arXiv subjects

Zihan Wang

Publications and source records attributed to Zihan Wang.

At least 181 records · Page 10Linked to original sources

arXiv2025

DNAMotifTokenizer: Towards Biologically Informed Tokenization of Genomic Sequences

DNA language models have advanced genomics, but their downstream performance varies widely due to differences in tokenization, pretraining data, and architecture. We argue that a major bottleneck lies in tokenizing sparse and unevenly distributed DNA sequence motifs, which are critical for accurate and interpretable models. To investigate, we systematically benchmark k-mer and Byte-Pair Encoding (BPE) tokenizers under controlled pretraining budget, evaluating across multiple downstream tasks from five datasets. We find that tokenizer choice induces task-specific trade-offs, and that vocabulary size and tokenizer training data strongly influence the biological knowledge captured. Notably, BPE tokenizers achieve strong performance when trained on smaller but biologically significant data. Building on these insights, we introduce DNAMotifTokenizer, which directly incorporates domain knowledge of DNA sequence motifs into the tokenization process. DNAMotifTokenizer consistently outperforms BPE across diverse benchmarks, demonstrating that knowledge-infused tokenization is crucial for learning powerful, interpretable, and generalizable genomic representations.

q-bio.GN↗

arXiv2025

TiViBench: Benchmarking Think-in-Video Reasoning for Video Generative Models

The rapid evolution of video generative models has shifted their focus from producing visually plausible outputs to tackling tasks requiring physical plausibility and logical consistency. However, despite recent breakthroughs such as Veo 3's chain-of-frames reasoning, it remains unclear whether these models can exhibit reasoning capabilities similar to large language models (LLMs). Existing benchmarks predominantly evaluate visual fidelity and temporal coherence, failing to capture higher-order reasoning abilities. To bridge this gap, we propose TiViBench, a hierarchical benchmark specifically designed to evaluate the reasoning capabilities of image-to-video (I2V) generation models. TiViBench systematically assesses reasoning across four dimensions: i) Structural Reasoning & Search, ii) Spatial & Visual Pattern Reasoning, iii) Symbolic & Logical Reasoning, and iv) Action Planning & Task Execution, spanning 24 diverse task scenarios across 3 difficulty levels. Through extensive evaluations, we show that commercial models (e.g., Sora 2, Veo 3.1) demonstrate stronger reasoning potential, while open-source models reveal untapped potential that remains hindered by limited training scale and data diversity. To further unlock this potential, we introduce VideoTPO, a simple yet effective test-time strategy inspired by preference optimization. By performing LLM self-analysis on generated candidates to identify strengths and weaknesses, VideoTPO significantly enhances reasoning performance without requiring additional training, data, or reward models. Together, TiViBench and VideoTPO pave the way for evaluating and advancing reasoning in video generation models, setting a foundation for future research in this emerging field.

cs.CV↗

arXiv2025

Non-unique decompositions of mixed states and deterministic energy transfers

We investigate the impact of non-unique decompositions of mixed states on energy transfer. Mixed states generally have non-unique decompositions into pure states in quantum theory and, by definition, in other non-classical probabilistic theories. We consider energy transfers constituting deterministic energy harvesting, wherein the source transfers energy to the harvester but not entropy. We use the possibility of non-unique decompositions to derive that if source states in a set jointly lead to deterministic energy harvesting for the given harvesting system and interaction, then that set can be expanded to include both mixtures and superpositions of the original states in the set. As a paradigmatic example, we model the source as an EM mode transferring energy to a 2-level system harvester via the Jaynes-Cummings model. We show that the set of coherent EM mode states with fixed $|α|$ that jointly achieve deterministic energy transfer can be expanded to include all mixtures and superpositions of those states. More generally, the results link the defining feature of a non-classical probability theory with the ability to achieve energy transfer without entropy transfer.

quant-ph↗

arXiv2025

D3D-VLP: Dynamic 3D Vision-Language-Planning Model for Embodied Grounding and Navigation

