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版本更新 · v2arXiv:2605.28655

AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation

Shanghua Gao, Ada Fang, Marinka Zitnik

原文摘要

Scientific research proceeds through iterative cycles of hypothesis generation, experiment design, execution, and revision. AI agents can automate parts of this process, but existing approaches typically follow a single research trajectory or coordinate through a central planner with fixed objectives. As a result, they struggle to sustain parallel exploration, adapt as experimental evidence changes, or preserve knowledge of failed directions over long-running experiments. We introduce AutoScientists, a decentralized team of AI agents for long-running computational scientific experimentation. Agents interpret a shared experimental state, self-organize into teams around promising hypotheses, critique proposals before using experimental compute, and share successes and failures to reduce redundant exploration. Under matched experimental budgets, AutoScientists improves over prior AI agents across biomedical machine learning, language-model training optimization, and protein fitness prediction. On BioML-Bench, spanning biomedical imaging, protein engineering, single-cell omics, and drug discovery, AutoScientists achieves a mean leaderboard percentile of 74.4% across 24 tasks, improving over the strongest AI agent by +8.33%. On GPT training optimization, AutoScientists reaches a target validation bits-per-byte 1.9x faster than Autoresearch and continues discovering improvements from a starting champion where the single-agent approach finds none (7 vs. 0 accepted improvements). On ProteinGym fitness prediction, AutoScientists discovers a method for ACE2-Spike binding that improves over the current state-of-the-art model by +12.5% in Spearman correlation. Applied without modification across all 217 ProteinGym assays, the same method improves over the prior state of the art by +6.5% (Spearman correlation).

cs.AI

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arXiv ↗PDF ↗
新论文 · v1arXiv:2611.11381

Does Predictive Performance Translate to Causal Performance? Evaluating tabular foundation models as nuisance learners for causal effect estimation

Andrew R Weckstein, Issa J Dahabreh, Marinka Zitnik, Sonia Hernández-Díaz, Sebastian Schneeweiss

原文摘要

Tabular foundation models based on prior-data fitted networks (PFNs) achieve strong predictive performance, but their value for causal inference is unclear. We evaluated whether PFNs, which predict through in-context learning, could match or outperform conventional nuisance learners in supporting accurate causal estimation and reliable uncertainty quantification (inference). Learners modeled propensity scores and outcome regressions within doubly robust estimators of average causal effects, with and without cross-fitting, across synthetic and semi-synthetic settings with varying confounding complexity and effect heterogeneity. Under simple parametric data-generating processes, the PFNs were competitive with correctly specified parametric regressions and ensembles containing them. In more complex settings, they outperformed all conventional learners evaluated, including richly specified Super Learner ensembles, for both accuracy and uncertainty quantification. As sample size increased, only the two PFN models (TabPFN and Mitra) consistently approached nominal confidence interval coverage, whereas under-coverage persisted for conventional learners. In some settings, PFNs achieved near-nominal coverage and well-calibrated standard errors even without cross-fitting. At the smallest sample size (n=200) and in the higher-dimensional semi-synthetic settings, PFNs and other flexible learners exhibited poor coverage without cross-fitting. For PFNs, this appeared to be driven by propensity score overfitting consistent with in-sample memorization of treatment labels. These findings highlight the promise of prior-data fitted networks as in-context nuisance learners for causal estimation, while underscoring the need for further evaluation in challenging settings.

stat.AP · cs.AI · cs.LG · stat.ME · stat.ML

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arXiv ↗PDF ↗
版本更新 · v3arXiv:2505.19337

Hindsight Relabeling is All You Need for Reach-Avoid Learning

Kevin Li, Marinka Zitnik

原文摘要

Offline goal-conditioned reinforcement learning methods have shown promise for reach-avoid tasks, where an agent must reach a target state while avoiding undesirable regions of the state space. Existing approaches typically encode avoid-region information into an augmented state space and cost function, which prevents flexible, dynamic specification of novel avoid-region information at evaluation time. They also rely heavily on meticulously designed reward and cost functions, limiting transferability to novel environments and specifications. We introduce RADT, a decision transformer approach for offline, reward-free, goal-conditioned, avoid-region-conditioned RL. RADT encodes goals and avoid-regions directly as prompt tokens, allowing any number of avoid-regions of arbitrary size to be specified at evaluation time. Using only suboptimal offline trajectories from a random policy, RADT can learn reach-avoid behavior in a completely data-driven manner using our novel avoid-region hindsight relabeling approach, without the need for reward/cost supervision. We benchmark RADT against existing offline goal-conditioned RL models across 17 tasks, environments, and experimental settings. RADT generalizes in a zero-shot manner to out-of-distribution avoid-region sizes and counts, outperforming baselines that require retraining. In one such zero-shot setting, RADT achieves 35.7% improvement in normalized cost over the best retrained baseline while maintaining high goal-reaching success. We also apply RADT to cell reprogramming in biology, demonstrating its versatility.

cs.LG · cs.AI · q-bio.QM

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arXiv ↗PDF ↗
新论文 · v1arXiv:2610.40447

从谱系上下文学习发育动力学

Learning developmental dynamics from lineage context

Gokul Gowri, Nic Fishman, William N. Colgan, Minming Wang, Yusuke Kijima, Sachin A. Kumar, Aleksandr Zimin, Luke W. Koblan 等 13 位作者

AI 速读 基于摘要

作者提出“谱系修补”（lineage inpainting）生成建模方法，利用树结构Transformer与随机插值从谱系上下文预测细胞状态动态。

q-bio.QM · cs.LG

arXiv ↗PDF ↗
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A central goal of biology is to predict the dynamics of multicellular systems. Lineage context (the states of a cell's sisters, cousins, etc.) could inform these predictions, but how best to leverage it remains unclear. Here we introduce lineage inpainting, a generative modeling approach that uses lineage context with tree-structured transformers and stochastic interpolants to model cell state dynamics across lineage trees. Applied to a lineage-traced transcriptional atlas of mouse embryogenesis, it recovers dynamics not resolved by gene expression alone, including multiple transcriptional convergence events where distinct lineages are drawn to a common state. Despite being fit on unperturbed development, lineage inpainting can generate hypotheses about perturbation responses by simulating counterfactuals. These simulations agree in many cases with observed developmental phenotypes, including a single-cell measurement of the Tbx5 knockout response. Our results show that lineage information provides a rich source of context for learning multicellular dynamics.

