arXiv subjects

Siyuan Li

Publications and source records attributed to Siyuan Li.

At least 109 records · Page 6Linked to original sources

arXiv2025

Multimodal Regression for Enzyme Turnover Rates Prediction

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental measurements. To address this gap, we propose a multimodal framework for predicting the enzyme turnover rate by integrating enzyme sequences, substrate structures, and environmental factors. Our model combines a pre-trained language model and a convolutional neural network to extract features from protein sequences, while a graph neural network captures informative representations from substrate molecules. An attention mechanism is incorporated to enhance interactions between enzyme and substrate representations. Furthermore, we leverage symbolic regression via Kolmogorov-Arnold Networks to explicitly learn mathematical formulas that govern the enzyme turnover rate, enabling interpretable and accurate predictions. Extensive experiments demonstrate that our framework outperforms both traditional and state-of-the-art deep learning approaches. This work provides a robust tool for studying enzyme kinetics and holds promise for applications in enzyme engineering, biotechnology, and industrial biocatalysis.

cs.LG↗

arXiv2025

Context-Driven Knowledge Graph Completion with Semantic-Aware Relational Message Passing

Semantic context surrounding a triplet $(h, r, t)$ is crucial for Knowledge Graph Completion (KGC), providing vital cues for prediction. However, traditional node-based message passing mechanisms, when applied to knowledge graphs, often introduce noise and suffer from information dilution or over-smoothing by indiscriminately aggregating information from all neighboring edges. To address this challenge, we propose a semantic-aware relational message passing. A core innovation of this framework is the introduction of a semantic-aware Top-K neighbor selection strategy. Specifically, this strategy first evaluates the semantic relevance between a central node and its incident edges within a shared latent space, selecting only the Top-K most pertinent ones. Subsequently, information from these selected edges is effectively fused with the central node's own representation using a multi-head attention aggregator to generate a semantically focused node message. In this manner, our model not only leverages the structure and features of edges within the knowledge graph but also more accurately captures and propagates the contextual information most relevant to the specific link prediction task, thereby effectively mitigating interference from irrelevant information. Extensive experiments demonstrate that our method achieves superior performance compared to existing approaches on several established benchmarks.

cs.AI↗

arXiv2025

3D-MOOD: Lifting 2D to 3D for Monocular Open-Set Object Detection

Monocular 3D object detection is valuable for various applications such as robotics and AR/VR. Existing methods are confined to closed-set settings, where the training and testing sets consist of the same scenes and/or object categories. However, real-world applications often introduce new environments and novel object categories, posing a challenge to these methods. In this paper, we address monocular 3D object detection in an open-set setting and introduce the first end-to-end 3D Monocular Open-set Object Detector (3D-MOOD). We propose to lift the open-set 2D detection into 3D space through our designed 3D bounding box head, enabling end-to-end joint training for both 2D and 3D tasks to yield better overall performance. We condition the object queries with geometry prior and overcome the generalization for 3D estimation across diverse scenes. To further improve performance, we design the canonical image space for more efficient cross-dataset training. We evaluate 3D-MOOD on both closed-set settings (Omni3D) and open-set settings (Omni3D to Argoverse 2, ScanNet), and achieve new state-of-the-art results. Code and models are available at royyang0714.github.io/3D-MOOD.