Embodied agents face a critical dilemma that end-to-end models lack interpretability and explicit 3D reasoning, while modular systems ignore cross-component interdependencies and synergies. To bridge this gap, we propose the Dynamic 3D Vision-Language-Planning Model (D3D-VLP). Our model introduces two key innovations: 1) A Dynamic 3D Chain-of-Thought (3D CoT) that unifies planning, grounding, navigation, and question answering within a single 3D-VLM and CoT pipeline; 2) A Synergistic Learning from Fragmented Supervision (SLFS) strategy, which uses a masked autoregressive loss to learn from massive and partially-annotated hybrid data. This allows different CoT components to mutually reinforce and implicitly supervise each other. To this end, we construct a large-scale dataset with 10M hybrid samples from 5K real scans and 20K synthetic scenes that are compatible with online learning methods such as RL and DAgger. Our D3D-VLP achieves state-of-the-art results on multiple benchmarks, including Vision-and-Language Navigation (R2R-CE, REVERIE-CE, NavRAG-CE), Object-goal Navigation (HM3D-OVON), and Task-oriented Sequential Grounding and Navigation (SG3D). Real-world mobile manipulation experiments further validate the effectiveness.

cs.CV↗

arXiv2025

SLOACI: Surrogate-Leveraged Online Adaptive Causal Inference

Adaptive experimental designs have gained increasing attention across a range of domains. In this paper, we propose a new methodological framework, surrogate-leveraged online adaptive causal inference (SLOACI), which integrates predictive surrogate outcomes into adaptive designs to enhance efficiency. For downstream analysis, we construct the adaptive augmented inverse probability weighting estimator for the average treatment effect using collected data. Our procedure remains robust even when surrogates are noisy or weak. We provide a comprehensive theoretical foundation for SLOACI. Under the asymptotic regime, we show that the proposed estimator attains the semiparametric efficiency bound. From a non-asymptotic perspective, we derive a regret bound to provide practical insights. We also develop a toolbox of sequential testing procedures that accommodates both asymptotic and non-asymptotic regimes, allowing experimenters to choose the perspective that best aligns with their practical needs. Extensive simulations and a synthetic case study are conducted to showcase the superior finite-sample performance of our method.

stat.ME↗

arXiv2025

The Effective Reproduction Number in the Kermack-McKendrick model with age of infection and reinfection

This study introduces a novel epidemiological model that expands upon the Kermack-McKendrick model by incorporating the age of infection and reinfection. By including infection age, we can classify participants, which enables a more targeted analysis within the modeling framework. The reinfection term addresses the real-world occurrences of secondary or recurrent viral infections. In the theoretical part, we apply the contraction mapping principle, the dominated convergence theorem, and the properties of Volterra integral equations to derive analytical expressions for the number of newly infected individuals denoted by $N(t)$. Then, we establish a Volterra integral equation for $N(t)$ and study its initial conditions for both a single cohort and multiple cohorts. From this equation, we derive a method for identifying the effective reproduction number, denoted as $\mathcal{R}(t)$. In the practical aspect, we present two distinct methods and separately apply them to analyze the daily new infection cases from the 2003 SARS outbreak in Singapore and the cumulative number of deaths from the COVID-19 epidemic in China. This work effectively bridges theoretical epidemiology and computational modeling, providing a robust framework for analyzing infection dynamics influenced by infection-age-structured transmission and reinfection mechanisms.

q-bio.PE↗

arXiv2025

KVReviver: Reversible KV Cache Compression with Sketch-Based Token Reconstruction

As the context length of current large language models (LLMs) rapidly increases, the memory demand for the Key-Value (KV) cache is becoming a bottleneck for LLM deployment and batch processing. Traditional KV cache compression methods typically involve permanently evicting or irreversibly merging "less important" tokens with low attention scores. This approach results in the unrecoverable loss of token information, which we call Contextual Amnesia, significantly degrading the model's information retrieval capability. To address this issue, we propose KVReviver, a reversible KV cache compression method based on the sketch algorithm. This method allows reconstructing compressed tokens from an additional data structure, thus enabling full-scale computation within limited memory. Experiments showed that in 2k-length contexts, it requires only 10% of KV Cache budget while maintaining identical end-to-end inference accuracy. For 32k-length contexts, it achieves equivalent or comparable accuracy ~2% accuracy loss) using merely 25% of KV Cache budget.

cs.CL↗

arXiv2025

KeepKV: Achieving Periodic Lossless KV Cache Compression for Efficient LLM Inference

