Haoyang Su

Yankai Jiang, Wenjie Lou, Lilong Wang et al.

We introduce SCP: the Science Context Protocol, an open-source standard designed to accelerate discovery by enabling a global network of autonomous scientific agents. SCP is built on two foundational pillars: (1) Unified Resource Integration: At its core, SCP provides a universal specification for describing and invoking scientific resources, spanning software tools, models, datasets, and physical instruments. This protocol-level standardization enables AI agents and applications to discover, call, and compose capabilities seamlessly across disparate platforms and institutional boundaries. (2) Orchestrated Experiment Lifecycle Management: SCP complements the protocol with a secure service architecture, which comprises a centralized SCP Hub and federated SCP Servers. This architecture manages the complete experiment lifecycle (registration, planning, execution, monitoring, and archival), enforces fine-grained authentication and authorization, and orchestrates traceable, end-to-end workflows that bridge computational and physical laboratories. Based on SCP, we have constructed a scientific discovery platform that offers researchers and agents a large-scale ecosystem of more than 1,600 tool resources. Across diverse use cases, SCP facilitates secure, large-scale collaboration between heterogeneous AI systems and human researchers while significantly reducing integration overhead and enhancing reproducibility. By standardizing scientific context and tool orchestration at the protocol level, SCP establishes essential infrastructure for scalable, multi-institution, agent-driven science.

Haoyang Su, Renqi Chen, Shixiang Tang et al.

The rapid advancement of scientific progress requires innovative tools that can accelerate knowledge discovery. Although recent AI methods, particularly large language models (LLMs), have shown promise in tasks such as hypothesis generation and experimental design, they fall short of replicating the collaborative nature of real-world scientific practices, where diverse experts work together in teams to tackle complex problems. To address the limitations, we propose an LLM-based multi-agent system, i.e., Virtual Scientists (VirSci), designed to mimic the teamwork inherent in scientific research. VirSci organizes a team of agents to collaboratively generate, evaluate, and refine research ideas. Through comprehensive experiments, we demonstrate that this multi-agent approach outperforms the state-of-the-art method in producing novel scientific ideas. We further investigate the collaboration mechanisms that contribute to its tendency to produce ideas with higher novelty, offering valuable insights to guide future research and illuminating pathways toward building a robust system for autonomous scientific discovery. The code is available at https://github.com/open-sciencelab/Virtual-Scientists.

Lisheng Zhang, Lilong Wang, Xiangyu Sun et al.

Computational drug discovery, particularly the complex workflows of drug molecule screening and optimization, requires orchestrating dozens of specialized tools in multi-step workflows, yet current AI agents struggle to maintain robust performance and consistently underperform in these high-complexity scenarios. Here we present MolClaw, an autonomous agent that leads drug molecule evaluation, screening, and optimization. It unifies over 30 specialized domain resources through a three-tier hierarchical skill architecture (70 skills in total) that facilitates agent long-term interaction at runtime: tool-level skills standardize atomic operations, workflow-level skills compose them into validated pipelines with quality check and reflection, and a discipline-level skill supplies scientific principles governing planning and verification across all scenarios in the field. Additionally, we introduce MolBench, a benchmark comprising molecular screening, optimization, and end-to-end discovery challenges spanning 8 to 50+ sequential tool calls. MolClaw achieves state-of-the-art performance across all metrics, and ablation studies confirm that gains concentrate on tasks that demand structured workflows while vanishing on those solvable with ad hoc scripting, establishing workflow orchestration competence as the primary capability bottleneck for AI-driven drug discovery.

Jie Ying, Zihong Chen, Zhefan Wang et al.

