Opportunities in AI/ML for the Rubin LSST Dark Energy Science Collaboration

The Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) will produce unprecedented volumes of heterogeneous astronomical data (images, catalogs, and alerts) that challenge traditional analysis pipelines. The LSST Dark Energy Science Collaboration (DESC) aims to derive robust constraints on dark energy and dark matter from these data, requiring methods that are statistically powerful, scalable, and operationally reliable. Artificial intelligence and machine learning (AI/ML) are already embedded across DESC science workflows, from photometric redshifts and transient classification to weak lensing inference and cosmological simulations. Yet their utility for precision cosmology hinges on trustworthy uncertainty quantification, robustness to covariate shift and model misspecification, and reproducible integration within scientific pipelines. This white paper surveys the current landscape of AI/ML across DESC's primary cosmological probes and cross-cutting analyses, revealing that the same core methodologies and fundamental challenges recur across disparate science cases. Since progress on these cross-cutting challenges would benefit multiple probes simultaneously, we identify key methodological research priorities, including Bayesian inference at scale, physics-informed methods, validation frameworks, and active learning for discovery. With an eye on emerging techniques, we also explore the potential of the latest foundation model methodologies and LLM-driven agentic AI systems to reshape DESC workflows, provided their deployment is coupled with rigorous evaluation and governance. Finally, we discuss critical software, computing, data infrastructure, and human capital requirements for the successful deployment of these new methodologies, and consider associated risks and opportunities for broader coordination with external actors.

Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

CYPRESS: Crop Yield Prediction via Regression on Prithvi's Encoder for Satellite Sensing

Accurate and timely crop yield prediction is crucial for global food security and modern agricultural management. Traditional methods often lack the scalability and granularity required for precision farming. This paper introduces CYPRESS (Crop Yield Prediction via Regression on Prithvi's Encoder for Satellite Sensing), a deep learning model designed for high-resolution, intra-field canola yield prediction. CYPRESS leverages a pre-trained, large-scale geospatial foundation model (Prithvi-EO-2.0-600M) and adapts it for a continuous regression task, transforming multi-temporal satellite imagery into dense, pixel-level yield maps. Evaluated on a comprehensive dataset from the Canadian Prairies, CYPRESS demonstrates superior performance over existing deep learning-based yield prediction models, highlighting the effectiveness of fine-tuning foundation models for specialized agricultural applications. By providing a continuous, high-resolution output, CYPRESS offers a more actionable tool for precision agriculture than conventional classification or county-level aggregation methods. This work validates a novel approach that bridges the gap between large-scale Earth observation and on-farm decision-making, offering a scalable solution for detailed agricultural monitoring.

Integrated Planning and Control on Manifolds: Factor Graph Representation and Toolkit

Model predictive control (MPC) faces significant limitations when applied to systems evolving on nonlinear manifolds, such as robotic attitude dynamics and constrained motion planning, where traditional Euclidean formulations struggle with singularities, over-parameterization, and poor convergence. To overcome these challenges, this paper introduces FactorMPC, a factor-graph based MPC toolkit that unifies system dynamics, constraints, and objectives into a modular, user-friendly, and efficient optimization structure. Our approach natively supports manifold-valued states with Gaussian uncertainties modeled in tangent spaces. By exploiting the sparsity and probabilistic structure of factor graphs, the toolkit achieves real-time performance even for high-dimensional systems with complex constraints. The velocity-extended on-manifold control barrier function (CBF)-based obstacle avoidance factors are designed for safety-critical applications. By bridging graphical models with safety-critical MPC, our work offers a scalable and geometrically consistent framework for integrated planning and control. The simulations and experimental results on the quadrotor demonstrate superior trajectory tracking and obstacle avoidance performance compared to baseline methods. To foster research reproducibility, we have provided open-source implementation offering plug-and-play factors.