Efficient inference of large language models (LLMs) is hindered by an ever-growing key-value (KV) cache, making KV cache compression a critical research direction. Traditional methods selectively evict less important KV cache entries, which leads to information loss and hallucinations. Recently, merging-based strategies have been explored to retain more information by merging KV pairs that would be discarded; however, these existing approaches inevitably introduce inconsistencies in attention distributions before and after merging, causing degraded generation quality. To overcome this challenge, we propose KeepKV, a novel adaptive KV cache merging method designed to preserve performance under strict memory constraints, achieving single-step lossless compression and providing error bounds for multi-step compression. KeepKV introduces the Electoral Votes mechanism that records merging history and adaptively adjusts attention scores. Moreover, it further leverages a novel Zero Inference-Perturbation Merging method, compensating for attention loss resulting from cache merging. Extensive experiments on various benchmarks and LLM architectures demonstrate that KeepKV substantially reduces memory usage while successfully retaining essential context information, achieving over 2x inference throughput improvement and maintaining superior generation quality even with only 10% KV cache budgets.

cs.LG↗

arXiv2025

On Meta-Evaluation

Evaluation is the foundation of empirical science, yet the evaluation of evaluation itself -- so-called meta-evaluation -- remains strikingly underdeveloped. While methods such as observational studies, design of experiments (DoE), and randomized controlled trials (RCTs) have shaped modern scientific practice, there has been little systematic inquiry into their comparative validity and utility across domains. Here we introduce a formal framework for meta-evaluation by defining the evaluation space, its structured representation, and a benchmark we call AxiaBench. AxiaBench enables the first large-scale, quantitative comparison of ten widely used evaluation methods across eight representative application domains. Our analysis reveals a fundamental limitation: no existing method simultaneously achieves accuracy and efficiency across diverse scenarios, with DoE and observational designs in particular showing significant deviations from real-world ground truth. We further evaluate a unified method of entire-space stratified sampling from previous evaluatology research, and the results report that it consistently outperforms prior approaches across all tested domains. These results establish meta-evaluation as a scientific object in its own right and provide both a conceptual foundation and a pragmatic tool set for advancing trustworthy evaluation in computational and experimental research.

stat.ME↗

arXiv2025

Zero-Shot Anomaly Detection with Dual-Branch Prompt Selection

Zero-shot anomaly detection (ZSAD) enables identifying and localizing defects in unseen categories by relying solely on generalizable features rather than requiring any labeled examples of anomalies. However, existing ZSAD methods, whether using fixed or learned prompts, struggle under domain shifts because their training data are derived from limited training domains and fail to generalize to new distributions. In this paper, we introduce PILOT, a framework designed to overcome these challenges through two key innovations: (1) a novel dual-branch prompt learning mechanism that dynamically integrates a pool of learnable prompts with structured semantic attributes, enabling the model to adaptively weight the most relevant anomaly cues for each input image; and (2) a label-free test-time adaptation strategy that updates the learnable prompt parameters using high-confidence pseudo-labels from unlabeled test data. Extensive experiments on 13 industrial and medical benchmarks demonstrate that PILOT achieves state-of-the-art performance in both anomaly detection and localization under domain shift.

cs.CV↗

arXiv2025

VPN: Visual Prompt Navigation

While natural language is commonly used to guide embodied agents, the inherent ambiguity and verbosity of language often hinder the effectiveness of language-guided navigation in complex environments. To this end, we propose Visual Prompt Navigation (VPN), a novel paradigm that guides agents to navigate using only user-provided visual prompts within 2D top-view maps. This visual prompt primarily focuses on marking the visual navigation trajectory on a top-down view of a scene, offering intuitive and spatially grounded guidance without relying on language instructions. It is more friendly for non-expert users and reduces interpretive ambiguity. We build VPN tasks in both discrete and continuous navigation settings, constructing two new datasets, R2R-VP and R2R-CE-VP, by extending existing R2R and R2R-CE episodes with corresponding visual prompts. Furthermore, we introduce VPNet, a dedicated baseline network to handle the VPN tasks, with two data augmentation strategies: view-level augmentation (altering initial headings and prompt orientations) and trajectory-level augmentation (incorporating diverse trajectories from large-scale 3D scenes), to enhance navigation performance. Extensive experiments evaluate how visual prompt forms, top-view map formats, and data augmentation strategies affect the performance of visual prompt navigation. The code is available at https://github.com/farlit/VPN.

