China

In real-world drug design, molecule optimization requires selectively improving multiple molecular properties up to pharmaceutically relevant levels, while maintaining others that already meet such criteria. However, existing computational approaches and instruction-tuned LLMs fail to capture such nuanced property-specific objectives, limiting their practical applicability. To address this, we introduce C-MuMOInstruct, the first instruction-tuning dataset focused on multi-property optimization with explicit, property-specific objectives. Leveraging C-MuMOInstruct, we develop mathttGeLLM⁴O-Cs, a series of instruction-tuned LLMs that can perform targeted property-specific optimization. Our experiments across 5 in-distribution and 5 out-of-distribution tasks show that mathttGeLLM⁴O-Cs consistently outperform strong baselines, achieving up to 126% higher success rate. Notably, mathttGeLLM⁴O-Cs exhibit impressive 0-shot generalization to novel optimization tasks and unseen instructions. This offers a step toward a foundational LLM to support realistic, diverse optimizations with property-specific objectives. C-MuMOInstruct and code are accessible through https://anonymous.4open.science/r/GeLLMO-C-BE1F.

EMNLP 2025

Large Language Models for Controllable Multi-property Multi-objective Molecule Optimization

poster

## 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."<br>

*Message from the General Chair, Dirk Hovy*

[**Link to Conference Handbook**](https://drive.google.com/file/d/1johU5QqVVYO4RfH7QcIORr7qrVBdzdwC/view?usp=sharing)





<br>

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

Long-context extension seeks to expand the contextual window in pre-trained large language models (LLMs), allowing them to handle several multiples of their original training context lengths. The primary method for extending the window length involves expanding the initial positional encodings, such as interpolating and extrapolation new positions based on Rotary Position Embedding (RoPE). This expansion inevitably disrupts the positional encodings learned during pre-training, thereby affecting the attention allotment and introducing unseen positional encoding distributions. To address this issue, we propose a new extension strategy based on RoPE, namely Periodic Extrapolation Positional Encodings (PEPE). This strategy expands pre-trained high dimensional components of positional encodings by replicating them in a periodic manner, thereby neither altering the learned positional encoding spaces nor introducing new positional encoding distributions. Experiments demonstrate that PEPE-based approaches can significantly improve long-context extension capabilities using just one-fourth the fine-tuning steps required by state-of-the-art methods. In addition, we analyze the characteristics of PEPE based methods and the key parameters that contribute to their effectiveness. The code will be available publicly.

PEPE: Long-context Extension for Large Language Models via Periodic Extrapolation Positional Encodings

Jailbreak attacks, where harmful prompts bypass generative models' built-in safety, raise serious concerns about model vulnerability. While many defense methods have been proposed, the trade-offs between safety and helpfulness, and their application to Large Vision-Language Models (LVLMs), are not well understood. This paper systematically examines jailbreak defenses by reframing the standard generation task as a binary classification problem to assess model refusal tendencies for both harmful and benign queries. We identify two key defense mechanisms: \textit{safety shift}, which increases refusal rates across all queries, and \textit{harmfulness discrimination}, which improves the model's ability to differentiate between harmful and benign inputs. Using these mechanisms, we develop two ensemble defense strategies—inter-mechanism and intra-mechanism ensembles—to balance safety and helpfulness. Experiments on the MM-SafetyBench and MOSSBench datasets with LLaVA-1.5 models show that these strategies effectively improve model safety or optimize the trade-off between safety and helpfulness.

