#01Nov 10, 2026
cs.AI
Re-Search: Dissecting LLM Ideation Through a Two-Player Questioning Game
Muhan Gao, Hangxiao Zhu, Xinqi Su and 3 more
Research ideation is iterative: researchers refine their ideas step by step based on feedback. Yet existing evaluations obscure this search process, making it difficult to understand how LLMs explore the space of research ideas and what limits their progress. We introduce Re-Search, which adapts the format of Twenty Questions to research ideation: given only the research problem of a published paper, a model must rediscover the paper's core idea by asking yes-or-no questions. Built from 200 ICML 2026 papers, Re-Search tracks how a model's idea evolves as it asks questions and receives binary oracle feedback, isolating ideation from execution. Across six recent LLMs, nearly all progress happens within the first 30 of 100 questions, which largely decide how the game ends; after that, most models plateau. Through controlled interventions on the candidate questions and the hypothesis space, we find that the bottleneck is generation, not judgment: models recognize a good idea or a good question when one is offered, but often cannot produce it on their own. We further analyze the ideation traces and find that models fail by either over-exploiting one direction or over-exploring too many. These findings point to concrete design principles for autoresearch systems: since models can judge candidates they cannot produce, enriching the search with externally sourced ideas and questions may be more effective than improving any single model's generation ability.
#02Nov 10, 2026
cs.LG
Pyrite: Building and Benchmarking Protein-Ligand Pose Ranking Agents
Megha Srivastava, Michael H. Lim, Allison M. Keys and 2 more
Predicting how a ligand binds to its target is central to small-molecule drug discovery. Modern cofolding models can generate diverse candidate poses, but reliably ranking these candidates remains challenging. We introduce Pyrite, a pairwise pose-ranking benchmark comprising 1,500 pose pairs across diverse protein-ligand complexes. Expert chemists equipped with 3D visualization tools and physics-based scores perform near chance, highlighting the difficulty of interpreting available chemical signals. To investigate automated ranking, we introduce PyriteRep, a structured representation of molecular geometry, protein-ligand interactions, and physicochemical scores, and develop two LLM-based agents: PyriteReasoner, which directly compares poses through text-based reasoning, and PyriteFeaturizer, which generates executable code to construct features for logistic regression, optionally incorporating features derived from LLM subcalls. These agents achieve up to 67% and 74% accuracy, respectively, exceeding observed expert performance. LLM-guided feature discovery generally outperforms direct reasoning, while Group Relative Policy Optimization (GRPO) improves open-weight models, enabling them to match or surpass closed-source frontier models in our evaluations. These results establish Pyrite as a challenging test of pose-ranking ability and highlight LLM-guided feature discovery as a promising approach to interpret and combine the outputs of computational chemistry tools.
#03Nov 10, 2026
cs.LG
A Theory of Policy Optimization in Post-Training: Coverage Collapse and Reference Resets
Audrey Huang, Nan Jiang, Sham M. Kakade and 3 more
Policy optimization is central to language model post-training, yet principled guidance remains limited. We revisit its theoretical foundations to identify algorithms that learn near-optimal policies using total samples and gradient steps governed by the base model's response coverage, a measure of how readily it generates optimal responses. We call such algorithms coverage-preserving. This guarantee captures the goal of amplifying capabilities accessible through sampling from the base model. (1) Coverage collapse. REINFORCE, the basis for PPO and GRPO, can drive the probability of optimal responses to near zero, even as reward improves. This coverage collapse stalls optimization, and convergence can require exponentially many steps despite good initial coverage. The failure arises even with exact gradients and persists under KL regularization to the base model. (2) Reference resets. We show that repeatedly resetting the KL reference to the most recent policy mitigates coverage collapse. We formalize this intervention in Approximate Policy Mirror Descent (APMD), a meta-algorithm that approximately solves a sequence of KL-regularized RL subproblems. APMD enables stronger regularization, making each subproblem easier to solve, while reference resets allow convergence to global optimality. (3) Coverage-preserving algorithms. For softmax linear policies over pretrained features, we use APMD to establish the first global convergence guarantees showing that widely used families of post-training algorithms are coverage-preserving. These include stylized PPO and GRPO variants with explicit KL regularization and reference resets, and squared-loss algorithms that implement them implicitly, including those used to train the Kimi models. These results clarify how regularization, clipping, and objective choice affect the sampling and optimization costs of post-training.
#04Nov 10, 2026
cs.LG
When Does the Real Wiring Win? Testing connectome structure-function claims against unmeasured physiology
Yeyuan Liu
Connectome-constrained models are often used to argue that a measured wiring diagram outperforms shuffled or rewired wiring, and hence that structure shapes function. Such comparisons can confound wiring with how the models are tuned: a connectome fixes who connects to whom, not the excitability, gains or plasticity rates the model also needs, and modellers often tune these until the real-wiring model works. We separate three estimands: physiology tuned on the real wiring and transferred to nulls (P1), each wiring tuned on its own (P2), and P2 restricted to physiology consistent with independent data (P3). The biases involved are known in machine learning (under-tuned baselines, inherited weights, winner's curse); we measure what they do to biological conclusions, using synthetic ground truth, placebo nulls and three Drosophila circuit models. Some claims survive every protocol we test: segregated reward and punishment dopamine improves learning, and head-direction topography is required for a persistent bump. Others do not. In the mushroom body, the real Kenyon-cell output wiring beats a cross-subtype identity shuffle by 0.09 under P1 and P2 but loses to it by 0.09 under P3 (95% CIs exclude zero; held-out runs confirm). The verdict is set by the share of alpha'beta' cells among active Kenyon cells, which P1 selects low; at the share implied by imaging (about 44%) the real-wiring model fails to learn, exposing a model inadequacy rather than a deficit of the fly's wiring. In flyvis, P1 penalises a mirrored connectome, which has a constructed solution within 0.07 (median) of the real error, more than a spatially shuffled one in 50 of 50 members; the ranking survives ten-fold longer retraining but depends on the checkpoint at fifty-fold. A credible structural claim needs matched optimisation, data-constrained physiology and a model that still works there.
#05Nov 10, 2026
cs.CL
Mechanistic Interpretability Needs a Logic of Inference
Zhimin Hu, Chen Jiang, Hanbo Xie and 2 more
Neural networks are increasingly studied not merely as predictive systems, but as complex systems whose internal computations are themselves objects of scientific inquiry. Recent progress in mechanistic interpretability (MI) has made it possible to identify neurons, features, circuits, population structures, and dynamical patterns associated with model behavior. As these tools improve, attention is shifting from what can be observed inside a model to how those observations support mechanistic explanations. We examine the parallel efforts of neuroscience and MI to address this question and identify recurring inferential bottlenecks when inferring mechanisms from complex neural systems. We propose five principles and organize them into a recursive logic for a more rigorous procedure of mechanistic inference. These principles provide a framework that supports scientific discovery in two senses: it helps turn local interpretability findings into cumulative knowledge of mechanisms within models, and it makes those mechanisms sufficiently precise to generate testable hypotheses about domains beyond the models. Evidence beyond MI is ultimately required to establish what model mechanisms reveal about the world.