cs.CV↗

arXiv2025

Video Finetuning Improves Reasoning Between Frames

Multimodal large language models (LLMs) have made rapid progress in visual understanding, yet their extension from images to videos often reduces to a naive concatenation of frame tokens. In this work, we investigate what video finetuning brings to multimodal LLMs. We propose Visual Chain-of-Thought (vCoT), an explicit reasoning process that generates transitional event descriptions between consecutive frames. Using vCoT, we systematically compare image-only LVLMs with their video-finetuned counterparts, both with and without access to these transitional cues. Our experiments show that vCoT significantly improves the performance of image-only models on long-form video question answering, while yielding only marginal gains for video-finetuned models. This suggests that the latter already capture frame-to-frame transitions implicitly. Moreover, we find that video models transfer this temporal reasoning ability to purely static settings, outperforming image models' baselines on relational visual reasoning tasks.

cs.CV↗

arXiv2025

Incorporating Spatial Information into Goal-Conditioned Hierarchical Reinforcement Learning via Graph Representations

The integration of graphs with Goal-conditioned Hierarchical Reinforcement Learning (GCHRL) has recently gained attention, as intermediate goals (subgoals) can be effectively sampled from graphs that naturally represent the overall task structure in most RL tasks. However, existing approaches typically rely on domain-specific knowledge to construct these graphs, limiting their applicability to new tasks. Other graph-based approaches create graphs dynamically during exploration but struggle to fully utilize them, because they have problems passing the information in the graphs to newly visited states. Additionally, current GCHRL methods face challenges such as sample inefficiency and poor subgoal representation. This paper proposes a solution to these issues by developing a graph encoder-decoder to evaluate unseen states. Our proposed method, Graph-Guided sub-Goal representation Generation RL (G4RL), can be incorporated into any existing GCHRL method when operating in environments with primarily symmetric and reversible transitions to enhance performance across this class of problems. We show that the graph encoder-decoder can be effectively implemented using a network trained on the state graph generated during exploration. Empirical results indicate that leveraging high and low-level intrinsic rewards from the graph encoder-decoder significantly enhances the performance of state-of-the-art GCHRL approaches with an extra small computational cost in dense and sparse reward environments.

cs.LG↗

arXiv2025

MTAttack: Multi-Target Backdoor Attacks against Large Vision-Language Models

Recent advances in Large Visual Language Models (LVLMs) have demonstrated impressive performance across various vision-language tasks by leveraging large-scale image-text pretraining and instruction tuning. However, the security vulnerabilities of LVLMs have become increasingly concerning, particularly their susceptibility to backdoor attacks. Existing backdoor attacks focus on single-target attacks, i.e., targeting a single malicious output associated with a specific trigger. In this work, we uncover multi-target backdoor attacks, where multiple independent triggers corresponding to different attack targets are added in a single pass of training, posing a greater threat to LVLMs in real-world applications. Executing such attacks in LVLMs is challenging since there can be many incorrect trigger-target mappings due to severe feature interference among different triggers. To address this challenge, we propose MTAttack, the first multi-target backdoor attack framework for enforcing accurate multiple trigger-target mappings in LVLMs. The core of MTAttack is a novel optimization method with two constraints, namely Proxy Space Partitioning constraint and Trigger Prototype Anchoring constraint. It jointly optimizes multiple triggers in the latent space, with each trigger independently mapping clean images to a unique proxy class while at the same time guaranteeing their separability. Experiments on popular benchmarks demonstrate a high success rate of MTAttack for multi-target attacks, substantially outperforming existing attack methods. Furthermore, our attack exhibits strong generalizability across datasets and robustness against backdoor defense strategies. These findings highlight the vulnerability of LVLMs to multi-target backdoor attacks and underscore the urgent need for mitigating such threats. Code is available at https://github.com/mala-lab/MTAttack.

