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Recent advances in large language models (LLMs) have highlighted the effectiveness of chain-of-thought reasoning in symbolic domains such as mathematics and programming. However, our study shows that directly transferring such text-based reasoning paradigms to protein function understanding is ineffective: reinforcement learning mainly amplifies superficial keyword patterns while failing to introduce new biological knowledge, resulting in limited generalization. We argue that protein function prediction is a knowledge-intensive scientific task that fundamentally relies on external biological priors and computational tools rather than purely internal reasoning. To address this gap, we propose Protein Function Understanding Agent (PFUA), a tool-augmented protein reasoning agent that unifies problem decomposition, tool invocation, and grounded answer generation. Instead of relying on long unconstrained reasoning traces, PFUA integrates domain-specific tools to produce verifiable intermediate evidence. Experiments on four benchmarks demonstrate that PFUA consistently outperforms text-only reasoning models with an average performance improvement of 103%. We believe PFUA has the potential to become a standard paradigm for agentic reasoning in knowledge-intensive life science domains.

ACL 2026

Interleaved Tool-Call Reasoning for Protein Function Understanding

## Welcome!
"I am excited to welcome you to this year’s edition of the Conference on Empirical Methods in Natural Language Processing! Importantly, it marks the 30th edition of EMNLP. With over 8,000 submissions, more than 3,000 accepted papers, and thousands of attendees, we have come a long way from that first
workshop, which had 14 accepted papers. As the field looks ahead, Suzhou is the fitting location for celebrating this milestone: rooted in a long literary tradition, yet modern and forward-looking, and home to a large share of the NLP community." 

*Message from the General Chair, Dirk Hovy*

EMNLP 2025

Celebrate 30 Years of EMNLP! 
EMNLP 2025 will be held in Suzhou, China from November 5th to November 9th, 2025.

poster

It is my great pleasure and honor to welcome you to the 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026), held in San Diego, California, USA, July 2–7, 2026. ACL 2026 continues our fields tradition of excellence in scholarship, innovation, and inclusivity, and I am deeply grateful to the many volunteers who have worked tirelessly to bring this event to life.

It is exciting to see the many developments in the field reflected at our conference, such as the advancement of large language models (born out of our community) into many application directions. This is not without challenges, partly due to unsolved problems, and partly due to misuse of the technology. All this is reflected well at ACL 2026. The conference also reflects that the field is not only about advancing technology, but also the science of fundamentally understanding language and how it is use by many different speaker communities. 
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The 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026) will take place in San Diego, California, from July 2 - 7, 2026.

Reliable failure detection and causal reasoning are critical in robotic manipulation, as their absence risks robot damage and endangers human safety.
Although recent Vision–Language Models (VLMs) are employed to attempt failure detection and causality reasoning, they typically make retrospective assessment only after task completion, and their reasoning accuracy is often limited.
To address these issues, we introduce RoboFailRing, which enables timely failure detection during task execution and enhances the reasoning accuracy of VLMs.
It achieves rapid failure detection by retrieving a pre-constructed failure memory and returning a similarity-based decision.
In addition, by providing grounded failure report to VLMs, it improves the accuracy of their reasoning about the failure causes and repair strategies.
We evaluate RoboFailRing on two large-scale simulated datasets comprising over 6,000 failure trajectories and covering 81 distinct manipulation tasks.
The results show that the average success rate of out-of-distribution failure detection reaches 80%, while the mean detection time is cut to roughly 50% of the baseline.
Moreover, evaluations on real-world systems show an average 35% gain in VLM failure-reasoning accuracy.
We make our code publicly available at: https://github.com/DynamicPoet/RoboFailRing.

 RoboFailRing: Retrieval-Augmented and Language Grounding Failure Detection for VLM-enabled Robotic Manipulation

Recent studies have identified "retrieval heads" in Large Language Models (LLMs) responsible for extracting information from input contexts. However, prior works largely rely on static statistics aggregated across datasets, identifying heads that perform retrieval on average. This perspective overlooks the fine-grained temporal dynamics of autoregressive generation. In this paper, we investigate retrieval heads from a dynamic perspective. Through extensive analysis, we establish three core claims: (1) Dynamism: Retrieval heads vary dynamically across timesteps; (2) Irreplaceability: Dynamic retrieval heads are specific at each timestep and cannot be effectively replaced by static retrieval heads; and (3) Correlation: The model's hidden state encodes a predictive signal for future retrieval head patterns, indicating an internal planning mechanism. We validate these findings on the Needle-in-a-Haystack task and a multi-hop QA task, and quantify the differences on the utility of dynamic and static retrieval heads in a Dynamic Retrieval-Augmented Generation framework. Our study provides new insights into the internal mechanisms of LLMs.