cs.CV↗

arXiv2025

MiniCPM4: Ultra-Efficient LLMs on End Devices

This paper introduces MiniCPM4, a highly efficient large language model (LLM) designed explicitly for end-side devices. We achieve this efficiency through systematic innovation in four key dimensions: model architecture, training data, training algorithms, and inference systems. Specifically, in terms of model architecture, we propose InfLLM v2, a trainable sparse attention mechanism that accelerates both prefilling and decoding phases for long-context processing. Regarding training data, we propose UltraClean, an efficient and accurate pre-training data filtering and generation strategy, and UltraChat v2, a comprehensive supervised fine-tuning dataset. These datasets enable satisfactory model performance to be achieved using just 8 trillion training tokens. Regarding training algorithms, we propose ModelTunnel v2 for efficient pre-training strategy search, and improve existing post-training methods by introducing chunk-wise rollout for load-balanced reinforcement learning and data-efficient tenary LLM, BitCPM. Regarding inference systems, we propose CPM.cu that integrates sparse attention, model quantization, and speculative sampling to achieve efficient prefilling and decoding. To meet diverse on-device requirements, MiniCPM4 is available in two versions, with 0.5B and 8B parameters, respectively. Furthermore, we construct a hybrid reasoning model, MiniCPM4.1, which can be used in both deep reasoning mode and non-reasoning mode. Evaluation results demonstrate that MiniCPM4 and MiniCPM4.1 outperform similar-sized open-source models across benchmarks, with the 8B variants showing significant speed improvements on long sequence understanding and generation.

cs.CL↗

arXiv2025

ResearchPulse: Building Method-Experiment Chains through Multi-Document Scientific Inference

Understanding how scientific ideas evolve requires more than summarizing individual papers-it demands structured, cross-document reasoning over thematically related research. In this work, we formalize multi-document scientific inference, a new task that extracts and aligns motivation, methodology, and experimental results across related papers to reconstruct research development chains. This task introduces key challenges, including temporally aligning loosely structured methods and standardizing heterogeneous experimental tables. We present ResearchPulse, an agent-based framework that integrates instruction planning, scientific content extraction, and structured visualization. It consists of three coordinated agents: a Plan Agent for task decomposition, a Mmap-Agent that constructs motivation-method mind maps, and a Lchart-Agent that synthesizes experimental line charts. To support this task, we introduce ResearchPulse-Bench, a citation-aware benchmark of annotated paper clusters. Experiments show that our system, despite using 7B-scale agents, consistently outperforms strong baselines like GPT-4o in semantic alignment, structural consistency, and visual fidelity. The dataset are available in https://huggingface.co/datasets/ResearchPulse/ResearchPulse-Bench.

cs.CL↗

arXiv2025

Flow-Modulated Scoring for Semantic-Aware Knowledge Graph Completion

Knowledge graph completion demands effective modeling of multifaceted semantic relationships between entities. Yet, prevailing methods, which rely on static scoring functions over learned embeddings, struggling to simultaneously capture rich semantic context and the dynamic nature of relations. To overcome this limitation, we propose the Flow-Modulated Scoring (FMS) framework, conceptualizing a relation as a dynamic evolutionary process governed by its static semantic environment. FMS operates in two stages: it first learns context-aware entity embeddings via a Semantic Context Learning module, and then models a dynamic flow between them using a Conditional Flow-Matching module. This learned flow dynamically modulates a base static score for the entity pair. By unifying context-rich static representations with a conditioned dynamic flow, FMS achieves a more comprehensive understanding of relational semantics. Extensive experiments demonstrate that FMS establishes a new state of the art across both canonical knowledge graph completion tasks: relation prediction and entity prediction. On the standard relation prediction benchmark FB15k-237, FMS achieves a near-perfect MRR of 99.8\% and Hits@1 of 99.7\% using a mere 0.35M parameters, while also attaining a 99.9\% MRR on WN18RR. Its dominance extends to entity prediction, where it secures a 25.2\% relative MRR gain in the transductive setting and substantially outperforms all baselines in challenging inductive settings. By unifying a dynamic flow mechanism with rich static contexts, FMS offers a highly effective and parameter-efficient new paradigm for knowledge graph completion. Code published at: https://github.com/yuanwuyuan9/FMS.

