Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and mathematical inference. Despite their effectiveness, Long-CoT reasoning models are often criticized for their limited ability and low efficiency in knowledge-intensive domains such as molecule discovery. Success in this field requires a precise understanding of domain knowledge, including molecular structures and chemical principles, which is challenging due to the inherent complexity of molecular data and the scarcity of high-quality expert annotations. To bridge this gap, we introduce Mol-R1, a novel framework designed to improve explainability and reasoning performance of R1-like Explicit Long-CoT reasoning LLMs in text-based molecule generation. Our approach begins with a high-quality reasoning dataset curated through Prior Regulation via In-context Distillation (PRID), a dedicated distillation strategy to effectively generate paired reasoning traces guided by prior regulations. Building upon this, we introduce MoIA, Molecular Iterative Adaptation, a sophisticated training strategy that iteratively combines Supervised Fine-tuning (SFT) with Reinforced Policy Optimization (RPO), tailored to boost the reasoning performance of R1-like reasoning models for molecule discovery. Finally, we examine the performance of Mol-R1 in the text-based molecule reasoning generation task, showing superior performance against existing baselines.

Investigation of Speech and Noise Latent Representations in Single-channel VAE-based Speech Enhancement

Recently, a variational autoencoder (VAE)-based single-channel speech enhancement system using Bayesian permutation training has been proposed, which uses two pretrained VAEs to obtain latent representations for speech and noise. Based on these pretrained VAEs, a noisy VAE learns to generate speech and noise latent representations from noisy speech for speech enhancement. Modifying the pretrained VAE loss terms affects the pretrained speech and noise latent representations. In this paper, we investigate how these different representations affect speech enhancement performance. Experiments on the DNS3, WSJ0-QUT, and VoiceBank-DEMAND datasets show that a latent space where speech and noise representations are clearly separated significantly improves performance over standard VAEs, which produce overlapping speech and noise representations.

Are LLMs Reliable Translators of Logical Reasoning Across Lexically Diversified Contexts?

Neuro-symbolic approaches combining large language models (LLMs) with solvers excels in logical reasoning problems need long reasoning chains. In this paradigm, LLMs serve as translators, converting natural language reasoning problems into formal logic formulas. Then reliable symbolic solvers return correct solutions. Despite their success, we find that LLMs, as translators, struggle to handle lexical diversification, a common linguistic phenomenon, indicating that LLMs as logic translators are unreliable in real-world scenarios. Moreover, existing logical reasoning benchmarks lack lexical diversity, failing to challenge LLMs' ability to translate such text and thus obscuring this issue. In this work, we propose SCALe, a benchmark designed to address this significant gap through **logic-invariant lexical diversification**. By using LLMs to transform original benchmark datasets into lexically diversified but logically equivalent versions, we evaluate LLMs' ability to consistently map diverse expressions to uniform logical symbols on these new datasets. Experiments using SCALe further confirm that current LLMs exhibit deficiencies in this capability. Building directly on the deficiencies identified through our benchmark, we propose a new method, MenTaL, to address this limitation. This method guides LLMs to first construct a table unifying diverse expressions before performing translation. Applying MenTaL through in-context learning and supervised fine-tuning (SFT) significantly improves the performance of LLM translators on lexically diversified text. Our code is now available at https://github.com/wufeiwuwoshihua/LexicalDiver.

Benchmarking Poisoning Attacks against Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) has proven effective in mitigating hallucinations in large language models by incorporating external knowledge during inference. However, this integration introduces new security vulnerabilities, particularly to poisoning attacks. Although prior work has explored various poisoning strategies, a thorough assessment of their practical threat to RAG systems remains missing. To address this gap, we propose the first comprehensive benchmark framework for evaluating poisoning attacks on RAG. Our benchmark covers 5 standard question answering (QA) datasets and 10 expanded variants, along with 13 poisoning attack methods and 7 defense mechanisms, representing a broad spectrum of existing techniques. Using this benchmark, we conduct a comprehensive evaluation of all included attacks and defenses across the full dataset spectrum. Our findings show that while existing attacks perform well on standard QA datasets, their effectiveness drops significantly on the expanded versions. Moreover, our results demonstrate that various advanced RAG architectures, such as sequential, branching, conditional, and loop RAG, as well as multi-turn conversational RAG, multimodal RAG systems, and RAG-based LLM agent systems, remain susceptible to poisoning attacks. Notably, current defense techniques fail to provide robust protection, underscoring the pressing need for more resilient and generalizable defense strategies.