How Jailbreak Defenses Work and Ensemble? A Mechanistic Investigation

Large language models have demonstrated considerable capabilities in various mathematical tasks, yet they often fall short in rigorous, proof-based reasoning essential for research-level mathematics. Retrieval-augmented generation presents a promising direction for enhancing these capabilities. This paper systematically explores RAG for natural language theorem proving, revealing that LLMs, when augmented with retrieved proofs rather than just theorems, can function as potent mimetic theorem provers: these models can effectively generalize proof techniques found in unstructured retrieved contexts to construct correct proofs for novel theorems. Building upon this finding, we introduce Dual RAG, a simple yet effective RAG framework. Dual RAG employs LLMs to identify underlying reasoning challenges within theorems, augmenting both queries and document contexts to improve retrieval performance. Our experiments show that Dual RAG achieves substantial improvements in retrieval performance, with gains of up to 34.19%. Expert evaluations further confirm that these retrieval enhancements directly translate into higher quality proof generation. Notably, when integrated with the arXiv API, Dual RAG demonstrates the ability to prove research-level theorems in theoretical machine learning, highlighting its strong potential as a foundational element for a practical mathematical copilot.

Retrieval-Augmented Language Models are Mimetic Theorem Provers

Speculative decoding has emerged as a promising approach to accelerating large language model (LLM) generation using a fast drafter while maintaining alignment with the target model's distribution. However, existing approaches face a trade-off: external drafters offer flexibility but can suffer from slower drafting, while self-speculation methods use drafters tailored to the target model but require re-training. In this paper, we introduce novel drafters based on Mamba, a state-of-the-art state space model (SSM), as a solution that combines the best aspects of both approaches. By leveraging the linear structure of SSMs, our approach avoids the quadratic complexity inherent in traditional Transformer-based methods, enabling faster drafting and lower memory usage while maintaining the flexibility to work across different target models. We further enhance efficiency with a novel test-time tree search algorithm for generating high-quality draft candidates. Our empirical evaluation demonstrates that Mamba-based drafters not only outperform existing external drafting methods but are also comparable to state-of-the-art self-speculation approaches while using less memory and maintaining their cross-model adaptability.

Mamba Drafters for Speculative Decoding

Recent large language models have shown promising capabilities in long-form reasoning, following structured chains of thought before arriving at a final answer. However, we observe that these reasoning paths tend to include substantial redundancy; analyzing attention patterns reveals that attention scores are widely scattered, particularly incorrect answers exhibit greater attention sparsity. In this paper, we demonstrate that deliberately removing this redundancy in the reasoning process significantly improves the performance through clear thinking (i.e., removing distraction). Specifically, we systematically identify such redundancy by measuring token-level attention scores to a special end-of-thinking token, which is appended to an explicit instruction inserted to conclude each intermediate reasoning step. Furthermore, we propose structure-aware pruning that prioritizes removing tokens in low-contributing reasoning chunks over individual tokens. After evicting redundant tokens, we remove the injected end-of-thinking instruction, then resume the reasoning generation. We demonstrate that our method significantly improves the over all accuracy across reasoning-intensive benchmarks without any training involved. In particular, our method shows strong performance on challenging mathematics competition benchmarks such as AIME and AMC, where reasoning redundancy is more prevalent.

Think Clearly: Improving Reasoning via Redundant Token Pruning

Automated Claim Verification (CV), where claim's veracity is assessed against explicitly provided reference materials, is crucial in combating escalating online misinformation. This survey carefully analyzed 198 studies published between January 2022 and March 2025 to summarize recent work on corpus creation, system architectures, and the integration of large language models. We also conducted two case studies: the first looks at the relationship between claims and references. The second examines issues in claim decomposition. Our findings illuminate common corpus construction strategies and emerging trends in system architectures while highlighting remaining challenges in CV research.

A Systematic Survey of Claim Verification: Corpora, Systems, and Case Studies

In dialogue intent detection, the challenge of acquiring sufficient corpora and the high cost of manual annotation often lead to incorrectly labeled or unrepresentative samples, which can hinder the generalization ability of classification models. Additionally, as using large language models for generating synthetic samples for data augmentation becomes more common, these synthetic samples may exacerbate the problem by introducing additional noise due to the models’ limited prior knowledge. To address this challenge, this paper proposes an interpretable Sample Filter by Topic Modeling (SFTM) framework. By evaluating the diversity and authenticity of the samples, SFTM effectively reduces the quantity of real and synthetic samples while improving the performance of the classification models.