cs.CL↗

arXiv2025

Multi-View 3D Point Tracking

We introduce the first data-driven multi-view 3D point tracker, designed to track arbitrary points in dynamic scenes using multiple camera views. Unlike existing monocular trackers, which struggle with depth ambiguities and occlusion, or prior multi-camera methods that require over 20 cameras and tedious per-sequence optimization, our feed-forward model directly predicts 3D correspondences using a practical number of cameras (e.g., four), enabling robust and accurate online tracking. Given known camera poses and either sensor-based or estimated multi-view depth, our tracker fuses multi-view features into a unified point cloud and applies k-nearest-neighbors correlation alongside a transformer-based update to reliably estimate long-range 3D correspondences, even under occlusion. We train on 5K synthetic multi-view Kubric sequences and evaluate on two real-world benchmarks: Panoptic Studio and DexYCB, achieving median trajectory errors of 3.1 cm and 2.0 cm, respectively. Our method generalizes well to diverse camera setups of 1-8 views with varying vantage points and video lengths of 24-150 frames. By releasing our tracker alongside training and evaluation datasets, we aim to set a new standard for multi-view 3D tracking research and provide a practical tool for real-world applications. Project page available at https://ethz-vlg.github.io/mvtracker.

cs.CV↗

arXiv2025

Enhancing Rumor Detection Methods with Propagation Structure Infused Language Model

Pretrained Language Models (PLMs) have excelled in various Natural Language Processing tasks, benefiting from large-scale pretraining and self-attention mechanism's ability to capture long-range dependencies. However, their performance on social media application tasks like rumor detection remains suboptimal. We attribute this to mismatches between pretraining corpora and social texts, inadequate handling of unique social symbols, and pretraining tasks ill-suited for modeling user engagements implicit in propagation structures. To address these issues, we propose a continue pretraining strategy called Post Engagement Prediction (PEP) to infuse information from propagation structures into PLMs. PEP makes models to predict root, branch, and parent relations between posts, capturing interactions of stance and sentiment crucial for rumor detection. We also curate and release large-scale Twitter corpus: TwitterCorpus (269GB text), and two unlabeled claim conversation datasets with propagation structures (UTwitter and UWeibo). Utilizing these resources and PEP strategy, we train a Twitter-tailored PLM called SoLM. Extensive experiments demonstrate PEP significantly boosts rumor detection performance across universal and social media PLMs, even in few-shot scenarios. On benchmark datasets, PEP enhances baseline models by 1.0-3.7\% accuracy, even enabling it to outperform current state-of-the-art methods on multiple datasets. SoLM alone, without high-level modules, also achieves competitive results, highlighting the strategy's effectiveness in learning discriminative post interaction features.

cs.CL↗

arXiv2025

Model-Agnostic Sentiment Distribution Stability Analysis for Robust LLM-Generated Texts Detection

The rapid advancement of large language models (LLMs) has resulted in increasingly sophisticated AI-generated content, posing significant challenges in distinguishing LLM-generated text from human-written language. Existing detection methods, primarily based on lexical heuristics or fine-tuned classifiers, often suffer from limited generalizability and are vulnerable to paraphrasing, adversarial perturbations, and cross-domain shifts. In this work, we propose SentiDetect, a model-agnostic framework for detecting LLM-generated text by analyzing the divergence in sentiment distribution stability. Our method is motivated by the empirical observation that LLM outputs tend to exhibit emotionally consistent patterns, whereas human-written texts display greater emotional variability. To capture this phenomenon, we define two complementary metrics: sentiment distribution consistency and sentiment distribution preservation, which quantify stability under sentiment-altering and semantic-preserving transformations. We evaluate SentiDetect on five diverse datasets and a range of advanced LLMs,including Gemini-1.5-Pro, Claude-3, GPT-4-0613, and LLaMa-3.3. Experimental results demonstrate its superiority over state-of-the-art baselines, with over 16% and 11% F1 score improvements on Gemini-1.5-Pro and GPT-4-0613, respectively. Moreover, SentiDetect also shows greater robustness to paraphrasing, adversarial attacks, and text length variations, outperforming existing detectors in challenging scenarios.

