Large Language Models have excelled in various domains but face efficiency challenges due to the growing Key-Value (KV) cache required for long-sequence inference. Recent efforts aim to reduce KV cache size by evicting vast non-critical cache elements during runtime while preserving generation quality. However, these methods typically allocate compression budgets uniformly across all attention heads, ignoring the unique attention patterns of each head. In this paper, we establish a theoretical loss upper bound between pre-and post-eviction attention output, explaining the optimization target of prior cache eviction methods, while guiding the optimization of adaptive budget allocation. Base on this, we propose {\it Ada-KV}, the first head-wise adaptive budget allocation strategy. It offers plug-and-play benefits, enabling seamless integration with prior cache eviction methods. Extensive evaluations on 13 datasets from Ruler and 16 datasets from LongBench, all conducted under both question-aware and question-agnostic scenarios, demonstrate substantial quality improvements over existing methods. Our code is available at https://github.com/FFY0/AdaKV.

Ordering-based approaches to causal discovery identify topological orders of causal graphs, providing scalable alternatives to combinatorial search methods. Under the Additive Noise Models (ANMs) assumption, recent causal ordering methods based on score matching require an accurate estimation of the Hessian diagonal of the log-densities. However, previous approaches mainly use Stein gradient estimators, which are computationally expensive and memory-intensive. Although DiffAN addresses these limitations by substituting kernel-based estimates with diffusion models, it remains numerically unstable due to the second-order derivatives of score models. To alleviate these problems, we propose Score-informed Neural Operator (SciNO), a probabilistic generative model in smooth function spaces designed to stably approximate the Hessian diagonal and to preserve structural information during the score modeling. Empirical results show that SciNO reduces order divergence by 42.7% on synthetic graphs and by 31.5% in real-world datasets on average compared to DiffAN, while maintaining memory efficiency and scalability. Furthermore, we propose a probabilistic control algorithm for causal reasoning with autoregressive models that integrates SciNO's probability estimates with autoregressive model priors, enabling reliable data-driven causal ordering informed by semantic information. Consequently, the proposed method enhances causal reasoning abilities of LLMs without additional fine-tuning or prompt engineering.

Despite the impressive performance of large language models (LLMs), the process of endowing them with new capabilities---such as mathematical reasoning---remains largely empirical and opaque. A critical open question is whether reasoning abilities stem from the entire model, specific modules, or are merely artifacts of overfitting. In this work, we hypothesize that the reasoning capabilities in well-trained LLMs are primarily attributed to the output projection module (o proj plays a central role in enabling reasoning, whereas other modules contribute more to fluent dialogue. These findings offer a new perspective on LLM interpretability and open avenues for more targeted training strategies, potentially enabling more efficient and specialized LLMs.

Large language models (LLMs) have demonstrated remarkable proficiency in mainstream academic disciplines such as mathematics, physics, and computer science. However, human knowledge encompasses over 200 specialized disciplines, far exceeding the scope of existing benchmarks. The capabilities of LLMs in many of these specialized fields-particularly in light industry, agriculture, and service-oriented disciplines-remain inadequately evaluated. To address this gap, we present SuperGPQA, a comprehensive benchmark that evaluates graduate-level knowledge and reasoning capabilities across 285 disciplines. Our benchmark employs a novel Human-LLM collaborative filtering mechanism to eliminate trivial or ambiguous questions through iterative refinement based on both LLM responses and expert feedback. Our experimental results reveal significant room for improvement in the performance of current state-of-the-art LLMs across diverse knowledge domains (e.g., the reasoning-focused model Gemini-2.5-Pro

Associative learning--forming links between co-occurring items--is fundamental to human cognition, reshaping internal representations in complex ways. Testing hypotheses on how representational changes occur in biological systems is challenging, but large language models (LLMs) offer a scalable alternative. Building on LLMs' in-context learning, we adapt a cognitive neuroscience associative learning paradigm and investigate how representations evolve across six models. Our initial findings reveal a non-monotonic pattern consistent with the Non-Monotonic Plasticity Hypothesis, with moderately similar items differentiating after learning. Leveraging the controllability of LLMs, we further show that this differentiation is modulated by the overlap of associated items with the broader vocabulary--a factor we term vocabulary interference, capturing how new associations compete with prior knowledge. We find that higher vocabulary interference amplifies differentiation, suggesting that representational change is influenced by both item similarity and global competition.

Chain of thought is a natural inference-time method for increasing the computational power of transformer-based large language models (LLMs), but comes at the cost of sequential decoding. Are there more efficient alternatives to expand a transformer's expressive power without adding parameters? We consider transformers with *padding* tokens as a form of parallelizable test-time compute. We show that averaging-hard-attention, masked-pre-norm transformers with polynomial padding recognize precisely the class $\mathsf{FO}$-uniform $\mathsf{TC}^0$ of extremely parallelizable problems. While the $\mathsf{TC}^0$ upper bound was known, proving a matching lower bound had been elusive. Further, our novel analysis reveals the precise expanded power of padded transformers when coupled with another form of inference-time compute, namely dynamically increasing depth via *looping*.

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems.

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology.

Inductive reasoning infers general rules from observed evidence, which is one of the most critical intelligence abilities. Previous works have succeeded in formal languages but suffer from onerous and error-prone conversions between a particular formal language and the working language. As large language models (LLMs) have emerged, direct reasoning with various kinds of languages, especially natural languages, without formal language involvement has become feasible. However, existing LLM-based inductive reasoning usually relies on LLM's intrinsic generation ability, which is prone to LLM's hallucination and lacks systematic guidance according to the nature of inductive reasoning. To this end, we propose HypoBootstrap, an integrated framework for inductive reasoning that generates and confirms hypotheses both in a bootstrapping manner. Regarding hypothesis generation, we propose a novel bootstrapping generation strategy, bootstrapping object hypotheses, relational hypotheses, and functional hypotheses successively, which assists LLM in observing the evidence from trivial patterns to non-trivial patterns. Regarding hypothesis confirmation, we utilize Glymour's theory of bootstrap confirmation, a hypothesis confirmation theory from the philosophy of science that can confirm a set of hypotheses. We use its principles to confirm the object hypotheses, relational hypotheses, and functional hypotheses. Empirical studies on four inductive reasoning scenarios of different natures, involving causal induction, concept learning, grammar learning, and abstract reasoning, demonstrate that HypoBootstrap significantly outperforms existing methods.

Large language models (LLMs) have enabled agents to perform complex reasoning and decision-making through free-form language interactions. However, in open-ended language action environments (e.g., negotiation or question-asking games), the action space can be formulated as a joint distribution over tokens, resulting in an extremely large and combinatorial action space. Sampling actions in such a space can lead to extreme reward sparsity, which brings large reward variance, hindering effective reinforcement learning (RL).