Seed science is essential for modern agriculture, directly influencing crop yields and global food security. However, challenges such as interdisciplinary complexity and high costs with limited returns hinder progress, leading to a shortage of experts and insufficient technological support. While large language models (LLMs) have shown promise across various fields, their application in seed science remains limited due to the scarcity of digital resources, complex gene-trait relationships, and the lack of standardized benchmarks. To address this gap, we introduce SeedBench -- the first multi-task benchmark specifically designed for seed science. Developed in collaboration with domain experts, SeedBench focuses on seed breeding and simulates key aspects of modern breeding processes. We conduct a comprehensive evaluation of 26 leading LLMs, encompassing proprietary, open-source, and domain-specific fine-tuned models. Our findings not only highlight the substantial gaps between the power of LLMs and the real-world seed science problems, but also make a foundational step for research on LLMs for seed design.

Renqi Chen, Haoyang Su, Shixiang Tang

The Segment Anything Model (SAM) has emerged as a powerful visual foundation model for image segmentation. However, adapting SAM to specific downstream tasks, such as medical and agricultural imaging, remains a significant challenge. To address this, Low-Rank Adaptation (LoRA) and its variants have been widely employed to enhancing SAM's adaptation performance on diverse domains. Despite advancements, a critical question arises: can we integrate inductive bias into the model? This is particularly relevant since the Transformer encoder in SAM inherently lacks spatial priors within image patches, potentially hindering the acquisition of high-level semantic information. In this paper, we propose NAS-LoRA, a new Parameter-Efficient Fine-Tuning (PEFT) method designed to bridge the semantic gap between pre-trained SAM and specialized domains. Specifically, NAS-LoRA incorporates a lightweight Neural Architecture Search (NAS) block between the encoder and decoder components of LoRA to dynamically optimize the prior knowledge integrated into weight updates. Furthermore, we propose a stage-wise optimization strategy to help the ViT encoder balance weight updates and architectural adjustments, facilitating the gradual learning of high-level semantic information. Various Experiments demonstrate our NAS-LoRA improves existing PEFT methods, while reducing training cost by 24.14% without increasing inference cost, highlighting the potential of NAS in enhancing PEFT for visual foundation models.

Haoyang Su, Ying Wen

Command line interface (CLI) agents are emerging as a practical paradigm for agent-computer interaction over evolving filesystems, executable command line programs, and online execution feedback. Recent work has used reinforcement learning (RL) to learn these interaction abilities from verifiable task feedback, yet few methods exploit the native structured attributes of CLI actions as learning signals. Beyond this underused action structure, CLI learning also couples two bottlenecks for coding agents. First, the agent must identify task-relevant evidence in a large codebase from partial observations. Second, sparse terminal rewards must be assigned to the actions that shape a long multi-turn trajectory. We study these bottlenecks through shell-driven information extraction and file editing tasks. For selective observation, we introduce $σ$-Reveal, an inference-time mechanism that selects token-budgeted context for the same CLI. For credit assignment, we propose Action Advantage Assignment ($\mathrm{A}^3$), a native agentic RL method that preserves the algorithmic complexity of standard agentic RL. $\mathrm{A}^3$ constructs turn-level advantages from episode-level relative feedback, abstract syntax tree (AST) based action sub-chain residuals, and tree-level trajectory margins. To further evaluate this problem setting, we construct ShellOps, a verifiable dataset suite covering CLI tasks in repository environments.

Renqi Chen, Xinzhe Zheng, Haoyang Su et al.

Accurate segmentation of ultrasound images is essential for reliable medical diagnoses but is challenged by poor image quality and scarce labeled data. Prior approaches have relied on manually designed, complex network architectures to improve multi-scale feature extraction. However, such handcrafted models offer limited gains when prior knowledge is inadequate and are prone to overfitting on small datasets. In this paper, we introduce DeNAS-ViT, a data-efficient NAS-optimized Vision Transformer, the first method to leverage neural architecture search (NAS) for ultrasound image segmentation by automatically optimizing model architecture through token-level search. Specifically, we propose an efficient NAS module that performs multi-scale token search prior to the ViT's attention mechanism, effectively capturing both contextual and local features while minimizing computational costs. Given ultrasound's data scarcity and NAS's inherent data demands, we further develop a NAS-guided semi-supervised learning (SSL) framework. This approach integrates network independence and contrastive learning within a stage-wise optimization strategy, significantly enhancing model robustness under limited-data conditions. Extensive experiments on public datasets demonstrate that DeNAS-ViT achieves state-of-the-art performance, maintaining robustness with minimal labeled data. Moreover, we highlight DeNAS-ViT's generalization potential beyond ultrasound imaging, underscoring its broader applicability.