cs.CL↗

arXiv2025

Neuro-MoBRE: Exploring Multi-subject Multi-task Intracranial Decoding via Explicit Heterogeneity Resolving

Neurophysiological decoding, fundamental to advancing brain-computer interface (BCI) technologies, has significantly benefited from recent advances in deep learning. However, existing decoding approaches largely remain constrained to single-task scenarios and individual subjects, limiting their broader applicability and generalizability. Efforts towards creating large-scale neurophysiological foundation models have shown promise, but continue to struggle with significant challenges due to pervasive data heterogeneity across subjects and decoding tasks. Simply increasing model parameters and dataset size without explicitly addressing this heterogeneity fails to replicate the scaling successes seen in natural language processing. Here, we introduce the Neural Mixture of Brain Regional Experts (Neuro-MoBRE), a general-purpose decoding framework explicitly designed to manage the ubiquitous data heterogeneity in neurophysiological modeling. Neuro-MoBRE incorporates a brain-regional-temporal embedding mechanism combined with a mixture-of-experts approach, assigning neural signals from distinct brain regions to specialized regional experts on a unified embedding basis, thus explicitly resolving both structural and functional heterogeneity. Additionally, our region-masked autoencoding pre-training strategy further enhances representational consistency among subjects, complemented by a task-disentangled information aggregation method tailored to effectively handle task-specific neural variations. Evaluations conducted on intracranial recordings from 11 subjects across five diverse tasks, including complex language decoding and epileptic seizure diagnosis, demonstrate that Neuro-MoBRE surpasses prior art and exhibits robust generalization for zero-shot decoding on unseen subjects.

eess.SP↗

arXiv2025

SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches

Hand-drawn sketches are a natural and efficient medium for capturing and conveying ideas. Despite significant advancements in controllable natural image generation, translating freehand sketches into structured, machine-readable diagrams remains a labor-intensive and predominantly manual task. The primary challenge stems from the inherent ambiguity of sketches, which lack the structural constraints and semantic precision required for automated diagram generation. To address this challenge, we introduce SketchAgent, a multi-agent system designed to automate the transformation of hand-drawn sketches into structured diagrams. SketchAgent integrates sketch recognition, symbolic reasoning, and iterative validation to produce semantically coherent and structurally accurate diagrams, significantly reducing the need for manual effort. To evaluate the effectiveness of our approach, we propose the Sketch2Diagram Benchmark, a comprehensive dataset and evaluation framework encompassing eight diverse diagram categories, such as flowcharts, directed graphs, and model architectures. The dataset comprises over 6,000 high-quality examples with token-level annotations, standardized preprocessing, and rigorous quality control. By streamlining the diagram generation process, SketchAgent holds great promise for applications in design, education, and engineering, while offering a significant step toward bridging the gap between intuitive sketching and machine-readable diagram generation. The benchmark is released at https://huggingface.co/datasets/DiagramAgent/Sketch2Diagram-Benchmark.

cs.AI↗

arXiv2025

Rep-MTL: Unleashing the Power of Representation-level Task Saliency for Multi-Task Learning

Despite the promise of Multi-Task Learning in leveraging complementary knowledge across tasks, existing multi-task optimization (MTO) techniques remain fixated on resolving conflicts via optimizer-centric loss scaling and gradient manipulation strategies, yet fail to deliver consistent gains. In this paper, we argue that the shared representation space, where task interactions naturally occur, offers rich information and potential for operations complementary to existing optimizers, especially for facilitating the inter-task complementarity, which is rarely explored in MTO. This intuition leads to Rep-MTL, which exploits the representation-level task saliency to quantify interactions between task-specific optimization and shared representation learning. By steering these saliencies through entropy-based penalization and sample-wise cross-task alignment, Rep-MTL aims to mitigate negative transfer by maintaining the effective training of individual tasks instead pure conflict-solving, while explicitly promoting complementary information sharing. Experiments are conducted on four challenging MTL benchmarks covering both task-shift and domain-shift scenarios. The results show that Rep-MTL, even paired with the basic equal weighting policy, achieves competitive performance gains with favorable efficiency. Beyond standard performance metrics, Power Law exponent analysis demonstrates Rep-MTL's efficacy in balancing task-specific learning and cross-task sharing. The project page is available at HERE.

