arXiv subjects

Siyuan Li

Publications and source records attributed to Siyuan Li.

At least 91 records · Page 5Linked to original sources

arXiv2026

Instructor-inspired Machine Learning for Robust Molecular Property Prediction

Machine learning catalyzes a revolution in chemical and biological science. However, its efficacy heavily depends on the availability of labeled data, and annotating biochemical data is extremely laborious. To surmount this data sparsity challenge, we present an instructive learning algorithm named InstructMol to measure pseudo-labels' reliability and help the target model leverage large-scale unlabeled data. InstructMol does not require transferring knowledge between multiple domains, which avoids the potential gap between the pretraining and fine-tuning stages. We demonstrated the high accuracy of InstructMol on several real-world molecular datasets and out-of-distribution (OOD) benchmarks. Code is available at~ https://github.com/smiles724/InstructMol.

cs.LG↗

arXiv2026

HoneyTrap: Deceiving Large Language Model Attackers to Honeypot Traps with Resilient Multi-Agent Defense

Jailbreak attacks pose significant threats to large language models (LLMs), enabling attackers to bypass safeguards. However, existing reactive defense approaches struggle to keep up with the rapidly evolving multi-turn jailbreaks, where attackers continuously deepen their attacks to exploit vulnerabilities. To address this critical challenge, we propose HoneyTrap, a novel deceptive LLM defense framework leveraging collaborative defenders to counter jailbreak attacks. It integrates four defensive agents, Threat Interceptor, Misdirection Controller, Forensic Tracker, and System Harmonizer, each performing a specialized security role and collaborating to complete a deceptive defense. To ensure a comprehensive evaluation, we introduce MTJ-Pro, a challenging multi-turn progressive jailbreak dataset that combines seven advanced jailbreak strategies designed to gradually deepen attack strategies across multi-turn attacks. Besides, we present two novel metrics: Mislead Success Rate (MSR) and Attack Resource Consumption (ARC), which provide more nuanced assessments of deceptive defense beyond conventional measures. Experimental results on GPT-4, GPT-3.5-turbo, Gemini-1.5-pro, and LLaMa-3.1 demonstrate that HoneyTrap achieves an average reduction of 68.77% in attack success rates compared to state-of-the-art baselines. Notably, even in a dedicated adaptive attacker setting with intensified conditions, HoneyTrap remains resilient, leveraging deceptive engagement to prolong interactions, significantly increasing the time and computational costs required for successful exploitation. Unlike simple rejection, HoneyTrap strategically wastes attacker resources without impacting benign queries, improving MSR and ARC by 118.11% and 149.16%, respectively.

cs.CR↗

arXiv2025

When Bayesian Tensor Completion Meets Multioutput Gaussian Processes: Functional Universality and Rank Learning

Functional tensor decomposition can analyze multi-dimensional data with real-valued indices, paving the path for applications in machine learning and signal processing. A limitation of existing approaches is the assumption that the tensor rank-a critical parameter governing model complexity-is known. However, determining the optimal rank is a non-deterministic polynomial-time hard (NP-hard) task and there is a limited understanding regarding the expressive power of functional low-rank tensor models for continuous signals. We propose a rank-revealing functional Bayesian tensor completion (RR-FBTC) method. Modeling the latent functions through carefully designed multioutput Gaussian processes, RR-FBTC handles tensors with real-valued indices while enabling automatic tensor rank determination during the inference process. We establish the universal approximation property of the model for continuous multi-dimensional signals, demonstrating its expressive power in a concise format. To learn this model, we employ the variational inference framework and derive an efficient algorithm with closed-form updates. Experiments on both synthetic and real-world datasets demonstrate the effectiveness and superiority of the RR-FBTC over state-of-the-art approaches. The code is available at https://github.com/OceanSTARLab/RR-FBTC.

