arXiv subjects

Mengdi Wang

Publications and source records attributed to Mengdi Wang.

At least 109 records · Page 6Linked to original sources

arXiv2025

Securing the Language of Life: Inheritable Watermarks from DNA Language Models to Proteins

DNA language models have revolutionized our ability to understand and design DNA sequences--the fundamental language of life--with unprecedented precision, enabling transformative applications in therapeutics, synthetic biology, and gene editing. However, this capability also poses substantial dual-use risks, including the potential for creating pathogens, viruses, and even bioweapons. To address these biosecurity challenges, we introduce two innovative watermarking techniques to reliably track the designed DNA: DNAMark and CentralMark. DNAMark employs synonymous codon substitutions to embed watermarks in DNA sequences while preserving the original function. CentralMark further advances this by creating inheritable watermarks that transfer from DNA to translated proteins, leveraging protein embeddings to ensure detection across the central dogma. Both methods utilize semantic embeddings to generate watermark logits, enhancing robustness against natural mutations, synthesis errors, and adversarial attacks. Evaluated on our therapeutic DNA benchmark, DNAMark and CentralMark achieve F1 detection scores above 0.85 under various conditions, while maintaining over 60% sequence similarity to ground truth and degeneracy scores below 15%. A case study on the CRISPR-Cas9 system underscores CentralMark's utility in real-world settings. This work establishes a vital framework for securing DNA language models, balancing innovation with accountability to mitigate biosecurity risks.

q-bio.GN↗

arXiv2025

CLASS: A Controller-Centric Layout Synthesizer for Dynamic Quantum Circuits

Layout Synthesis for Quantum Computing (LSQC) is a critical component of quantum design tools. Traditional LSQC studies primarily focus on optimizing for reduced circuit depth by adopting a device-centric design methodology. However, these approaches overlook the impact of classical processing and communication time, thereby being insufficient for Dynamic Quantum Circuits (DQC). To address this, we introduce CLASS, a controller-centric layout synthesizer designed to reduce inter-controller communication latency in a distributed control system. It consists of a two-stage framework featuring a hypergraph-based modeling and a heuristic-based graph partitioning algorithm. Evaluations demonstrate that CLASS effectively reduces communication latency by up to 100% with only a 2.10% average increase in the number of additional operations.

quant-ph↗

arXiv2025

Preacher: Paper-to-Video Agentic System

The paper-to-video task converts a research paper into a structured video abstract, distilling key concepts, methods, and conclusions into an accessible, well-organized format. While state-of-the-art video generation models demonstrate potential, they are constrained by limited context windows, rigid video duration constraints, limited stylistic diversity, and an inability to represent domain-specific knowledge. To address these limitations, we introduce Preacher, the first paper-to-video agentic system. Preacher employs a topdown approach to decompose, summarize, and reformulate the paper, followed by bottom-up video generation, synthesizing diverse video segments into a coherent abstract. To align cross-modal representations, we define key scenes and introduce a Progressive Chain of Thought (P-CoT) for granular, iterative planning. Preacher successfully generates high-quality video abstracts across five research fields, demonstrating expertise beyond current video generation models. Code will be released at: https://github.com/Gen-Verse/Paper2Video

cs.CV↗

arXiv2025

Revolutionizing Reinforcement Learning Framework for Diffusion Large Language Models

We propose TraceRL, a trajectory-aware reinforcement learning framework for diffusion language models (DLMs) that incorporates preferred inference trajectory into post-training, and is applicable across different architectures. Equipped with a diffusion-based value model that enhances training stability, we demonstrate improved reasoning performance on complex math and coding tasks. Besides, it can also be applied to adapt block-specific models to larger blocks, which improves sampling flexibility. Employing TraceRL, we derive a series of state-of-the-art diffusion language models, namely TraDo. Although smaller than 7B-scale AR models, TraDo-4B-Instruct still consistently outperforms them across complex math reasoning tasks. TraDo-8B-Instruct achieves relative accuracy improvements of 6.1% over Qwen2.5-7B-Instruct and 51.3% over Llama3.1-8B-Instruct on mathematical reasoning benchmarks. Through curriculum learning, we also derive the first long-CoT DLM, outperforming Qwen2.5-7B-Instruct on MATH500 with an 18.1% relative accuracy gain. To facilitate reproducible research and practical applications, we release a comprehensive open-source framework for building, training, and deploying diffusion LLMs across diverse architectures. The framework integrates accelerated KV-cache techniques and inference engines for both inference and reinforcement learning, and includes implementations of various supervised fine-tuning and RL methods for mathematics, coding, and general tasks. Code and Models: https://github.com/Gen-Verse/dLLM-RL