cs.CV↗

arXiv2025

Order Matters: Rethinking Prompt Construction in In-Context Learning

In-context learning (ICL) enables large language models to perform new tasks by conditioning on a sequence of examples. Most prior work reasonably and intuitively assumes that which examples are chosen has a far greater effect on performance than how those examples are ordered, leading to a focus on example selection. We revisit this assumption and conduct a systematic comparison between the effect of selection and ordering. Through controlled experiments on both classification and generation tasks, using multiple open-source model families (0.5B to 27B parameters) and GPT-5, we find that the variance in performance due to different example orderings is comparable to that from using entirely different example sets. Furthermore, we show that strong orderings can be identified using only a development set, achieving performance close to an oracle that selects the best ordering based on test labels. Our findings highlight the equal and intertwined importance of example selection and ordering in prompt design, calling for a reexamination of the assumptions held in ICL.

cs.CL↗

arXiv2025

MPMA: Preference Manipulation Attack Against Model Context Protocol

Model Context Protocol (MCP) standardizes interface mapping for large language models (LLMs) to access external data and tools, which revolutionizes the paradigm of tool selection and facilitates the rapid expansion of the LLM agent tool ecosystem. However, as the MCP is increasingly adopted, third-party customized versions of the MCP server expose potential security vulnerabilities. In this paper, we first introduce a novel security threat, which we term the MCP Preference Manipulation Attack (MPMA). An attacker deploys a customized MCP server to manipulate LLMs, causing them to prioritize it over other competing MCP servers. This can result in economic benefits for attackers, such as revenue from paid MCP services or advertising income generated from free servers. To achieve MPMA, we first design a Direct Preference Manipulation Attack (DPMA) that achieves significant effectiveness by inserting the manipulative word and phrases into the tool name and description. However, such a direct modification is obvious to users and lacks stealthiness. To address these limitations, we further propose Genetic-based Advertising Preference Manipulation Attack (GAPMA). GAPMA employs four commonly used strategies to initialize descriptions and integrates a Genetic Algorithm (GA) to enhance stealthiness. The experiment results demonstrate that GAPMA balances high effectiveness and stealthiness. Our study reveals a critical vulnerability of the MCP in open ecosystems, highlighting an urgent need for robust defense mechanisms to ensure the fairness of the MCP ecosystem.

cs.CR↗

arXiv2025

ConfGuard: A Simple and Effective Backdoor Detection for Large Language Models

Backdoor attacks pose a significant threat to Large Language Models (LLMs), where adversaries can embed hidden triggers to manipulate LLM's outputs. Most existing defense methods, primarily designed for classification tasks, are ineffective against the autoregressive nature and vast output space of LLMs, thereby suffering from poor performance and high latency. To address these limitations, we investigate the behavioral discrepancies between benign and backdoored LLMs in output space. We identify a critical phenomenon which we term sequence lock: a backdoored model generates the target sequence with abnormally high and consistent confidence compared to benign generation. Building on this insight, we propose ConfGuard, a lightweight and effective detection method that monitors a sliding window of token confidences to identify sequence lock. Extensive experiments demonstrate ConfGuard achieves a near 100\% true positive rate (TPR) and a negligible false positive rate (FPR) in the vast majority of cases. Crucially, the ConfGuard enables real-time detection almost without additional latency, making it a practical backdoor defense for real-world LLM deployments.

cs.CR↗

arXiv2025

Self-Adaptive Cognitive Debiasing for Large Language Models in Decision-Making

Large language models (LLMs) have shown potential in supporting decision-making applications, particularly as personal assistants in the financial, healthcare, and legal domains. While prompt engineering strategies have enhanced the capabilities of LLMs in decision-making, cognitive biases inherent to LLMs present significant challenges. Cognitive biases are systematic patterns of deviation from norms or rationality in decision-making that can lead to the production of inaccurate outputs. Existing cognitive bias mitigation strategies assume that input prompts only contain one type of cognitive bias, limiting their effectiveness in more challenging scenarios involving multiple cognitive biases. To fill this gap, we propose a cognitive debiasing approach, self-adaptive cognitive debiasing (SACD), that enhances the reliability of LLMs by iteratively refining prompts. Our method follows three sequential steps - bias determination, bias analysis, and cognitive debiasing - to iteratively mitigate potential cognitive biases in prompts. We evaluate SACD on finance, healthcare, and legal decision-making tasks using both open-weight and closed-weight LLMs. Compared to advanced prompt engineering methods and existing cognitive debiasing techniques, SACD achieves the lowest average bias scores in both single-bias and multi-bias settings.

cs.CL↗