cs.LG↗

arXiv2025

UniDepthV2: Universal Monocular Metric Depth Estimation Made Simpler

Accurate monocular metric depth estimation (MMDE) is crucial to solving downstream tasks in 3D perception and modeling. However, the remarkable accuracy of recent MMDE methods is confined to their training domains. These methods fail to generalize to unseen domains even in the presence of moderate domain gaps, which hinders their practical applicability. We propose a new model, UniDepthV2, capable of reconstructing metric 3D scenes from solely single images across domains. Departing from the existing MMDE paradigm, UniDepthV2 directly predicts metric 3D points from the input image at inference time without any additional information, striving for a universal and flexible MMDE solution. In particular, UniDepthV2 implements a self-promptable camera module predicting a dense camera representation to condition depth features. Our model exploits a pseudo-spherical output representation, which disentangles the camera and depth representations. In addition, we propose a geometric invariance loss that promotes the invariance of camera-prompted depth features. UniDepthV2 improves its predecessor UniDepth model via a new edge-guided loss which enhances the localization and sharpness of edges in the metric depth outputs, a revisited, simplified and more efficient architectural design, and an additional uncertainty-level output which enables downstream tasks requiring confidence. Thorough evaluations on ten depth datasets in a zero-shot regime consistently demonstrate the superior performance and generalization of UniDepthV2. Code and models are available at https://github.com/lpiccinelli-eth/UniDepth

cs.CV↗

arXiv2025

Decouple to Generalize: Context-First Self-Evolving Learning for Data-Scarce Vision-Language Reasoning

Recent vision-language models (VLMs) achieve remarkable reasoning through reinforcement learning (RL), which provides a feasible solution for realizing continuous self-evolving large vision-language models (LVLMs) in the era of experience. However, RL for VLMs requires abundant high-quality multimodal data, especially challenging in specialized domains like chemistry, earth sciences, and multimodal mathematics. Existing strategies such as synthetic data and self-rewarding mechanisms suffer from limited distributions and alignment difficulties, ultimately causing reward hacking: models exploit high-reward patterns, collapsing policy entropy and destabilizing training. We propose DoGe (Decouple to Generalize), a dual-decoupling framework that guides models to first learn from context rather than problem solving by refocusing on the problem context scenarios overlooked by synthetic data methods. By decoupling learning process into dual components (Thinker and Solver), we reasonably quantify the reward signals of this process and propose a two-stage RL post-training approach from freely exploring context to practically solving tasks. Second, to increase the diversity of training data, DoGe constructs an evolving curriculum learning pipeline: an expanded native domain knowledge corpus and an iteratively evolving seed problems pool. Experiments show that our method consistently outperforms the baseline across various benchmarks, providing a scalable pathway for realizing self-evolving LVLMs.

cs.AI↗

arXiv2025

Envision: Benchmarking Unified Understanding & Generation for Causal World Process Insights

Current multimodal models aim to transcend the limitations of single-modality representations by unifying understanding and generation, often using text-to-image (T2I) tasks to calibrate semantic consistency. However, their reliance on static, single-image generation in training and evaluation leads to overfitting to static pattern matching and semantic fusion, while fundamentally hindering their ability to model dynamic processes that unfold over time. To address these constraints, we propose Envision-a causal event progression benchmark for chained text-to-multi-image generation. Grounded in world knowledge and structured by spatiotemporal causality, it reorganizes existing evaluation dimensions and includes 1,000 four-stage prompts spanning six scientific and humanities domains. To transition evaluation from single images to sequential frames and assess whether models truly internalize world knowledge while adhering to causal-temporal constraints, we introduce Envision-Score, a holistic metric integrating multi-dimensional consistency, physicality, and aesthetics. Comprehensive evaluation of 15 models (10 specialized T2I models, 5 unified models) uncovers: specialized T2I models demonstrate proficiency in aesthetic rendering yet lack intrinsic world knowledge. Unified multimodal models bridge this gap, consistently outperforming specialized counterparts in causal narrative coherence. However, even these unified architectures remain subordinate to closed-source models and struggle to overcome the core challenge of spatiotemporal consistency. This demonstrates that a focus on causally-isolated single images impedes multi-frame reasoning and generation, promoting static pattern matching over dynamic world modeling-ultimately limiting world knowledge internalization, generation.