From Noise to Clarity: Filtering Real and LLM-Generated Samples for Enhanced Intent Detection

The advancement of large language models (LLMs) has enabled the construction of multi-agent systems to solve complex tasks by dividing responsibilities among specialized agents, such as a planning agent for subgoal generation and a grounding agent for executing tool-use actions. Most existing methods typically fine-tune these agents independently, leading to capability gaps among them with poor coordination. To address this, we propose MOAT, a Multi-Agent Joint Alignment Tuning framework that improves agents collaboration through iterative alignment. MOAT alternates between two key stages: (1) Planning Agent Alignment, which optimizes the planning agent to generate subgoal sequences that better guide the grounding agent; and (2) Grounding Agent Improving, which fine-tunes the grounding agent using diverse subgoal-action pairs generated by the agent itself to enhance its generalization capablity. Theoretical analysis proves that MOAT ensures a non-decreasing and progressively convergent training process. Experiments across six benchmarks demonstrate that MOAT outperforms state-of-the-art baselines, achieving average improvements of 3.1% on held-in tasks and 4.4% on held-out tasks.

Bridging the Capability Gap: Joint Alignment Tuning for Harmonizing LLM-based Multi-Agent Systems

Retrieval-augmented generation (RAG) with foundation models has demonstrated notable capabilities across various tasks and domains, showcasing advanced problem-solving skills in natural language understanding, generation, and complex decision-making processes. However, their proficiency in addressing expert-level reasoning, such as solving mathematical physics problems, remains relatively unexplored. This paper investigates the potential of RAG techniques to solve Olympic-level mathematical physics problems, motivated by students' natural inclination to reference past problems when preparing for competitions. We propose PhOPile, a high-quality, multimodal, physics-specific dataset tailored for Olympic-level challenges. In this dataset, problems from 2021 serve as the evaluation set, while data from other years form the knowledge base for RAG. Additionally, we benchmark RAG methods with foundation models to report and analyze results that can inform future research. Additionally, we highlight the significant role of reflection through experimental results. Furthermore, we conduct a high-granularity evaluation of the performance of popular LLMs and large multimodal models (LMMs) on our dataset, assessing their physics reasoning and RAG capabilities.

Benchmarking Foundation Models with Retrieval-Augmented Generation in Olympic-Level Physics Problem Solving

Auto-regressive Large Language Models (LLMs) demonstrate remarkable performance across different domains such as vision and language processing. However, due to sequential processing through a stack of transformer layers, autoregressive decoding faces significant computation/latency challenges, particularly in resource-constrained environments like mobile and edge devices. Existing approaches in literature that aim to improve latency via skipping layers have two distinct flavors - 1) Early exit, and 2) Input-agnostic heuristics where tokens exit at pre-determined layers irrespective of input sequence. Both the above strategies have limitations - the former cannot be applied to handle KV Caching necessary for speed-ups in modern framework and the latter does not capture the variation in layer importance across tasks or more generally, across input sequences. To address both limitations, we propose FiRST, an algorithm that reduces inference latency by using layer-specific routers to select a subset of transformer layers adaptively for each input sequence - the prompt (during the prefill stage) decides which layers will be skipped during decoding. FiRST preserves compatibility with KV caching enabling faster inference while being quality-aware. FiRST is model-agnostic and can be easily enabled on any pre-trained LLM. Our approach reveals that input adaptivity is critical - indeed, different task-specific middle layers play a crucial role in evolving hidden representations depending on tasks. Extensive experiments show that FiRST significantly reduces latency while outperforming other layer selection strategies in quality metics. It retains competitive performance to base model (without layer skipping) and in some cases, even improves upon it. FiRST is thus a promising and efficient solution for LLM deployment in low-resource environments.

Premium content

Downloads

Next from EMNLP 2025

PEPE: Long-context Extension for Large Language Models via Periodic Extrapolation Positional Encodings

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES