Suiren-1.0 Technical Report: A Family of Molecular Foundation Models

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

DyJR: Preserving Diversity in Reinforcement Learning with Verifiable Rewards via Dynamic Jensen-Shannon Replay

While Reinforcement Learning (RL) enhances Large Language Model reasoning, on-policy algorithms like GRPO are sample-inefficient as they discard past rollouts. Existing experience replay methods address this by reusing accurate samples for direct policy updates, but this often incurs high computational costs and causes mode collapse via overfitting. We argue that historical data should prioritize sustaining diversity rather than simply reinforcing accuracy. To this end, we propose Dynamic Jensen-Shannon Replay (DyJR), a simple yet effective regularization framework using a dynamic reference distribution from recent trajectories. DyJR introduces two innovations: (1) A Time-Sensitive Dynamic Buffer that uses FIFO and adaptive sizing to retain only temporally proximal samples, synchronizing with model evolution; and (2) Jensen-Shannon Divergence Regularization, which replaces direct gradient updates with a distributional constraint to prevent diversity collapse. Experiments on mathematical reasoning and Text-to-SQL benchmarks demonstrate that DyJR significantly outperforms GRPO as well as baselines such as RLEP and Ex-GRPO, while maintaining training efficiency comparable to the original GRPO. Furthermore, from the perspective of Rank-$k$ token probability evolution, we show that DyJR enhances diversity and mitigates over-reliance on Rank-1 tokens, elucidating how specific sub-modules of DyJR influence the training dynamics.

InterveneBench: Benchmarking LLMs for Intervention Reasoning and Causal Study Design in Real Social Systems

Causal inference in social science relies on end-to-end, intervention-centered research-design reasoning grounded in real-world policy interventions, but current benchmarks fail to evaluate this capability of large language models (LLMs). We present InterveneBench, a benchmark designed to assess such reasoning in realistic social settings. Each instance in InterveneBench is derived from an empirical social science study and requires models to reason about policy interventions and identification assumptions without access to predefined causal graphs or structural equations. InterveneBench comprises 744 peer-reviewed studies across diverse policy domains. Experimental results show that state-of-the-art LLMs struggle under this setting. To address this limitation, we further propose a multi-agent framework, STRIDES. It achieves significant performance improvements over state-of-the-art reasoning models. Our code and data are available at https://github.com/Sii-yuning/STRIDES.

PA-Net: Precipitation-Adaptive Mixture-of-Experts for Long-Tail Rainfall Nowcasting

Precipitation nowcasting is vital for flood warning, agricultural management, and emergency response, yet two bottlenecks persist: the prohibitive cost of modeling million-scale spatiotemporal tokens from multi-variate atmospheric fields, and the extreme long-tailed rainfall distribution where heavy-to-torrential events -- those of greatest societal impact -- constitute fewer than 0.1% of all samples. We propose the Precipitation-Adaptive Network (PA-Net), a Transformer framework whose computational budget is explicitly governed by rainfall intensity. Its core component, Precipitation-Adaptive MoE (PA-MoE), dynamically scales the number of activated experts per token according to local precipitation magnitude, channeling richer representational capacity toward the rare yet critical heavy-rainfall tail. A Dual-Axis Compressed Latent Attention mechanism factorizes spatiotemporal attention with convolutional reduction to manage massive context lengths, while an intensity-aware training protocol progressively amplifies learning signals from extreme-rainfall samples. Experiment on ERA5 demonstrate consistent improvements over state-of-the-art baselines, with particularly significant gains in heavy-rain and rainstorm regimes.

Developing Foundation Models for Universal Segmentation from 3D Whole-Body Positron Emission Tomography

Positron emission tomography (PET) is a key nuclear medicine imaging modality that visualizes radiotracer distributions to quantify in vivo physiological and metabolic processes, playing an irreplaceable role in disease management. Despite its clinical importance, the development of deep learning models for quantitative PET image analysis remains severely limited, driven by both the inherent segmentation challenge from PET's paucity of anatomical contrast and the high costs of data acquisition and annotation. To bridge this gap, we develop generalist foundational models for universal segmentation from 3D whole-body PET imaging. We first build the largest and most comprehensive PET dataset to date, comprising 11041 3D whole-body PET scans with 59831 segmentation masks for model development. Based on this dataset, we present SegAnyPET, an innovative foundational model with general-purpose applicability to diverse segmentation tasks. Built on a 3D architecture with a prompt engineering strategy for mask generation, SegAnyPET enables universal and scalable organ and lesion segmentation, supports efficient human correction with minimal effort, and enables a clinical human-in-the-loop workflow. Extensive evaluations on multi-center, multi-tracer, multi-disease datasets demonstrate that SegAnyPET achieves strong zero-shot performance across a wide range of segmentation tasks, highlighting its potential to advance the clinical applications of molecular imaging.