cs.CV↗

arXiv2025

Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains underexplored. This paper follows the guidance of the central dogma to redesign both the data and model pipeline and offers a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions between coding and non-coding regions through masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive experiments show that Life-Code achieves state-of-the-art results on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

cs.LG↗

arXiv2025

MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

q-bio.GN↗

arXiv2025

MrCoM: A Meta-Regularized World-Model Generalizing Across Multi-Scenarios

Model-based reinforcement learning (MBRL) is a crucial approach to enhance the generalization capabilities and improve the sample efficiency of RL algorithms. However, current MBRL methods focus primarily on building world models for single tasks and rarely address generalization across different scenarios. Building on the insight that dynamics within the same simulation engine share inherent properties, we attempt to construct a unified world model capable of generalizing across different scenarios, named Meta-Regularized Contextual World-Model (MrCoM). This method first decomposes the latent state space into various components based on the dynamic characteristics, thereby enhancing the accuracy of world-model prediction. Further, MrCoM adopts meta-state regularization to extract unified representation of scenario-relevant information, and meta-value regularization to align world-model optimization with policy learning across diverse scenario objectives. We theoretically analyze the generalization error upper bound of MrCoM in multi-scenario settings. We systematically evaluate our algorithm's generalization ability across diverse scenarios, demonstrating significantly better performance than previous state-of-the-art methods.

cs.LG↗

arXiv2025

Every Activation Boosted: Scaling General Reasoner to 1 Trillion Open Language Foundation

We introduce Ling 2.0, a series reasoning-oriented language foundation built upon the principle that every activation boosts reasoning capability. Designed to scale from tens of billions to one trillion parameters under a unified Mixture-of-Experts (MoE) paradigm, Ling 2.0 emphasizes high sparsity, cross-scale consistency, and efficiency guided by empirical scaling laws. The series includes three non-thinking (instruct) models - Ling-mini-2.0, Ling-flash-2.0, and Ling-1T - ranging from 16B to 1T total parameters and achieving up to 7-fold active-compute efficiency compared with dense counterparts. Ling 2.0 integrates coordinated innovations across model architecture, pre-training, post-training, and infrastructure: a high-sparsity MoE with MTP for efficient reasoning, reasoning-oriented data and mid-training CoT activation, reinforcement-based fine-tuning (DFT, Evo-CoT), and full-scale FP8 training with fine-grained heterogeneous pipelines. At the trillion scale, Ling-1T establishes a new Pareto frontier of reasoning accuracy versus computational efficiency, demonstrating that sparse activation, when properly aligned with reasoning objectives, enables scalable and efficient intelligence. Collectively, Ling 2.0 provides a coherent, open, and efficient foundation for advancing future reasoning and thinking models, including the Ring series built upon the same base.

cs.CL↗

arXiv2025

Less Is More: Generating Time Series with LLaMA-Style Autoregression in Simple Factorized Latent Spaces

Generative models for multivariate time series are essential for data augmentation, simulation, and privacy preservation, yet current state-of-the-art diffusion-based approaches are slow and limited to fixed-length windows. We propose FAR-TS, a simple yet effective framework that combines disentangled factorization with an autoregressive Transformer over a discrete, quantized latent space to generate time series. Each time series is decomposed into a data-adaptive basis that captures static cross-channel correlations and temporal coefficients that are vector-quantized into discrete tokens. A LLaMA-style autoregressive Transformer then models these token sequences, enabling fast and controllable generation of sequences with arbitrary length. Owing to its streamlined design, FAR-TS achieves orders-of-magnitude faster generation than Diffusion-TS while preserving cross-channel correlations and an interpretable latent space, enabling high-quality and flexible time series synthesis.

cs.LG↗

arXiv2025

Lares: LLM-driven Code Slice Semantic Search for Patch Presence Testing

In modern software ecosystems, 1-day vulnerabilities pose significant security risks due to extensive code reuse. Identifying vulnerable functions in target binaries alone is insufficient; it is also crucial to determine whether these functions have been patched. Existing methods, however, suffer from limited usability and accuracy. They often depend on the compilation process to extract features, requiring substantial manual effort and failing for certain software. Moreover, they cannot reliably differentiate between code changes caused by patches or compilation variations. To overcome these limitations, we propose Lares, a scalable and accurate method for patch presence testing. Lares introduces Code Slice Semantic Search, which directly extracts features from the patch source code and identifies semantically equivalent code slices in the pseudocode of the target binary. By eliminating the need for the compilation process, Lares improves usability, while leveraging large language models (LLMs) for code analysis and SMT solvers for logical reasoning to enhance accuracy. Experimental results show that Lares achieves superior precision, recall, and usability. Furthermore, it is the first work to evaluate patch presence testing across optimization levels, architectures, and compilers. The datasets and source code used in this article are available at https://github.com/Siyuan-Li201/Lares.

