arXiv subjects

Siyuan Li

Publications and source records attributed to Siyuan Li.

At least 145 records · Page 8Linked to original sources

arXiv2024

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov Chain Monte Carlo methods face slow convergence and computational burdens. Existing Variational Inference methods, which require pre-generated topologies and typically treat tree structures and branch lengths independently, may overlook critical sequence features, limiting their accuracy and flexibility. We propose PhyloGen, a novel method leveraging a pre-trained genomic language model to generate and optimize phylogenetic trees without dependence on evolutionary models or aligned sequence constraints. PhyloGen views phylogenetic inference as a conditionally constrained tree structure generation problem, jointly optimizing tree topology and branch lengths through three core modules: (i) Feature Extraction, (ii) PhyloTree Construction, and (iii) PhyloTree Structure Modeling. Meanwhile, we introduce a Scoring Function to guide the model towards a more stable gradient descent. We demonstrate the effectiveness and robustness of PhyloGen on eight real-world benchmark datasets. Visualization results confirm PhyloGen provides deeper insights into phylogenetic relationships.

q-bio.PE↗

arXiv2024

$2^{++}$ Di-gluonium from LSR at higher order

We improve the determination of the mass and coupling of the $2^{++}$ tensor di-gluonium by using relativistic QCD Laplace sum rules (LSR). In so doing, we evaluate the next-to-leading order (NLO) corrections to the perturbative (PT) and $\langle α_s G^2 \rangle$ condensate and the lowest order (LO) $\langle G^3 \rangle$ contributions to the $2^{++}$ di-gluonium two-point correlator. Within a vacuum saturation estimate ($k_G=1$) of the dimension-eight gluon condensates, we obtain: $M_{T}=3028(287)\mbox{MeV}$ and the renormalization group invariant (RGI) coupling $\hat{f}_T=224(33)\mbox{MeV}$. Assuming that the factorization hypothesis can be violated, we study the effect of the violation factor $k_G$ on the results and obtain: $M_T=3188(337)\mbox{MeV}$ and $\hat{f}_T=245(32)\mbox{MeV}$ for $k_G=(3\pm 2)$. Our estimation does not favour the interpretation of the observed $f_2(2010)$, $f_2(2300)$ and $f_2(2340)$ as pure glueball state.

hep-ph↗

arXiv2024

Artificial Intelligence for Central Dogma-Centric Multi-Omics: Challenges and Breakthroughs

With the rapid development of high-throughput sequencing platforms, an increasing number of omics technologies, such as genomics, metabolomics, and transcriptomics, are being applied to disease genetics research. However, biological data often exhibit high dimensionality and significant noise, making it challenging to effectively distinguish disease subtypes using a single-omics approach. To address these challenges and better capture the interactions among DNA, RNA, and proteins described by the central dogma, numerous studies have leveraged artificial intelligence to develop multi-omics models for disease research. These AI-driven models have improved the accuracy of disease prediction and facilitated the identification of genetic loci associated with diseases, thus advancing precision medicine. This paper reviews the mathematical definitions of multi-omics, strategies for integrating multi-omics data, applications of artificial intelligence and deep learning in multi-omics, the establishment of foundational models, and breakthroughs in multi-omics technologies, drawing insights from over 130 related articles. It aims to provide practical guidance for computational biologists to better understand and effectively utilize AI-based multi-omics machine learning algorithms in the context of central dogma.

q-bio.GN↗

arXiv2024

SimVPv2: Towards Simple yet Powerful Spatiotemporal Predictive Learning

Recent years have witnessed remarkable advances in spatiotemporal predictive learning, with methods incorporating auxiliary inputs, complex neural architectures, and sophisticated training strategies. While SimVP has introduced a simpler, CNN-based baseline for this task, it still relies on heavy Unet-like architectures for spatial and temporal modeling, which still suffers from high complexity and computational overhead. In this paper, we propose SimVPv2, a streamlined model that eliminates the need for Unet architectures and demonstrates that plain stacks of convolutional layers, enhanced with an efficient Gated Spatiotemporal Attention mechanism, can deliver state-of-the-art performance. SimVPv2 not only simplifies the model architecture but also improves both performance and computational efficiency. On the standard Moving MNIST benchmark, SimVPv2 achieves superior performance compared to SimVP, with fewer FLOPs, about half the training time, and 60% faster inference efficiency. Extensive experiments across eight diverse datasets, including real-world tasks such as traffic forecasting and climate prediction, further demonstrate that SimVPv2 offers a powerful yet straightforward solution, achieving robust generalization across various spatiotemporal learning scenarios. We believe the proposed SimVPv2 can serve as a solid baseline to benefit the spatiotemporal predictive learning community.