Visual Instruction Bottleneck Tuning

Despite widespread adoption, multimodal large language models (MLLMs) suffer performance degradation when encountering unfamiliar queries under distribution shifts. Existing methods to improve MLLM generalization typically require either more instruction data or larger advanced model architectures, both of which incur non-trivial human labor or computational costs. In this work, we take an alternative approach to enhance the robustness of MLLMs under distribution shifts, from a representation learning perspective. Inspired by the information bottleneck (IB) principle, we derive a variational lower bound of the IB for MLLMs and devise a practical implementation, Visual Instruction Bottleneck Tuning (Vittle). We then provide a theoretical justification of Vittle by revealing its connection to an information-theoretic robustness metric of MLLM. Empirical validation of three MLLMs on open-ended and closed-form question answering and object hallucination detection tasks over 45 datasets, including 30 shift scenarios, demonstrates that Vittle consistently improves the MLLM's robustness under shifts by pursuing the learning of a minimal sufficient representation.

am-ELO: A Stable Framework for Arena-based LLM Evaluation

Arena-based evaluation is a fundamental yet significant evaluation paradigm for modern AI models, especially large language models (LLMs). Existing framework based on ELO rating system suffers from the inevitable instability problem due to ranking inconsistency and the lack of attention to the varying abilities of annotators. In this paper, we introduce a novel stable arena framework to address these issues by enhancing the ELO Rating System. Specifically, we replace the iterative update method with a Maximum Likelihood Estimation (MLE) approach, m-ELO, and provide theoretical proof of the consistency and stability of the MLE approach for model ranking. Additionally, we proposed the am-ELO, which modify the Elo Rating's probability function to incorporate annotator abilities, enabling the simultaneous estimation of model scores and annotator reliability. Experiments demonstrate that this method ensures stability, proving that this framework offers a more robust, accurate, and stable evaluation method for LLMs.

TOMG-Bench: Evaluating LLMs on Text-based Open Molecule Generation

In this paper, we propose Text-based Open Molecule Generation Benchmark (TOMG-Bench), the first benchmark to evaluate the open-domain molecule generation capability of LLMs. TOMG-Bench encompasses a dataset of three major tasks: molecule editing (MolEdit), molecule optimization (MolOpt), and customized molecule generation (MolCustom). Each task further contains three subtasks, with each subtask comprising 5,000 test samples. Given the inherent complexity of open molecule generation, we have also developed an automated evaluation system that helps measure both the quality and the accuracy of the generated molecules. Our comprehensive benchmarking of 25 LLMs reveals the current limitations and potential areas for improvement in text-guided molecule discovery. Furthermore, with the assistance of OpenMolIns, a specialized instruction tuning dataset proposed for solving challenges raised by TOMG-Bench, Llama3.1-8B could outperform all the open-source general LLMs, even surpassing GPT-3.5-turbo by 46.5\% on TOMG-Bench. Our codes and datasets are available through https://github.com/phenixace/TOMG-Bench.

Critic-V: VLM Critics Help Catch VLM Errors in Multimodal Reasoning

Vision-language models (VLMs) have shown remarkable advancements in multimodal reasoning tasks. However, they still often generate inaccurate or irrelevant responses due to issues like hallucinated image understandings or unrefined reasoning paths. To address these challenges, we introduce Critic-V, a novel framework inspired by the Actor-Critic paradigm to boost the reasoning capability of VLMs. This framework decouples the reasoning process and critic process by integrating two independent components: the Reasoner, which generates reasoning paths based on visual and textual inputs, and the Critic, which provides constructive critique to refine these paths. In this approach, the Reasoner generates reasoning responses according to text prompts, which can evolve iteratively as a policy based on feedback from the Critic. This interaction process was theoretically driven by a reinforcement learning framework where the Critic offers natural language critiques instead of scalar rewards, enabling more nuanced feedback to boost the Reasoner's capability on complex reasoning tasks. The Critic model is trained using Direct Preference Optimization (DPO), leveraging a preference dataset of critiques ranked by Rule-based Reward~(RBR) to enhance its critic capabilities. Evaluation results show that the Critic-V framework significantly outperforms existing methods, including GPT-4V, on 5 out of 8 benchmarks, especially regarding reasoning accuracy and efficiency. Combining a dynamic text-based policy for the Reasoner and constructive feedback from the preference-optimized Critic enables a more reliable and context-sensitive multimodal reasoning process. Our approach provides a promising solution to enhance the reliability of VLMs, improving their performance in real-world reasoning-heavy multimodal applications such as autonomous driving and embodied intelligence.

MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

Leveraging LLMs for Hypothetical Deduction in Logical Inference: A Neuro-Symbolic Approach

Large Language Models (LLMs) have exhibited remarkable potential across a wide array of reasoning tasks, including logical reasoning. Although massive efforts have been made to empower the logical reasoning ability of LLMs via external logical symbolic solvers, crucial challenges of the poor generalization ability to questions with different features and inevitable question information loss of symbolic solver-driven approaches remain unresolved. To mitigate these issues, we introduce LINA, a LLM-driven neuro-symbolic approach for faithful logical reasoning. By enabling an LLM to autonomously perform the transition from propositional logic extraction to sophisticated logical reasoning, LINA not only bolsters the resilience of the reasoning process but also eliminates the dependency on external solvers. Additionally, through its adoption of a hypothetical-deductive reasoning paradigm, LINA effectively circumvents the expansive search space challenge that plagues traditional forward reasoning methods. Empirical evaluations demonstrate that LINA substantially outperforms both established propositional logic frameworks and conventional prompting techniques across a spectrum of five logical reasoning tasks. Specifically, LINA achieves an improvement of 24.34% over LINC on the FOLIO dataset, while also surpassing prompting strategies like CoT and CoT-SC by up to 24.02%. Our code is available at https://github.com/wufeiwuwoshihua/nshy.