cs.SE↗

arXiv2025

TopoFR: A Closer Look at Topology Alignment on Face Recognition

The field of face recognition (FR) has undergone significant advancements with the rise of deep learning. Recently, the success of unsupervised learning and graph neural networks has demonstrated the effectiveness of data structure information. Considering that the FR task can leverage large-scale training data, which intrinsically contains significant structure information, we aim to investigate how to encode such critical structure information into the latent space. As revealed from our observations, directly aligning the structure information between the input and latent spaces inevitably suffers from an overfitting problem, leading to a structure collapse phenomenon in the latent space. To address this problem, we propose TopoFR, a novel FR model that leverages a topological structure alignment strategy called PTSA and a hard sample mining strategy named SDE. Concretely, PTSA uses persistent homology to align the topological structures of the input and latent spaces, effectively preserving the structure information and improving the generalization performance of FR model. To mitigate the impact of hard samples on the latent space structure, SDE accurately identifies hard samples by automatically computing structure damage score (SDS) for each sample, and directs the model to prioritize optimizing these samples. Experimental results on popular face benchmarks demonstrate the superiority of our TopoFR over the state-of-the-art methods. Code and models are available at: https://github.com/modelscope/facechain/tree/main/face_module/TopoFR.

cs.CV↗

arXiv2025

StyleDecipher: Robust and Explainable Detection of LLM-Generated Texts with Stylistic Analysis

With the increasing integration of large language models (LLMs) into open-domain writing, detecting machine-generated text has become a critical task for ensuring content authenticity and trust. Existing approaches rely on statistical discrepancies or model-specific heuristics to distinguish between LLM-generated and human-written text. However, these methods struggle in real-world scenarios due to limited generalization, vulnerability to paraphrasing, and lack of explainability, particularly when facing stylistic diversity or hybrid human-AI authorship. In this work, we propose StyleDecipher, a robust and explainable detection framework that revisits LLM-generated text detection using combined feature extractors to quantify stylistic differences. By jointly modeling discrete stylistic indicators and continuous stylistic representations derived from semantic embeddings, StyleDecipher captures distinctive style-level divergences between human and LLM outputs within a unified representation space. This framework enables accurate, explainable, and domain-agnostic detection without requiring access to model internals or labeled segments. Extensive experiments across five diverse domains, including news, code, essays, reviews, and academic abstracts, demonstrate that StyleDecipher consistently achieves state-of-the-art in-domain accuracy. Moreover, in cross-domain evaluations, it surpasses existing baselines by up to 36.30%, while maintaining robustness against adversarial perturbations and mixed human-AI content. Further qualitative and quantitative analysis confirms that stylistic signals provide explainable evidence for distinguishing machine-generated text. Our source code can be accessed at https://github.com/SiyuanLi00/StyleDecipher.

cs.CL↗

arXiv2025

An Imitative Reinforcement Learning Framework for Pursuit-Lock-Launch Missions

Unmanned Combat Aerial Vehicle (UCAV) Within-Visual-Range (WVR) engagement, referring to a fight between two or more UCAVs at close quarters, plays a decisive role on the aerial battlefields. With the development of artificial intelligence, WVR engagement progressively advances towards intelligent and autonomous modes. However, autonomous WVR engagement policy learning is hindered by challenges such as weak exploration capabilities, low learning efficiency, and unrealistic simulated environments. To overcome these challenges, we propose a novel imitative reinforcement learning framework, which efficiently leverages expert data while enabling autonomous exploration. The proposed framework not only enhances learning efficiency through expert imitation, but also ensures adaptability to dynamic environments via autonomous exploration with reinforcement learning. Therefore, the proposed framework can learn a successful policy of `pursuit-lock-launch' for UCAVs. To support data-driven learning, we establish an environment based on the Harfang3D sandbox. The extensive experiment results indicate that the proposed framework excels in this multistage task, and significantly outperforms state-of-the-art reinforcement learning and imitation learning methods. Thanks to the ability of imitating experts and autonomous exploration, our framework can quickly learn the critical knowledge in complex aerial combat tasks, achieving up to a 100% success rate and demonstrating excellent robustness.