Ziyu Sun, Haoyang Su, Hanqi Sun et al.

Mobile Crowd Sensing (MCS) is a promising paradigm that leverages mobile users and their smart portable devices to perform various real-world tasks. However, due to budget constraints and the inaccessibility of certain areas, Sparse MCS has emerged as a more practical alternative, collecting data from a limited number of target subareas and utilizing inference algorithms to complete the full sensing map. While existing approaches typically assume a time-discrete setting with data remaining constant within each sensing cycle, this simplification can introduce significant errors, especially when dealing with long cycles, as real-world sensing data often changes continuously. In this paper, we go from fine-grained completion, i.e., the subdivision of sensing cycles into minimal time units, towards a more accurate, time-continuous completion. We first introduce Deep Matrix Factorization (DMF) as a neural network-enabled framework and enhance it with a Recurrent Neural Network (RNN-DMF) to capture temporal correlations in these finer time slices. To further deal with the continuous data, we propose TIME-DMF, which captures temporal information across unequal intervals, enabling time-continuous completion. Additionally, we present the Query-Generate (Q-G) strategy within TIME-DMF to model the infinite states of continuous data. Extensive experiments across five types of sensing tasks demonstrate the effectiveness of our models and the advantages of time-continuous completion.

Shaohao Rui, Haoyang Su, Jinyi Xiang et al.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

Renqi Chen, Wenwei Han, Haohao Zhang et al.

Genomic selection (GS), as a critical crop breeding strategy, plays a key role in enhancing food production and addressing the global hunger crisis. The predominant approaches in GS currently revolve around employing statistical methods for prediction. However, statistical methods often come with two main limitations: strong statistical priors and linear assumptions. A recent trend is to capture the non-linear relationships between markers by deep learning. However, as crop datasets are commonly long sequences with limited samples, the robustness of deep learning models, especially Transformers, remains a challenge. In this work, to unleash the unexplored potential of attention mechanism for the task of interest, we propose a simple yet effective Transformer-based framework that enables end-to-end training of the whole sequence. Via experiments on rice3k and wheat3k datasets, we show that, with simple tricks such as k-mer tokenization and random masking, Transformer can achieve overall superior performance against seminal methods on GS tasks of interest.

Haoyang Su, Shaohao Rui, Jinyi Xiang et al.

Accurate and contrast-free Major Adverse Cardiac Events (MACE) prediction from Cine MRI sequences remains a critical challenge. Existing methods typically necessitate supervised learning based on human-refined masks in the ventricular myocardium, which become impractical without contrast agents. We introduce a self-supervised framework, namely Codebook-based Temporal-Spatial Learning (CTSL), that learns dynamic, spatiotemporal representations from raw Cine data without requiring segmentation masks. CTSL decouples temporal and spatial features through a multi-view distillation strategy, where the teacher model processes multiple Cine views, and the student model learns from reduced-dimensional Cine-SA sequences. By leveraging codebook-based feature representations and dynamic lesion self-detection through motion cues, CTSL captures intricate temporal dependencies and motion patterns. High-confidence MACE risk predictions are achieved through our model, providing a rapid, non-invasive solution for cardiac risk assessment that outperforms traditional contrast-dependent methods, thereby enabling timely and accessible heart disease diagnosis in clinical settings.