cs.CL↗

arXiv2025

FutureX: An Advanced Live Benchmark for LLM Agents in Future Prediction

Future prediction is a complex task for LLM agents, requiring a high level of analytical thinking, information gathering, contextual understanding, and decision-making under uncertainty. Agents must not only gather and interpret vast amounts of dynamic information but also integrate diverse data sources, weigh uncertainties, and adapt predictions based on emerging trends, just as human experts do in fields like politics, economics, and finance. Despite its importance, no large-scale benchmark exists for evaluating agents on future prediction, largely due to challenges in handling real-time updates and retrieving timely, accurate answers. To address this, we introduce $\textbf{FutureX}$, a dynamic and live evaluation benchmark specifically designed for LLM agents performing future prediction tasks. FutureX is the largest and most diverse live benchmark for future prediction, supporting real-time daily updates and eliminating data contamination through an automated pipeline for question gathering and answer collection. We evaluate 25 LLM/agent models, including those with reasoning, search capabilities, and integration of external tools such as the open-source Deep Research Agent and closed-source Deep Research models. This comprehensive evaluation assesses agents' adaptive reasoning and performance in dynamic environments. Additionally, we provide in-depth analyses of agents' failure modes and performance pitfalls in future-oriented tasks, including the vulnerability to fake web pages and the temporal validity. Our goal is to establish a dynamic, contamination-free evaluation standard that drives the development of LLM agents capable of performing at the level of professional human analysts in complex reasoning and predictive thinking.

cs.AI↗

arXiv2025

TreeBoN: Enhancing Inference-Time Alignment with Speculative Tree-Search and Best-of-N Sampling

Inference-time alignment enhances the performance of large language models without requiring additional training or fine-tuning but presents challenges due to balancing computational efficiency with high-quality output. Best-of-N (BoN) sampling, as a simple yet powerful approach, generates multiple responses and selects the best one, achieving improved performance but with a high computational cost. We propose TreeBoN, a novel framework that integrates a speculative tree-search strategy into Best-of-N (BoN) Sampling. TreeBoN maintains a set of parent nodes, iteratively branching and pruning low-quality responses, thereby reducing computational overhead while maintaining high output quality. Our approach also leverages token-level rewards from Direct Preference Optimization (DPO) to guide tree expansion and prune low-quality paths. We evaluate TreeBoN using AlpacaFarm, HH-RLHF, UltraFeedback, GSM8K, and TutorEval datasets, demonstrating consistent improvements. Specifically, TreeBoN achieves the highest win rate of 65% on TutorEval and around 60% win rates across other different datasets, outperforming standard BoN with the same computational cost and showcasing its scalability and alignment efficacy.

cs.CL↗

arXiv2025

Physics Supernova: AI Agent Matches Elite Gold Medalists at IPhO 2025

Physics provides fundamental laws that describe and predict the natural world. AI systems aspiring toward more general, real-world intelligence must therefore demonstrate strong physics problem-solving abilities: to formulate and apply physical laws for explaining and predicting physical processes. The International Physics Olympiad (IPhO)--the world's most prestigious physics competition--offers a rigorous benchmark for this purpose. We introduce Physics Supernova, an AI agent system with superior physics problem-solving abilities that match elite IPhO gold medalists. In IPhO 2025 theory problems, Physics Supernova attains 23.5/30 points, ranking 14th of 406 contestants and surpassing the median performance of human gold medalists. We extensively analyzed Physics Supernova's capabilities and flexibility across diverse physics tasks. These results show that principled tool integration within agent systems can deliver competitive improvements in solving challenging science problems. The codes are available at https://github.com/CharlesQ9/Physics-Supernova.

cs.AI↗

arXiv2025

CRISPR-GPT for Agentic Automation of Gene-editing Experiments

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks. The published version of this draft is available at https://www.nature.com/articles/s41551-025-01463-z.

cs.AI↗

arXiv2025

A First-order Generative Bilevel Optimization Framework for Diffusion Models

Diffusion models, which iteratively denoise data samples to synthesize high-quality outputs, have achieved empirical success across domains. However, optimizing these models for downstream tasks often involves nested bilevel structures, such as tuning hyperparameters for fine-tuning tasks or noise schedules in training dynamics, where traditional bilevel methods fail due to the infinite-dimensional probability space and prohibitive sampling costs. We formalize this challenge as a generative bilevel optimization problem and address two key scenarios: (1) fine-tuning pre-trained models via an inference-only lower-level solver paired with a sample-efficient gradient estimator for the upper level, and (2) training diffusion model from scratch with noise schedule optimization by reparameterizing the lower-level problem and designing a computationally tractable gradient estimator. Our first-order bilevel framework overcomes the incompatibility of conventional bilevel methods with diffusion processes, offering theoretical grounding and computational practicality. Experiments demonstrate that our method outperforms existing fine-tuning and hyperparameter search baselines.