PET-F2I: A Comprehensive Benchmark and Parameter-Efficient Fine-Tuning of LLMs for PET/CT Report Impression Generation

PET/CT imaging is pivotal in oncology and nuclear medicine, yet summarizing complex findings into precise diagnostic impressions is labor-intensive. While LLMs have shown promise in medical text generation, their capability in the highly specialized domain of PET/CT remains underexplored. We introduce PET-F2I-41K (PET Findings-to-Impression Benchmark), a large-scale benchmark for PET/CT impression generation using LLMs, constructed from over 41k real-world reports. Using PET-F2I-41K, we conduct a comprehensive evaluation of 27 models across proprietary frontier LLMs, open-source generalist models, and medical-domain LLMs, and we develop a domain-adapted 7B model (PET-F2I-7B) fine-tuned from Qwen2.5-7B-Instruct via LoRA. Beyond standard NLG metrics (e.g., BLEU-4, ROUGE-L, BERTScore), we propose three clinically grounded metrics - Entity Coverage Rate (ECR), Uncovered Entity Rate (UER), and Factual Consistency Rate (FCR) - to assess diagnostic completeness and factual reliability. Experiments reveal that neither frontier nor medical-domain LLMs perform adequately in zero-shot settings. In contrast, PET-F2I-7B achieves substantial gains (e.g., 0.708 BLEU-4) and a 3.0x improvement in entity coverage over the strongest baseline, while offering advantages in cost, latency, and privacy. Beyond this modeling contribution, PET-F2I-41K establishes a standardized evaluation framework to accelerate the development of reliable and clinically deployable reporting systems for PET/CT.

Equivariant Asynchronous Diffusion: An Adaptive Denoising Schedule for Accelerated Molecular Conformation Generation

Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between training and inference. Conversely, synchronous diffusion models denoise all atoms at once, offering a molecule-level horizon but failing to capture the causal relationships inherent in hierarchical molecular structures. We introduce Equivariant Asynchronous Diffusion (EAD) to overcome these limitations. EAD is a novel diffusion model that combines the strengths of both approaches: it uses an asynchronous denoising schedule to better capture molecular hierarchy while maintaining a molecule-level horizon. Since these relationships are often complex, we propose a dynamic scheduling mechanism to adaptively determine the denoising timestep. Experimental results show that EAD achieves state-of-the-art performance in 3D molecular generation.

AI-for-Science Low-code Platform with Bayesian Adversarial Multi-Agent Framework

Large Language Models (LLMs) demonstrate potentials for automating scientific code generation but face challenges in reliability, error propagation in multi-agent workflows, and evaluation in domains with ill-defined success metrics. We present a Bayesian adversarial multi-agent framework specifically designed for AI for Science (AI4S) tasks in the form of a Low-code Platform (LCP). Three LLM-based agents are coordinated under the Bayesian framework: a Task Manager that structures user inputs into actionable plans and adaptive test cases, a Code Generator that produces candidate solutions, and an Evaluator providing comprehensive feedback. The framework employs an adversarial loop where the Task Manager iteratively refines test cases to challenge the Code Generator, while prompt distributions are dynamically updated using Bayesian principles by integrating code quality metrics: functional correctness, structural alignment, and static analysis. This co-optimization of tests and code reduces dependence on LLM reliability and addresses evaluation uncertainty inherent to scientific tasks. LCP also streamlines human-AI collaboration by translating non-expert prompts into domain-specific requirements, bypassing the need for manual prompt engineering by practitioners without coding backgrounds. Benchmark evaluations demonstrate LCP's effectiveness in generating robust code while minimizing error propagation. The proposed platform is also tested on an Earth Science cross-disciplinary task and demonstrates strong reliability, outperforming competing models.

Uncovering Modality Discrepancy and Generalization Illusion for General-Purpose 3D Medical Segmentation

While emerging 3D medical foundation models are envisioned as versatile tools with offer general-purpose capabilities, their validation remains largely confined to regional and structural imaging, leaving a significant modality discrepancy unexplored. To provide a rigorous and objective assessment, we curate the UMD dataset comprising 490 whole-body PET/CT and 464 whole-body PET/MRI scans ($\sim$675k 2D images, $\sim$12k 3D organ annotations) and conduct a thorough and comprehensive evaluation of representative 3D segmentation foundation models. Through intra-subject controlled comparisons of paired scans, we isolate imaging modality as the primary independent variable to evaluate model robustness in real-world applications. Our evaluation reveals a stark discrepancy between literature-reported benchmarks and real-world efficacy, particularly when transitioning from structural to functional domains. Such systemic failures underscore that current 3D foundation models are far from achieving truly general-purpose status, necessitating a paradigm shift toward multi-modal training and evaluation to bridge the gap between idealized benchmarking and comprehensive clinical utility. This dataset and analysis establish a foundational cornerstone for future research to develop truly modality-agnostic medical foundation models.

Structure-based RNA Design by Step-wise Optimization of Latent Diffusion Model

RNA inverse folding, designing sequences to form specific 3D structures, is critical for therapeutics, gene regulation, and synthetic biology. Current methods, focused on sequence recovery, struggle to address structural objectives like secondary structure consistency (SS), minimum free energy (MFE), and local distance difference test (LDDT), leading to suboptimal structural accuracy. To tackle this, we propose a reinforcement learning (RL) framework integrated with a latent diffusion model (LDM). Drawing inspiration from the success of diffusion models in RNA inverse folding, which adeptly model complex sequence-structure interactions, we develop an LDM incorporating pre-trained RNA-FM embeddings from a large-scale RNA model. These embeddings capture co-evolutionary patterns, markedly improving sequence recovery accuracy. However, existing approaches, including diffusion-based methods, cannot effectively handle non-differentiable structural objectives. By contrast, RL excels in this task by using policy-driven reward optimization to navigate complex, non-gradient-based objectives, offering a significant advantage over traditional methods. In summary, we propose the Step-wise Optimization of Latent Diffusion Model (SOLD), a novel RL framework that optimizes single-step noise without sampling the full diffusion trajectory, achieving efficient refinement of multiple structural objectives. Experimental results demonstrate SOLD surpasses its LDM baseline and state-of-the-art methods across all metrics, establishing a robust framework for RNA inverse folding with profound implications for biotechnological and therapeutic applications.