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新论文 · v1arXiv:2611.17323

AgentSSL: Can MLE Agents Leverage Unlabeled Data?

Ethan Lin, Akanksha Sarkar, Ziang Liu, Kristin Branson, Jennifer J. Sun

原文摘要

Applying machine learning systems to new domains introduces bottlenecks in both labeled data acquisition and manual pipeline engineering. While recent MLE agents show promise in automating pipeline design, they have been studied almost exclusively in fully supervised settings, leaving them untested in realistic regimes where labeled data is scarce but unlabeled data is abundant. In this work, we introduce Agentic Semi-Supervised Learning (AgentSSL), framing SSL as a program search problem and studying how agents navigate this space under limited supervision. We find that even under weak feedback and matched compute, agents can synthesize code that combines and adapts established SSL techniques, exceeding the strongest human-engineered baselines in 8 of 12 settings by up to +21.8%. However, our results identify program selection as a critical bottleneck in AgentSSL, where performance drops by as much as 47% when selecting based on the agent's feedback metric. To systematically study this bottleneck, we introduce ProgramSelectBench, a large-scale benchmark with a combined total of 16,977 agent-generated and human-engineered SSL programs, and evaluate both unsupervised and active program selection methods. We further evaluate AgentSSL on real-world ecology detection tasks, highlighting the opportunities and challenges of transferring agent-discovered strategies beyond controlled benchmarks.

cs.AI · cs.LG

新论文 · v1arXiv:2611.16099

CupOFMoCA: Coupled Objective-Guided Discrete Flows for Molecular Conjugate Assembly

Ruoxi Rosie Zhang, Ziang Li, Jiatao Gu, Pranam Chatterjee

原文摘要

Molecular conjugates, including PROTACs and peptide-drug conjugates (PDCs), derive their function from the joint behavior of multiple coupled components, yet most generative approaches design these components independently and combine them only after generation. Such staged pipelines ignore cross-component dependencies and often produce conjugates that are chemically invalid, fall outside empirical conjugate distributions, or lose function upon assembly. In this work, we introduce Coupled Objective-Guided Discrete Flows for Molecular Conjugate Assembly (CupOFMoCA), a discrete generative method that enforces cross-component chemical constraints during conjugate generation. CupOFMoCA restricts guided updates to chemically feasible conjugate states and reweights local transitions using molecular design objectives. Across three PDC systems, coupled generation achieved 100% conjugation validity among valid peptides and increased valid yield over matched post-hoc filtering, with comparable predicted binding scores across the full valid sets. In three-seed evaluations of three PROTAC systems, CupOFMoCA achieved the highest assembly validity on two systems and generated more assembly-valid molecules per second than the evaluated baselines. We further evaluated the generated PROTACs with post-hoc DegradeMaster scoring and explicit-solvent molecular dynamics, supporting their predicted activity and conformational properties. Together, these results establish CupOFMoCA as an efficient generator of molecular conjugates, supporting therapeutic development via coordinated control of assembly and molecular properties.

q-bio.BM · cs.LG

新论文 · v1arXiv:2611.14514

对比式发现:在竞争性解释中进行开放式科学发现

Contrastive Discovery: Open-Ended Scientific Discovery over Competing Explanations

Ziang Liu, James J. Kim, Yijia Dai, Jennifer J. Sun

AI 速读 基于摘要

提出 Contrastive Discovery,用互斥且完备的竞争解释集合替代单一假设,让 LLM 智能体在相同证据与实验预算下把被否定的假设进一步归结到具体替代解释。

cs.AI · cs.CL · cs.LG

查看原文摘要

LLM agents are increasingly used for open-ended, data-driven scientific discovery, yet most of them evaluate hypotheses pointwise, testing an empirical claim $h$ only against its complement $\neg h$. When evidence rejects $h$, the agent learns that one explanation is unlikely but not which alternative the evidence supports. To recover that alternative, we introduce Contrastive Discovery, which replaces the single hypothesis with a contrast set, a scientific question paired with mutually exclusive and collectively exhaustive competing explanations. Each experiment is scored by how its evidence redistributes belief across the set, and the question is resolved when belief concentrates on one explanation. Because contrast sets change only the unit an agent proposes and scores, an existing agent can use them to re-evaluate evidence it has already collected or to guide its search. Across six domains, $89\%$ of the pointwise candidates with the largest belief shifts are rejections. On the same evidence, contrast sets resolve $73\%$ of these candidates to a specific alternative. When contrast sets guide search, the agent resolves $67\%$ more questions than pointwise surprisal under the same experiment budget. In a blinded study, $38$ human experts chose the same explanation on $78\%$ of resolved questions and on $82\%$ of questions where the pointwise agent rejected its hypothesis and stopped. Together, these results support explicit competing explanations as a way for discovery agents to resolve more scientific questions from the same evidence and validation budget.

版本更新 · v2arXiv:2609.19134

ScienceIDE: Turning World's Scientific Codebase into Agent Learnable Environments

Hejia Geng, Zesen Huang, Haoyang Li, Wenbin Li, Koutian Wu, Zihan Zhou, Yuanbo Pang, Weihao Liu 等 63 位作者

原文摘要

Scientific code repositories encode decades of human knowledge in executable models, methods, and tools. Yet fragmented toolchains, implicit domain conventions, and specialized correctness criteria make this knowledge difficult to convert into reliable learning experience-a challenge we call the scientific experience bottleneck. We introduce ScienceIDE, infrastructure for turning the world's scientific code into programmable environments for scientific agents. Guided by expert-defined scientific cases and acceptance criteria, agents transform repositories into executable environments that support task generation, execution, and scientific verification. These environments provide a shared foundation for supervised fine-tuning, reinforcement learning, and evaluation. Using verified interaction trajectories, we train PhAI-IDE-72B/9B/4B. The model family shows gains in held-out scientific-code repair and across selected general-purpose benchmarks in code, reasoning, and knowledge, providing evidence of positive transfer from scientific experience to broader capabilities. ScienceIDE lays the foundation for an integrated workspace for agent learning and scientific practice, making humanity's scientific software a shared substrate for developing scientific intelligence. Code: https://github.com/aitofound/ScienceIDE

cs.CL · cs.CY