cs.LG↗

arXiv2025

SpecDec++: Boosting Speculative Decoding via Adaptive Candidate Lengths

Speculative decoding reduces the inference latency of a target large language model via utilizing a smaller and faster draft model. Its performance depends on a hyperparameter K -- the candidate length, i.e., the number of candidate tokens for the target model to verify in each round. However, previous methods often use simple heuristics to choose K, which may result in sub-optimal performance. We study the choice of the candidate length K and formulate it as a Markov Decision Process. We theoretically show that the optimal policy of this Markov decision process takes the form of a threshold policy, i.e., the current speculation should stop and be verified when the probability of getting a rejection exceeds a threshold value. Motivated by this theory, we propose SpecDec++, an enhanced version of speculative decoding that adaptively determines the candidate length on the fly. We augment the draft model with a trained acceptance prediction head to predict the conditional acceptance probability of the candidate tokens. SpecDec++ will stop the current speculation when the predicted probability that at least one token gets rejected exceeds a threshold. We implement SpecDec++ and apply it to the llama-2-chat 7B & 70B model pair. Our adaptive method achieves a 2.04x speedup on the Alpaca dataset (7.2% improvement over the baseline speculative decoding). On the GSM8K and HumanEval datasets, our method achieves a 2.26x speedup (9.4% improvement) and 2.23x speedup (11.1% improvement), respectively. The code of this paper is available at https://github.com/Kaffaljidhmah2/SpecDec_pp.

cs.CL↗

arXiv2025

LIAR: Leveraging Inference Time Alignment (Best-of-N) to Jailbreak LLMs in Seconds

Jailbreak attacks expose vulnerabilities in safety-aligned LLMs by eliciting harmful outputs through carefully crafted prompts. Existing methods rely on discrete optimization or trained adversarial generators, but are slow, compute-intensive, and often impractical. We argue that these inefficiencies stem from a mischaracterization of the problem. Instead, we frame jailbreaks as inference-time misalignment and introduce LIAR (Leveraging Inference-time misAlignment to jailbReak), a fast, black-box, best-of-$N$ sampling attack requiring no training. LIAR matches state-of-the-art success rates while reducing perplexity by $10\times$ and Time-to-Attack from hours to seconds. We also introduce a theoretical "safety net against jailbreaks" metric to quantify safety alignment strength and derive suboptimality bounds. Our work offers a simple yet effective tool for evaluating LLM robustness and advancing alignment research.

cs.CL↗

arXiv2025

STELLA: Self-Evolving LLM Agent for Biomedical Research

The rapid growth of biomedical data, tools, and literature has created a fragmented research landscape that outpaces human expertise. While AI agents offer a solution, they typically rely on static, manually curated toolsets, limiting their ability to adapt and scale. Here, we introduce STELLA, a self-evolving AI agent designed to overcome these limitations. STELLA employs a multi-agent architecture that autonomously improves its own capabilities through two core mechanisms: an evolving Template Library for reasoning strategies and a dynamic Tool Ocean that expands as a Tool Creation Agent automatically discovers and integrates new bioinformatics tools. This allows STELLA to learn from experience. We demonstrate that STELLA achieves state-of-the-art accuracy on a suite of biomedical benchmarks, scoring approximately 26\% on Humanity's Last Exam: Biomedicine, 54\% on LAB-Bench: DBQA, and 63\% on LAB-Bench: LitQA, outperforming leading models by up to 6 percentage points. More importantly, we show that its performance systematically improves with experience; for instance, its accuracy on the Humanity's Last Exam benchmark almost doubles with increased trials. STELLA represents a significant advance towards AI Agent systems that can learn and grow, dynamically scaling their expertise to accelerate the pace of biomedical discovery.

cs.AI↗

arXiv2025

On Path to Multimodal Historical Reasoning: HistBench and HistAgent

Recent advances in large language models (LLMs) have led to remarkable progress across domains, yet their capabilities in the humanities, particularly history, remain underexplored. Historical reasoning poses unique challenges for AI, involving multimodal source interpretation, temporal inference, and cross-linguistic analysis. While general-purpose agents perform well on many existing benchmarks, they lack the domain-specific expertise required to engage with historical materials and questions. To address this gap, we introduce HistBench, a new benchmark of 414 high-quality questions designed to evaluate AI's capacity for historical reasoning and authored by more than 40 expert contributors. The tasks span a wide range of historical problems-from factual retrieval based on primary sources to interpretive analysis of manuscripts and images, to interdisciplinary challenges involving archaeology, linguistics, or cultural history. Furthermore, the benchmark dataset spans 29 ancient and modern languages and covers a wide range of historical periods and world regions. Finding the poor performance of LLMs and other agents on HistBench, we further present HistAgent, a history-specific agent equipped with carefully designed tools for OCR, translation, archival search, and image understanding in History. On HistBench, HistAgent based on GPT-4o achieves an accuracy of 27.54% pass@1 and 36.47% pass@2, significantly outperforming LLMs with online search and generalist agents, including GPT-4o (18.60%), DeepSeek-R1(14.49%) and Open Deep Research-smolagents(20.29% pass@1 and 25.12% pass@2). These results highlight the limitations of existing LLMs and generalist agents and demonstrate the advantages of HistAgent for historical reasoning.