新论文 · v1arXiv:2610.38709

Latent Decision Flow Rewards for Clinical Guideline Reasoning

Gaurav Bhatt, Marinka Zitnik

原文摘要

Clinical practice guidelines encode evidence-based recommendations as conditional decision flows, which makes them a natural source of process supervision for training reasoning models. Two properties of clinical reasoning make this supervision difficult to use. A decision flow consistent with a guideline does not by itself determine the correct answer for a given patient, which we call the path--answer gap, and several valid decision flows can support the same clinical decision, which we call path multiplicity. Current training approaches address parts of this problem. Answer rewards supervise the final decision, and process rewards computed against a reference flow supervise one valid decision flow per case. Supervised fine-tuning on annotated flows teaches guideline-consistent reasoning but constrains the model to one trajectory per case and can reduce answer accuracy. We introduce GUIDER, a method that jointly optimizes a decision flow controller and a reasoning policy. The controller learns to generate plausible decision flows from guideline-derived supervision, and the policy learns to generate a decision flow and a final answer for each patient case. GUIDER computes the process reward for the policy over several controller-generated flows, which accounts for path multiplicity, and gates this reward on answer correctness, which addresses the path--answer gap. Joint training allows the process supervision to evolve with the policy. On MedGUIDE, GUIDER with Qwen3-14B achieves 82.5 weighted accuracy and 73.5 guideline adherence, 3.3 and 3.1 points above the strongest clinical reinforcement learning baseline. With Qwen3-14B and Gemma4-12B backbones, GUIDER also improves over CRPO, MRPO, and FaithMed on the out-of-domain benchmarks AMEGA-LLM, RealMedQA, and CancerGUIDE.

cs.LG · cs.AI

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arXiv ↗PDF ↗
版本更新 · v2arXiv:2602.10156

STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations

Boyang Fu, Sameer Gabbita, George Dasoulas, Xiang Lin, Shanghua Gao, Xiaorui Su, Soumya Ghosh, Marinka Zitnik

原文摘要

Prediction of the transcriptional response of a cell to a genetic perturbation is a central problem in the computational modeling of gene regulation. Perturbations of the same gene can produce different transcriptional responses depending on the targeted locus, such as an alternative transcription start site or a distal regulatory element, and gene-level perturbation models represent these distinct interventions with a single gene identifier. We introduce STRAND, a generative model that encodes the regulatory DNA sequence at the perturbation locus and uses this encoding to parameterize a conditional transport process from control to perturbed single-cell states. Sequence conditioning enables zero-shot prediction for perturbation targets absent from training and supports locus-resolved inputs at 128 bp model resolution within a 524 kb sequence window. On CRISPRi screens in K562, Jurkat, and RPE1 cells, STRAND achieves the best average rank on few-shot and unseen-gene benchmarks, with gains of up to 33% in perturbation discrimination, and improves transfer to held-out cell lines by up to 0.12 in $Δ$Pearson. Ablation studies attribute these gains to sequence conditioning and to conditional transport. At the locus level, STRAND distinguishes alternative transcription start sites and validated regulatory elements that gene-identifier models represent as a single perturbation. STRAND is available at https://github.com/mims-harvard/STRAND.

q-bio.GN · cs.LG · q-bio.CB

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arXiv ↗PDF ↗
首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.714ACL Anthology · ACL 2026

Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval

Joaquin Polonuer, Lucas Vittor Harvard University, Iñaki Arango Harvard Medical School, Harvard University, Ayush Noori University of Oxford and Harvard Medical School, Harvard University, David A. Clifton University of Oxford, Luciano Del Corro Universidad de San Andres and Lumina Labs, Marinka Zitnik Harvard University

原文摘要

Retrieving evidence for language model queries from knowledge graphs requires balancing broad search across the graph with multi-hop traversal to follow relational links. Similarity-based retrievers provide coverage but remain shallow, whereas traversal-based methods rely on selecting seed nodes to start exploration, which can fail when queries span multiple entities and relations. We introduce ARK: Adaptive Retriever of Knowledge, a tool-using KG retriever that gives a language model control over this breadth-depth tradeoff using a two-operation toolset: global lexical search over node descriptors and one-hop neighborhood exploration that composes into multi-hop traversal. ARK alternates between breadth-oriented discovery and depth-oriented expansion without depending on a fragile seed selection, a pre-set hop depth, or requiring retrieval training. ARK adapts tool use to queries, using global search for language-heavy queries and neighborhood exploration for relation-heavy queries.On STaRK, ARK reaches 59.1% average Hit@1 and 67.4 average MRR, improving average Hit@1 by up to 31.4% and average MRR by up to 28.0% over retrieval-based and agent-based training-free methods.Finally, we distill ARK’s tool-use trajectories from a large teacher into an 8B model via label-free imitation, improving Hit@1 by +7.0, +26.6, and +13.5 absolute points over the base 8B model on AMAZON, MAG, and PRIME datasets, respectively, while retaining up to 98.5% of the teacher’s Hit@1 rate.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表