cs.LG↗

arXiv2025

KnowMT-Bench: Benchmarking Knowledge-Intensive Long-Form Question Answering in Multi-Turn Dialogues

Multi-Turn Long-Form Question Answering (MT-LFQA) is a key application paradigm of Large Language Models (LLMs) in knowledge-intensive domains. However, existing benchmarks are limited to single-turn dialogue, while multi-turn dialogue benchmarks typically assess other orthogonal capabilities rather than knowledge-intensive factuality. To bridge this critical gap, we introduce \textbf{KnowMT-Bench}, the \textit{first-ever} benchmark designed to systematically evaluate MT-LFQA for LLMs across knowledge-intensive fields, including medicine, finance, and law. To faithfully assess the model's real-world performance, KnowMT-Bench employs a dynamic evaluation setting where models generate their own multi-turn dialogue histories given logically progressive question sequences. The factual capability and information delivery efficiency of the \textit{final-turn} answer are then evaluated using a human-validated automated pipeline. Our experiments reveal that multi-turn contexts degrade performance: factual capability declines due to the contextual noise from self-generated histories, while information efficiency drops as models become more verbose with increasing dialogue length. We then investigate mitigation strategies, demonstrating that retrieval-augmented generation (RAG) can effectively alleviate and even reverse this factual degradation. These findings underscore the importance of our benchmark in evaluating and enhancing the conversational factual capabilities of LLMs in real-world knowledge-intensive applications. Code is available at \href{https://github.com/hardenyu21/KnowMT-Bench}{\textcolor{cyan}{\texttt{KnowMT-Bench}}}.

cs.CL↗

arXiv2025

Boosting Zero-Shot VLN via Abstract Obstacle Map-Based Waypoint Prediction with TopoGraph-and-VisitInfo-Aware Prompting

With the rapid progress of foundation models and robotics, vision-language navigation (VLN) has emerged as a key task for embodied agents with broad practical applications. We address VLN in continuous environments, a particularly challenging setting where an agent must jointly interpret natural language instructions, perceive its surroundings, and plan low-level actions. We propose a zero-shot framework that integrates a simplified yet effective waypoint predictor with a multimodal large language model (MLLM). The predictor operates on an abstract obstacle map, producing linearly reachable waypoints, which are incorporated into a dynamically updated topological graph with explicit visitation records. The graph and visitation information are encoded into the prompt, enabling reasoning over both spatial structure and exploration history to encourage exploration and equip MLLM with local path planning for error correction. Extensive experiments on R2R-CE and RxR-CE show that our method achieves state-of-the-art zero-shot performance, with success rates of 41% and 36%, respectively, outperforming prior state-of-the-art methods.

cs.RO↗

arXiv2025

ProDyG: Progressive Dynamic Scene Reconstruction via Gaussian Splatting from Monocular Videos

Achieving truly practical dynamic 3D reconstruction requires online operation, global pose and map consistency, detailed appearance modeling, and the flexibility to handle both RGB and RGB-D inputs. However, existing SLAM methods typically merely remove the dynamic parts or require RGB-D input, while offline methods are not scalable to long video sequences, and current transformer-based feedforward methods lack global consistency and appearance details. To this end, we achieve online dynamic scene reconstruction by disentangling the static and dynamic parts within a SLAM system. The poses are tracked robustly with a novel motion masking strategy, and dynamic parts are reconstructed leveraging a progressive adaptation of a Motion Scaffolds graph. Our method yields novel view renderings competitive to offline methods and achieves on-par tracking with state-of-the-art dynamic SLAM methods.

cs.CV↗