cs.LG↗

arXiv2025

DHEvo: Data-Algorithm Based Heuristic Evolution for Generalizable MILP Solving

Primal heuristics play a critical role in improving the efficiency of mixed integer programming (MILP) solvers. As large language models (LLMs) have demonstrated superior code generation abilities, recent MILP works are devoted to leveraging the evolutionary computation approaches with LLMs to generate effective primal heuristics. Although the generated heuristics have achieved better solving performance than the hand-crafted ones with little adaptability, the advantage of current LLM-based methods is limited to few MILP instances in one problem class, as they fail to capture the instance characteristics in the problem class (the MILP instances generated from the same mathematical model are defined as a problem class). Since MILP instances often differ significantly in structure and feature distribution, the neglect of their characteristics in the evolution process results in poor generalization within the same problem class. To overcome this challenge, we propose a data-algorithm co-evolution framework (DHEvo) that iteratively selects representative instances and evolves corresponding heuristics. With the initial instance distribution, we develop an LLM-based multi-agent system to generate data-code pairs simultaneously. These data-code pairs are iteratively refined based on their fitness scores, leading to the identification of the most effective heuristic over the entire problem class. Extensive experiments across diverse MILP benchmarks demonstrate that our approach significantly outperforms both human-designed heuristics and existing LLM-based methods.

cs.NE↗

arXiv2025

MogaNet: Multi-order Gated Aggregation Network

By contextualizing the kernel as global as possible, Modern ConvNets have shown great potential in computer vision tasks. However, recent progress on multi-order game-theoretic interaction within deep neural networks (DNNs) reveals the representation bottleneck of modern ConvNets, where the expressive interactions have not been effectively encoded with the increased kernel size. To tackle this challenge, we propose a new family of modern ConvNets, dubbed MogaNet, for discriminative visual representation learning in pure ConvNet-based models with favorable complexity-performance trade-offs. MogaNet encapsulates conceptually simple yet effective convolutions and gated aggregation into a compact module, where discriminative features are efficiently gathered and contextualized adaptively. MogaNet exhibits great scalability, impressive efficiency of parameters, and competitive performance compared to state-of-the-art ViTs and ConvNets on ImageNet and various downstream vision benchmarks, including COCO object detection, ADE20K semantic segmentation, 2D&3D human pose estimation, and video prediction. Notably, MogaNet hits 80.0% and 87.8% accuracy with 5.2M and 181M parameters on ImageNet-1K, outperforming ParC-Net and ConvNeXt-L, while saving 59% FLOPs and 17M parameters, respectively. The source code is available at https://github.com/Westlake-AI/MogaNet.

cs.CV↗

arXiv2025

FieldFormer: Self-supervised Reconstruction of Physical Fields via Tensor Attention Prior

Reconstructing physical field tensors from \textit{in situ} observations, such as radio maps and ocean sound speed fields, is crucial for enabling environment-aware decision making in various applications, e.g., wireless communications and underwater acoustics. Field data reconstruction is often challenging, due to the limited and noisy nature of the observations, necessitating the incorporation of prior information to aid the reconstruction process. Deep neural network-based data-driven structural constraints (e.g., ``deeply learned priors'') have showed promising performance. However, this family of techniques faces challenges such as model mismatches between training and testing phases. This work introduces FieldFormer, a self-supervised neural prior learned solely from the limited {\it in situ} observations without the need of offline training. Specifically, the proposed framework starts with modeling the fields of interest using the tensor Tucker model of a high multilinear rank, which ensures a universal approximation property for all fields. In the sequel, an attention mechanism is incorporated to learn the sparsity pattern that underlies the core tensor in order to reduce the solution space. In this way, a ``complexity-adaptive'' neural representation, grounded in the Tucker decomposition, is obtained that can flexibly represent various types of fields. A theoretical analysis is provided to support the recoverability of the proposed design. Moreover, extensive experiments, using various physical field tensors, demonstrate the superiority of the proposed approach compared to state-of-the-art baselines.

