High-Resolution Pathological Images

Breast cancer survival prediction in computational pathology presents a remarkable challenge due to tumor heterogeneity. For instance, different regions of the same tumor in the pathology image can show distinct morphological and molecular characteristics. This makes it difficult to extract representative features from whole slide images (WSIs) that truly reflect the tumor's aggressive potential and likely survival outcomes. In this paper, we present PathoHR, a novel pipeline for accurate breast cancer survival prediction that enhances any size of pathological images to enable more effective feature learning. Our approach entails (1) the incorporation of a plug-and-play high-resolution Vision Transformer (ViT) to enhance patch-wise WSI representation, enabling more detailed and comprehensive feature extraction, (2) the systematic evaluation of multiple advanced similarity metrics for comparing WSI-extracted features, optimizing the representation learning process to better capture tumor characteristics, (3) the demonstration that smaller image patches enhanced follow the proposed pipeline can achieve equivalent or superior prediction accuracy compared to raw larger patches, while significantly reducing computational overhead. Experimental findings valid that PathoHR provides the potential way of integrating enhanced image resolution with optimized feature learning to advance computational pathology, offering a promising direction for more accurate and efficient breast cancer survival prediction. Code will be available at https://github.com/AIGeeksGroup/PathoHR.

  • 10 authors
·
Mar 23, 2025 2

An Automatic Approach for Generating Rich, Linked Geo-Metadata from Historical Map Images

Historical maps contain detailed geographic information difficult to find elsewhere covering long-periods of time (e.g., 125 years for the historical topographic maps in the US). However, these maps typically exist as scanned images without searchable metadata. Existing approaches making historical maps searchable rely on tedious manual work (including crowd-sourcing) to generate the metadata (e.g., geolocations and keywords). Optical character recognition (OCR) software could alleviate the required manual work, but the recognition results are individual words instead of location phrases (e.g., "Black" and "Mountain" vs. "Black Mountain"). This paper presents an end-to-end approach to address the real-world problem of finding and indexing historical map images. This approach automatically processes historical map images to extract their text content and generates a set of metadata that is linked to large external geospatial knowledge bases. The linked metadata in the RDF (Resource Description Framework) format support complex queries for finding and indexing historical maps, such as retrieving all historical maps covering mountain peaks higher than 1,000 meters in California. We have implemented the approach in a system called mapKurator. We have evaluated mapKurator using historical maps from several sources with various map styles, scales, and coverage. Our results show significant improvement over the state-of-the-art methods. The code has been made publicly available as modules of the Kartta Labs project at https://github.com/kartta-labs/Project.

  • 7 authors
·
Dec 2, 2021

deadtrees.earth-aerial: A Multi-Resolution Aerial Image Dataset for Tree Cover and Mortality Detection

Forests worldwide are increasingly threatened by climate change and disturbances such as fire, pests, and pathogens, creating an urgent need for scalable monitoring of tree cover and tree mortality. Aerial imagery from drones and aircraft is a key data source for detailed and large-scale mapping of tree crowns and mortality. However, related progress is limited by the lack of globally representative, harmonized datasets for joint segmentation of tree cover and mortality. We introduce two novel, open, machine-learning-ready datasets to enable joint segmentation of tree cover and tree mortality from centimeter-scale aerial imagery for the first time at global scales. With DTE-aerial-train, we provide a training dataset comprising 385K image patches of size 1024x1024 pixels, with resolutions ranging from 2.5 to 20 cm. It includes multi-class expert-annotated and -audited pseudo-labels for tree cover and mortality. With DTE-aerial-bench, we provide a geographically balanced benchmark test set of 25 globally distributed orthoimages totaling 525 patches with high-quality expert annotations for both tree cover and mortality. Both the training and benchmark datasets span tropical, temperate, boreal, and dryland biomes and cover a wide range of forest structures and mortality patterns. Using the benchmark test set for evaluation, we establish strong reference baselines that improve mortality segmentation across all biomes and scales with significant gains in challenging regions, such as boreal forests, where the F1 score increases from 0.40 to 0.58 with around 45% relative improvement. All data, models, and code will be publicly released under permissive open-source licenses. An interactive visualization of the benchmark dataset is available at deadtrees.earth/releases/dte-aerial-bench.