 Retrieval Heads are Dynamic

Large transformer-based language models dominate modern NLP, yet our understanding of how they encode linguistic information relies primarily on studies of early models like BERT and GPT-2. We systematically probe 25 models from BERT Base to Qwen2.5-7B focusing on two linguistic properties: lexical identity and inflectional features across 6 diverse languages. We find a consistent pattern: inflectional features are linearly decodable throughout the model, while lexical identity is prominent early but increasingly weakens with depth. Further analysis of the representation geometry reveals that models with aggressive mid-layer dimensionality compression show reduced steering effectiveness in those layers, despite probe accuracy remaining high. Pretraining analysis shows that inflectional structure stabilizes early while lexical identity representations continue evolving. Taken together, our findings suggest that transformers maintain inflectional features across layers, while trading off lexical identity for compact, predictive representations.

 Model Internal Sleuthing: Finding Lexical Identity and Inflectional Features in Modern Language Models

Guideline-following is increasingly important in compliance, customer support, and other regulated workflows, where correctness is defined by explicit rule systems rather than heuristics. Learning to follow guidelines is challenging because guidelines are interdependent: rules can trigger, suppress, or conflict with one another, while locally plausible responses may violate global constraints. Most existing methods treat guidelines as static text and rely on implicit reasoning or deeper decoding, making rule interactions and satisfaction status hard to observe and control. A more feasible approach is to model guideline execution with an explicit state that tracks evolving rule evidence across steps. However, conventional world models are a poor fit: they typically assume privileged feedback or well-defined transition dynamics, assumptions that do not hold when reasoning occurs purely in language space under ambiguous, text-defined constraints. As a solution, we propose RGCWM, a Rule-Grounded Causal World Model that builds an explicit state space from the guideline text itself. RGCWM represents rule applicability and satisfaction as a continuously updated evidence state, externalizes inter-rule dependencies as a causal structure, and plans at inference time by counterfactually evaluating candidate responses under model-estimated state transitions. Experiments show that this shift from implicit text reasoning to state-based reasoning enables stable, controllable execution of complex interacting rules across diverse domains.

Guidelines as Environments: A World Model Approach to Rule Following

Language model (LM) probability is not a reliable quality estimator, as natural language is ambiguous. When multiple output options are valid, the model's probability distribution is spread across them, which can misleadingly indicate low output quality. This issue is caused by two reasons: (1) LMs' final output activation is softmax, which does not allow multiple correct options to receive high probabilities simultaneuously and (2) LMs' training data is single, one-hot encoded references, indicating that there is only one correct option at each output step. We propose training a module for Quality Estimation on top of pre-trained LMs to address these limitations. The module, called Sigmoid Head, is an extra unembedding head with sigmoid activation to tackle the first limitation. To tackle the second limitation, during the negative sampling process to train the Sigmoid Head, we use a heuristic to avoid selecting potentially alternative correct tokens. Our Sigmoid Head is computationally efficient during training and inference. The probability from Sigmoid Head is notably better quality signal compared to the original softmax head. As the Sigmoid Head does not rely on human-annotated quality data, it is more robust to out-of-domain settings compared to supervised QE.

 Sigmoid Head for Quality Estimation under Language Ambiguity

We introduce **Doublespeak**, a simple in-context representation hijacking attack against language models. The attack works by systematically replacing a harmful keyword (e.g., *bomb*) with a benign token (e.g., *carrot*) across multiple in-context examples, provided as a prefix to a harmful request. We demonstrate that this substitution leads to the internal representation of the benign token converging toward that of the harmful one, effectively embedding the harmful semantics under a euphemism. As a result, superficially innocuous prompts (e.g., *"How to build a carrot?"*) are internally interpreted as disallowed instructions (*"How to build a bomb?"*), thereby bypassing the model's safety alignment. We use interpretability tools to show this semantic shift occurs progressively across layers. Doublespeak is optimization-free, broadly transferable across model families, and achieves strong success rates on closed-source systems, reaching 74% on Llama-3.3-70B-Instruct with a single-sentence context override. Our findings highlight a new attack surface in LM latent space, indicating that current alignment strategies are insufficient and should instead operate at the representation level.