eess.SP↗

arXiv2025

AlphaFold Database Debiasing for Robust Inverse Folding

The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein design. However, its direct use in training deep models that are sensitive to fine-grained atomic geometry, such as inverse folding, exposes a critical limitation. Comparative analysis of structural feature distributions reveals that AFDB structures exhibit distinct statistical regularities, reflecting a systematic geometric bias that deviates from the conformational diversity found in experimentally determined structures from the Protein Data Bank (PDB). While AFDB structures are cleaner and more idealized, PDB structures capture the intrinsic variability and physical realism essential for generalization in downstream tasks. To address this discrepancy, we introduce a Debiasing Structure AutoEncoder (DeSAE) that learns to reconstruct native-like conformations from intentionally corrupted backbone geometries. By training the model to recover plausible structural states, DeSAE implicitly captures a more robust and natural structural manifold. At inference, applying DeSAE to AFDB structures produces debiased structures that significantly improve inverse folding performance across multiple benchmarks. This work highlights the critical impact of subtle systematic biases in predicted structures and presents a principled framework for debiasing, significantly boosting the performance of structure-based learning tasks like inverse folding.

cs.LG↗

arXiv2025

Taming LLMs by Scaling Learning Rates with Gradient Grouping

Training large language models (LLMs) poses challenges due to their massive scale and heterogeneous architectures. While adaptive optimizers like AdamW help address gradient variations, they still struggle with efficient and effective parameter-wise learning rate estimation, resulting in training instability, slow convergence, and poor compatibility with parameter-efficient fine-tuning (PEFT) techniques. This work introduces Scaling with Gradient Grouping (SGG), an optimizer wrapper that improves adaptive learning rate estimation by dynamic grouping and group-specific scaling. SGG first groups gradient statistics in each layer into clusters and then applies cluster-specific scaling to calibrate learning rates for each parameter, thus imposing collective group-wise constraints while maintaining precise per-parameter adaptation. Experiments on diverse (M)LLM benchmarks show that SGG integrates seamlessly with existing optimizers, and offers consistent gains and faster convergence over baselines, with various model sizes. Its stability across varying batch sizes and learning rates establishes SGG as a robust choice for LLM optimization.

cs.LG↗

arXiv2025

Towards Unified Neural Decoding with Brain Functional Network Modeling

Recent achievements in implantable brain-computer interfaces (iBCIs) have demonstrated the potential to decode cognitive and motor behaviors with intracranial brain recordings; however, individual physiological and electrode implantation heterogeneities have constrained current approaches to neural decoding within single individuals, rendering interindividual neural decoding elusive. Here, we present Multi-individual Brain Region-Aggregated Network (MIBRAIN), a neural decoding framework that constructs a whole functional brain network model by integrating intracranial neurophysiological recordings across multiple individuals. MIBRAIN leverages self-supervised learning to derive generalized neural prototypes and supports group-level analysis of brain-region interactions and inter-subject neural synchrony. To validate our framework, we recorded stereoelectroencephalography (sEEG) signals from a cohort of individuals performing Mandarin syllable articulation. Both real-time online and offline decoding experiments demonstrated significant improvements in both audible and silent articulation decoding, enhanced decoding accuracy with increased multi-subject data integration, and effective generalization to unseen subjects. Furthermore, neural predictions for regions without direct electrode coverage were validated against authentic neural data. Overall, this framework paves the way for robust neural decoding across individuals and offers insights for practical clinical applications.

q-bio.NC↗