  • 12 authors
·
May 18

OncoReason: Structuring Clinical Reasoning in LLMs for Robust and Interpretable Survival Prediction

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP, they often lack structured reasoning capabilities critical for high-stakes decision support. We present a unified, multi-task learning framework that aligns autoregressive LLMs with clinical reasoning for outcome prediction on the MSK-CHORD dataset. Our models are trained to jointly perform binary survival classification, continuous survival time regression, and natural language rationale generation. We evaluate three alignment strategies: (1) standard supervised fine-tuning (SFT), (2) SFT with Chain-of-Thought (CoT) prompting to elicit step-by-step reasoning, and (3) Group Relative Policy Optimization (GRPO), a reinforcement learning method that aligns model outputs to expert-derived reasoning trajectories. Experiments with LLaMa3-8B and Med42-8B backbones demonstrate that CoT prompting improves F1 by +6.0 and reduces MAE by 12%, while GRPO achieves state-of-the-art interpretability and predictive performance across BLEU, ROUGE, and BERTScore. We further show that existing biomedical LLMs often fail to produce valid reasoning traces due to architectural constraints. Our findings underscore the importance of reasoning-aware alignment in multi-task clinical modeling and set a new benchmark for interpretable, trustworthy LLMs in precision oncology.

  • 4 authors
·
Oct 20, 2025

OTSurv: A Novel Multiple Instance Learning Framework for Survival Prediction with Heterogeneity-aware Optimal Transport

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

  • 5 authors
·
Jun 25, 2025

CanadaFireSat: Toward high-resolution wildfire forecasting with multiple modalities

Canada experienced in 2023 one of the most severe wildfire seasons in recent history, causing damage across ecosystems, destroying communities, and emitting large quantities of CO2. This extreme wildfire season is symptomatic of a climate-change-induced increase in the length and severity of the fire season that affects the boreal ecosystem. Therefore, it is critical to empower wildfire management in boreal communities with better mitigation solutions. Wildfire probability maps represent an important tool for understanding the likelihood of wildfire occurrence and the potential severity of future wildfires. The massive increase in the availability of Earth observation data has enabled the development of deep learning-based wildfire forecasting models, aiming at providing precise wildfire probability maps at different spatial and temporal scales. A main limitation of such methods is their reliance on coarse-resolution environmental drivers and satellite products, leading to wildfire occurrence prediction of reduced resolution, typically around sim 0.1{\deg}. This paper presents a benchmark dataset: CanadaFireSat, and baseline methods for high-resolution: 100 m wildfire forecasting across Canada, leveraging multi-modal data from high-resolution multi-spectral satellite images (Sentinel-2 L1C), mid-resolution satellite products (MODIS), and environmental factors (ERA5 reanalysis data). Our experiments consider two major deep learning architectures. We observe that using multi-modal temporal inputs outperforms single-modal temporal inputs across all metrics, achieving a peak performance of 60.3% in F1 score for the 2023 wildfire season, a season never seen during model training. This demonstrates the potential of multi-modal deep learning models for wildfire forecasting at high-resolution and continental scale.

  • 4 authors
·
Jun 10, 2025

Forecasting Clinical Risk from Textual Time Series: Structuring Narratives for Temporal AI in Healthcare

Clinical case reports encode temporal patient trajectories that are often underexploited by traditional machine learning methods relying on structured data. In this work, we introduce the forecasting problem from textual time series, where timestamped clinical findings -- extracted via an LLM-assisted annotation pipeline -- serve as the primary input for prediction. We systematically evaluate a diverse suite of models, including fine-tuned decoder-based large language models and encoder-based transformers, on tasks of event occurrence prediction, temporal ordering, and survival analysis. Our experiments reveal that encoder-based models consistently achieve higher F1 scores and superior temporal concordance for short- and long-horizon event forecasting, while fine-tuned masking approaches enhance ranking performance. In contrast, instruction-tuned decoder models demonstrate a relative advantage in survival analysis, especially in early prognosis settings. Our sensitivity analyses further demonstrate the importance of time ordering, which requires clinical time series construction, as compared to text ordering, the format of the text inputs that LLMs are classically trained on. This highlights the additional benefit that can be ascertained from time-ordered corpora, with implications for temporal tasks in the era of widespread LLM use.