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Exploring Strategies for Personalized Radiation Therapy: Part III Identifying genetic determinants for Radiation Response with Meta Learning

Radiation response in cancer is shaped by complex, patient specific biology, yet current treatment strategies often rely on uniform dose prescriptions without accounting for tumor heterogeneity. In this study, we introduce a meta learning framework for one-shot prediction of radiosensitivity measured by SF2 using cell line level gene expression data. Unlike the widely used Radiosensitivity Index RSI a rank-based linear model trained on a fixed 10-gene signature, our proposed meta-learned model allows the importance of each gene to vary by sample through fine tuning. This flexibility addresses key limitations of static models like RSI, which assume uniform gene contributions across tumor types and discard expression magnitude and gene gene interactions. Our results show that meta learning offers robust generalization to unseen samples and performs well in tumor subgroups with high radiosensitivity variability, such as adenocarcinoma and large cell carcinoma. By learning transferable structure across tasks while preserving sample specific adaptability, our approach enables rapid adaptation to individual samples, improving predictive accuracy across diverse tumor subtypes while uncovering context dependent patterns of gene influence that may inform personalized therapy.

From High-SNR Radar Signal to ECG: A Transfer Learning Model with Cardio-Focusing Algorithm for Scenarios with Limited Data

Electrocardiogram (ECG), as a crucial find-grained cardiac feature, has been successfully recovered from radar signals in the literature, but the performance heavily relies on the high-quality radar signal and numerous radar-ECG pairs for training, restricting the applications in new scenarios due to data scarcity. Therefore, this work will focus on radar-based ECG recovery in new scenarios with limited data and propose a cardio-focusing and -tracking (CFT) algorithm to precisely track the cardiac location to ensure an efficient acquisition of high-quality radar signals. Furthermore, a transfer learning model (RFcardi) is proposed to extract cardio-related information from the radar signal without ECG ground truth based on the intrinsic sparsity of cardiac features, and only a few synchronous radar-ECG pairs are required to fine-tune the pre-trained model for the ECG recovery. The experimental results reveal that the proposed CFT can dynamically identify the cardiac location, and the RFcardi model can effectively generate faithful ECG recoveries after using a small number of radar-ECG pairs for training. The code and dataset are available after the publication.

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.

Recover from Horcrux: A Spectrogram Augmentation Method for Cardiac Feature Monitoring from Radar Signal Components

Radar-based wellness monitoring is becoming an effective measurement to provide accurate vital signs in a contactless manner, but data scarcity retards the related research on deep-learning-based methods. Data augmentation is commonly used to enrich the dataset by modifying the existing data, but most augmentation techniques can only couple with classification tasks. To enable the augmentation for regression tasks, this research proposes a spectrogram augmentation method, Horcrux, for radar-based cardiac feature monitoring (e.g., heartbeat detection, electrocardiogram reconstruction) with both classification and regression tasks involved. The proposed method is designed to increase the diversity of input samples while the augmented spectrogram is still faithful to the original ground truth vital sign. In addition, Horcrux proposes to inject zero values in specific areas to enhance the awareness of the deep learning model on subtle cardiac features, improving the performance for the limited dataset. Experimental result shows that Horcrux achieves an overall improvement of 16.20% in cardiac monitoring and has the potential to be extended to other spectrogram-based tasks. The code will be released upon publication.

Biomedical Foundation Model: A Survey

Foundation models, first introduced in 2021, are large-scale pre-trained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling them to excel in diverse downstream tasks. These models, like GPT, can be adapted to various applications such as question answering and visual understanding, outperforming task-specific AI models and earning their name due to broad applicability across fields. The development of biomedical foundation models marks a significant milestone in leveraging artificial intelligence (AI) to understand complex biological phenomena and advance medical research and practice. This survey explores the potential of foundation models across diverse domains within biomedical fields, including computational biology, drug discovery and development, clinical informatics, medical imaging, and public health. The purpose of this survey is to inspire ongoing research in the application of foundation models to health science.