cs.AI↗

arXiv2025

AgentDistill: Training-Free Agent Distillation with Generalizable MCP Boxes

While knowledge distillation has become a mature field for compressing large language models (LLMs) into smaller ones by aligning their outputs or internal representations, the distillation of LLM-based agents, which involve planning, memory, and tool use, remains relatively underexplored. Existing agent distillation methods typically replay full teacher trajectories or imitate step-by-step teacher tool usage, but they often struggle to train student agents to dynamically plan and act in novel environments. We propose AgentDistill, a novel, training-free agent distillation framework that enables efficient and scalable knowledge transfer via direct reuse of Model-Context-Protocols (MCPs), which are structured and reusable task-solving modules autonomously generated by teacher agents. The reuse of these distilled MCPs enables student agents to generalize their capabilities across domains and solve new problems with minimal supervision or human intervention. Experiments on biomedical and mathematical benchmarks demonstrate that our distilled student agents, built on small language models, can achieve performance comparable to advanced systems using large LLMs such as OctoTools (GPT-4o), highlighting the effectiveness of our framework in building scalable and cost-efficient intelligent agents.

cs.AI↗

arXiv2025

Immune: Improving Safety Against Jailbreaks in Multi-modal LLMs via Inference-Time Alignment

With the widespread deployment of Multimodal Large Language Models (MLLMs) for visual-reasoning tasks, improving their safety has become crucial. Recent research indicates that despite training-time safety alignment, these models remain vulnerable to jailbreak attacks. In this work, we first highlight an important safety gap to describe that alignment achieved solely through safety training may be insufficient against jailbreak attacks. To address this vulnerability, we propose Immune, an inference-time defense framework that leverages a safe reward model through controlled decoding to defend against jailbreak attacks. Additionally, we provide a mathematical characterization of Immune, offering insights on why it improves safety against jailbreaks. Extensive evaluations on diverse jailbreak benchmarks using recent MLLMs reveal that Immune effectively enhances model safety while preserving the model's original capabilities. For instance, against text-based jailbreak attacks on LLaVA-1.6, Immune reduces the attack success rate by 57.82% and 16.78% compared to the base MLLM and state-of-the-art defense strategy, respectively.

cs.CR↗

arXiv2025

Training-Free Guidance Beyond Differentiability: Scalable Path Steering with Tree Search in Diffusion and Flow Models

Training-free guidance enables controlled generation in diffusion and flow models, but most methods rely on gradients and assume differentiable objectives. This work focuses on training-free guidance addressing challenges from non-differentiable objectives and discrete data distributions. We propose TreeG: Tree Search-Based Path Steering Guidance, applicable to both continuous and discrete settings in diffusion and flow models. TreeG offers a unified framework for training-free guidance by proposing, evaluating, and selecting candidates at each step, enhanced with tree search over active paths and parallel exploration. We comprehensively investigate the design space of TreeG over the candidate proposal module and the evaluation function, instantiating TreeG into three novel algorithms. Our experiments show that TreeG consistently outperforms top guidance baselines in symbolic music generation, small molecule design, and enhancer DNA design with improvements of 29.01%, 16.6%, and 18.43%. Additionally, we identify an inference-time scaling law showing TreeG's scalability in inference-time computation.

cs.LG↗

arXiv2025

Emergent Symbolic Mechanisms Support Abstract Reasoning in Large Language Models

Many recent studies have found evidence for emergent reasoning capabilities in large language models (LLMs), but debate persists concerning the robustness of these capabilities, and the extent to which they depend on structured reasoning mechanisms. To shed light on these issues, we study the internal mechanisms that support abstract reasoning in LLMs. We identify an emergent symbolic architecture that implements abstract reasoning via a series of three computations. In early layers, symbol abstraction heads convert input tokens to abstract variables based on the relations between those tokens. In intermediate layers, symbolic induction heads perform sequence induction over these abstract variables. Finally, in later layers, retrieval heads predict the next token by retrieving the value associated with the predicted abstract variable. These results point toward a resolution of the longstanding debate between symbolic and neural network approaches, suggesting that emergent reasoning in neural networks depends on the emergence of symbolic mechanisms.

cs.CL↗

arXiv2025

Toward Scientific Reasoning in LLMs: Training from Expert Discussions via Reinforcement Learning

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

cs.AI↗