Planetary Prediction Engine: Autonomous Geospatial Prediction via Intelligent Data Selection and Foundation Model Embeddings

Addressing critical global challenges, from food security and disaster risk to disease outbreaks and socio-economic vulnerability, demands high-fidelity geospatial modeling. However, building predictive planetary models remains bottlenecked by a fragmented data ecosystem, requiring manual data retrieval, multimodal data curation and fusion along with iterative model selection. We present the Planetary Prediction Engine (PPE), an autonomous AI system that executes this end-to-end workflow directly from natural-language queries. PPE synthesizes multimodal datasets on the fly, retrieving spatiotemporally relevant covariates across open-web and Earth observation platforms (Data Commons, Google Earth Engine) and fusing them with geospatial foundation model embeddings (PDFM, AlphaEarth). Simultaneously, it searches over task-tailored model architecture families with automated overfitting guards. Across diverse tasks, geographies, and scientific domains, PPE consistently outperforms state-of-the-art or manually tuned expert baselines. For US spatial regression, PPE improves mean R^2 across 21 CDC health indicators (76.8% vs. 60.0%), FEMA national risk indices (64.9% vs. 60.0%), and the Social Vulnerability Index (66.2% vs. 58.6%). For spatial downscaling in data-scarce settings, PPE integrates localized proxies to double baseline accuracy in Nigerian food security indicators (R^2 of 66.1% vs. 31.5%). For epidemiological nowcasting of the 2026 DRC Bundibugyo Ebola outbreak, PPE achieves a Recall@10 of 83.3% (identifying 15 of 18 newly invaded health zones across five weekly forecasts), a +10.3 percentage-point improvement over the public state-of-the-art modeling (~73%). By combining autonomous multimodal planetary data discovery with targeted model optimization, PPE lowers the technical barrier to planetary-scale analytics, enabling rapid, customized, expert-level deployment.

  • 28 authors
·
Aug 25

PEACE: Empowering Geologic Map Holistic Understanding with MLLMs

Geologic map, as a fundamental diagram in geology science, provides critical insights into the structure and composition of Earth's subsurface and surface. These maps are indispensable in various fields, including disaster detection, resource exploration, and civil engineering. Despite their significance, current Multimodal Large Language Models (MLLMs) often fall short in geologic map understanding. This gap is primarily due to the challenging nature of cartographic generalization, which involves handling high-resolution map, managing multiple associated components, and requiring domain-specific knowledge. To quantify this gap, we construct GeoMap-Bench, the first-ever benchmark for evaluating MLLMs in geologic map understanding, which assesses the full-scale abilities in extracting, referring, grounding, reasoning, and analyzing. To bridge this gap, we introduce GeoMap-Agent, the inaugural agent designed for geologic map understanding, which features three modules: Hierarchical Information Extraction (HIE), Domain Knowledge Injection (DKI), and Prompt-enhanced Question Answering (PEQA). Inspired by the interdisciplinary collaboration among human scientists, an AI expert group acts as consultants, utilizing a diverse tool pool to comprehensively analyze questions. Through comprehensive experiments, GeoMap-Agent achieves an overall score of 0.811 on GeoMap-Bench, significantly outperforming 0.369 of GPT-4o. Our work, emPowering gEologic mAp holistiC undErstanding (PEACE) with MLLMs, paves the way for advanced AI applications in geology, enhancing the efficiency and accuracy of geological investigations.

  • 11 authors
·
Jan 10, 2025

The Impact of Medication Non-adherence on Adverse Outcomes: Evidence from Schizophrenia Patients via Survival Analysis

This study quantifies the association between non-adherence to antipsychotic medications and adverse outcomes in individuals with schizophrenia. We frame the problem using survival analysis, focusing on the time to the earliest of several adverse events (early death, involuntary hospitalization, jail booking). We extend standard causal inference methods (T-learner, S-learner, nearest neighbor matching) to utilize various survival models to estimate individual and average treatment effects, where treatment corresponds to medication non-adherence. Analyses are repeated using different amounts of longitudinal information (3, 6, 9, and 12 months). Using data from Allegheny County in western Pennsylvania, we find strong evidence that non-adherence advances adverse outcomes by approximately 1 to 4 months. Ablation studies confirm that county-provided risk scores adjust for key confounders, as their removal amplifies the estimated effects. Subgroup analyses by medication formulation (injectable vs. oral) and medication type consistently show that non-adherence is associated with earlier adverse events. These findings highlight the clinical importance of adherence in delaying psychiatric crises and show that integrating survival analysis with causal inference tools can yield policy-relevant insights. We caution that although we apply causal inference, we only make associative claims and discuss assumptions needed for causal interpretation.