 In-Context Representation Hijacking

Large Language Models (LLMs) excel at code-related tasks but often struggle in realistic software repositories, where project-specific APIs and cross-file dependencies are crucial. Retrieval-augmented methods mitigate this by injecting repository context at inference time. Low inference time latency budget either affects retrieval quality or the added latency impacts user experience adversely. We address this limitation with SpecAgent, an agent that enhances both latency and code-generation quality by proactively exploring repository files during indexing and constructing speculative context that anticipates future edits in each file. This indexing-time asynchrony allows thorough context computation masking latency and the speculative nature of the context improves code-generation quality. Additionally, we identify the problem of future context leakage in existing benchmarks, which can inflate reported performance. To address this, we construct a synthetic, leakage-free benchmark that enables a more realistic evaluation of our agent against baselines. Experiments show that SpecAgent consistently achieves absolute gains of 9–11% (48–58% relative) compared to the best-performing baselines, while significantly reducing inference latency.

SpecAgent: A Speculative Retrieval and Forecasting Agent for Code Completion

Reasoning benchmarks such as the Abstraction and Reasoning Corpus (ARC) and ARC-AGI are widely used to assess progress in artificial intelligence and are often interpreted as probes of core, so-called ``fluid'' reasoning abilities. Despite their apparent simplicity for humans, these tasks remain challenging for frontier vision-language models (VLMs), a gap commonly attributed to deficiencies in machine reasoning. We challenge this interpretation and hypothesize that the gap arises primarily from limitations in visual perception rather than from shortcomings in inductive reasoning.

To verify this hypothesis, we introduce a two-stage experimental pipeline that explicitly separates perception and reasoning. In the perception stage, each image is independently converted into a natural-language description, while in the reasoning stage a model induces and applies rules using these descriptions. This design prevents leakage of cross-image inductive signals and isolates reasoning from perception bottlenecks. Across three ARC-style datasets, Mini-ARC, ACRE, and Bongard-LOGO, we show that the perception capability is the dominant factor underlying the observed performance gap by comparing the two-stage pipeline with against standard end-to-end one-stage evaluation. Manual inspection of reasoning traces in the VLM outputs further reveals that approximately 80 percent of model failures stem from perception errors. Together, these results demonstrate that ARC-style benchmarks conflate perceptual and reasoning challenges and that observed performance gaps may overstate deficiencies in machine reasoning. Our findings underscore the need for evaluation protocols that disentangle perception from reasoning when assessing progress in machine intelligence.

 Your Reasoning Benchmark May Not Test Reasoning: Revealing Perception Bottleneck in Abstract Reasoning Benchmarks

Autonomous web agents powered by large language models (LLMs) show strong potential for performing goal-oriented tasks such as information retrieval, report generation, and online transactions. These agents mark a key step toward practical embodied reasoning in open web environments. However, existing approaches remain limited in reasoning depth and efficiency: vanilla linear methods fail at multi-step reasoning and lack effective backtracking, while other search strategies are coarse-grained and computationally costly. We introduce \emph{Branch-and-Browse}, a fine-grained web agent framework that unifies structured reasoning-acting, contextual memory, and efficient execution. It (i) employs explicit subtask management with tree-structured exploration for controllable multi-branch reasoning, (ii) bootstraps exploration through efficient web state replay with background reasoning, and (iii) leverages a page action memory to share explored actions within and across sessions. 
On the WebArena benchmark, Branch-and-Browse achieves a task success rate of 35.8\% and reduces execution time by up to 40.4\% relative to state-of-the-art methods. These results demonstrate that Branch-and-Browse is a reliable and efficient framework for LLM-based web agents. Code is available at https://anonymous.4open.science/r/Branch_and_Browse/.

Branch-and-Browse: Efficient and Controllable Web Exploration with Tree-Structured Reasoning and Action Memory

Symbolic logical reasoning is a critical yet underexplored capability of large language models (LLMs), providing reliable and verifiable decision-making in high-stakes domains such as mathematical reasoning and legal judgment. In this study, we present a systematic analysis of logical reasoning under controlled increases in logical complexity, and reveal a previously unrecognized phenomenon, which we term **Logical Phase Transitions**: rather than degrading smoothly, logical reasoning performance remains stable within a regime but collapses abruptly beyond a critical logical depth, mirroring physical phase transitions such as water freezing beyond a critical temperature threshold. Building on this insight, we propose **Neuro-Symbolic Curriculum Tuning**, a principled framework that adaptively aligns natural language with logical symbols to establish a shared representation, and reshapes training dynamics around phase-transition boundaries to progressively strengthen reasoning at increasing logical depths. Experiments on five benchmarks show that our approach effectively mitigates logical reasoning collapse at high complexity, yielding average accuracy gains of +1.26 in naive prompting and +3.95 in CoT, while improving generalization to unseen logical compositions.

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RoboFailRing: Retrieval-Augmented and Language Grounding Failure Detection for VLM-enabled Robotic Manipulation

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