Haoyang Su, Shaoting Zhang, Xiaosong Wang

The emergence of tool-calling-based agent systems introduces a more evidence-driven paradigm for pathology image analysis in contrast to the coarse-grained text-image diagnostic approaches. With the recent large-scale experimental adoption of spatial transcriptomics technologies, molecularly validated pathological diagnosis is becoming increasingly open and accessible. In this work, we propose LAMMI-Pathology (LVLM-Agent System for Molecularly Informed Medical Intelligence in Pathology), a scalable agent framework for domain-specific agent tool-calling. LAMMI-Pathology adopts a tool-centric, bottom-up architecture in which customized domain-adaptive tools serve as the foundation. These tools are clustered by domain style to form component agents, which are then coordinated through a top-level planner hierarchically, avoiding excessively long context lengths that could induce task drift. Based on that, we introduce a novel trajectory construction mechanism based on Atomic Execution Nodes (AENs), which serve as reliable and composable units for building semi-simulated reasoning trajectories that capture credible agent-tool interactions. Building on this foundation, we develop a trajectory-aware fine-tuning strategy that aligns the planner's decision-making process with these multi-step reasoning trajectories, thereby enhancing inference robustness in pathology understanding and its adaptive use of the customized toolset.

Haoyang Su, Jin-Yi Xiang, Shaohao Rui et al.

Accurate prediction of major adverse cardiac events (MACE) remains a central challenge in cardiovascular prognosis. We present PRISM (Prompt-guided Representation Integration for Survival Modeling), a self-supervised framework that integrates visual representations from non-contrast cardiac cine magnetic resonance imaging with structured electronic health records (EHRs) for survival analysis. PRISM extracts temporally synchronized imaging features through motion-aware multi-view distillation and modulates them using medically informed textual prompts to enable fine-grained risk prediction. Across four independent clinical cohorts, PRISM consistently surpasses classical survival prediction models and state-of-the-art (SOTA) deep learning baselines under internal and external validation. Further clinical findings demonstrate that the combined imaging and EHR representations derived from PRISM provide valuable insights into cardiac risk across diverse cohorts. Three distinct imaging signatures associated with elevated MACE risk are uncovered, including lateral wall dyssynchrony, inferior wall hypersensitivity, and anterior elevated focus during diastole. Prompt-guided attribution further identifies hypertension, diabetes, and smoking as dominant contributors among clinical and physiological EHR factors.

Renqi Chen, Haoyang Su, Shixiang Tang et al.

The Science of Science (SoS) explores the mechanisms underlying scientific discovery, and offers valuable insights for enhancing scientific efficiency and fostering innovation. Traditional approaches often rely on simplistic assumptions and basic statistical tools, such as linear regression and rule-based simulations, which struggle to capture the complexity and scale of modern research ecosystems. The advent of artificial intelligence (AI) presents a transformative opportunity for the next generation of SoS, enabling the automation of large-scale pattern discovery and uncovering insights previously unattainable. This paper offers a forward-looking perspective on the integration of Science of Science with AI for automated research pattern discovery and highlights key open challenges that could greatly benefit from AI. We outline the advantages of AI over traditional methods, discuss potential limitations, and propose pathways to overcome them. Additionally, we present a preliminary multi-agent system as an illustrative example to simulate research societies, showcasing AI's ability to replicate real-world research patterns and accelerate progress in Science of Science research.

Dingning Liu, Jinzhe Li, Haoyang Su et al.

Weed control is a critical challenge in modern agriculture, as weeds compete with crops for essential nutrient resources, significantly reducing crop yield and quality. Traditional weed control methods, including chemical and mechanical approaches, have real-life limitations such as associated environmental impact and efficiency. An emerging yet effective approach is laser weeding, which uses a laser beam as the stem cutter. Although there have been studies that use deep learning in weed recognition, its application in intelligent laser weeding still requires a comprehensive understanding. Thus, this study represents the first empirical investigation of weed recognition for laser weeding. To increase the efficiency of laser beam cut and avoid damaging the crops of interest, the laser beam shall be directly aimed at the weed root. Yet, weed stem detection remains an under-explored problem. We integrate the detection of crop and weed with the localization of weed stem into one end-to-end system. To train and validate the proposed system in a real-life scenario, we curate and construct a high-quality weed stem detection dataset with human annotations. The dataset consists of 7,161 high-resolution pictures collected in the field with annotations of 11,151 instances of weed. Experimental results show that the proposed system improves weeding accuracy by 6.7% and reduces energy cost by 32.3% compared to existing weed recognition systems.