cs.LG↗

arXiv2024

TransferFuzz: Fuzzing with Historical Trace for Verifying Propagated Vulnerability Code

Code reuse in software development frequently facilitates the spread of vulnerabilities, making the scope of affected software in CVE reports imprecise. Traditional methods primarily focus on identifying reused vulnerability code within target software, yet they cannot verify if these vulnerabilities can be triggered in new software contexts. This limitation often results in false positives. In this paper, we introduce TransferFuzz, a novel vulnerability verification framework, to verify whether vulnerabilities propagated through code reuse can be triggered in new software. Innovatively, we collected runtime information during the execution or fuzzing of the basic binary (the vulnerable binary detailed in CVE reports). This process allowed us to extract historical traces, which proved instrumental in guiding the fuzzing process for the target binary (the new binary that reused the vulnerable function). TransferFuzz introduces a unique Key Bytes Guided Mutation strategy and a Nested Simulated Annealing algorithm, which transfers these historical traces to implement trace-guided fuzzing on the target binary, facilitating the accurate and efficient verification of the propagated vulnerability. Our evaluation, conducted on widely recognized datasets, shows that TransferFuzz can quickly validate vulnerabilities previously unverifiable with existing techniques. Its verification speed is 2.5 to 26.2 times faster than existing methods. Moreover, TransferFuzz has proven its effectiveness by expanding the impacted software scope for 15 vulnerabilities listed in CVE reports, increasing the number of affected binaries from 15 to 53. The datasets and source code used in this article are available at https://github.com/Siyuan-Li201/TransferFuzz.

cs.SE↗

arXiv2024

BinEnhance: An Enhancement Framework Based on External Environment Semantics for Binary Code Search

Binary code search plays a crucial role in applications like software reuse detection. Currently, existing models are typically based on either internal code semantics or a combination of function call graphs (CG) and internal code semantics. However, these models have limitations. Internal code semantic models only consider the semantics within the function, ignoring the inter-function semantics, making it difficult to handle situations such as function inlining. The combination of CG and internal code semantics is insufficient for addressing complex real-world scenarios. To address these limitations, we propose BinEnhance, a novel framework designed to leverage the inter-function semantics to enhance the expression of internal code semantics for binary code search. Specifically, BinEnhance constructs an External Environment Semantic Graph (EESG), which establishes a stable and analogous external environment for homologous functions by using different inter-function semantic relations (e.g., call, location, data-co-use). After the construction of EESG, we utilize the embeddings generated by existing internal code semantic models to initialize nodes of EESG. Finally, we design a Semantic Enhancement Model (SEM) that uses Relational Graph Convolutional Networks (RGCNs) and a residual block to learn valuable external semantics on the EESG for generating the enhanced semantics embedding. In addition, BinEnhance utilizes data feature similarity to refine the cosine similarity of semantic embeddings. We conduct experiments under six different tasks (e.g., under function inlining scenario) and the results illustrate the performance and robustness of BinEnhance. The application of BinEnhance to HermesSim, Asm2vec, TREX, Gemini, and Asteria on two public datasets results in an improvement of Mean Average Precision (MAP) from 53.6% to 69.7%. Moreover, the efficiency increases fourfold.

cs.SE↗

arXiv2024

Event USKT : U-State Space Model in Knowledge Transfer for Event Cameras

Event cameras, as an emerging imaging technology, offer distinct advantages over traditional RGB cameras, including reduced energy consumption and higher frame rates. However, the limited quantity of available event data presents a significant challenge, hindering their broader development. To alleviate this issue, we introduce a tailored U-shaped State Space Model Knowledge Transfer (USKT) framework for Event-to-RGB knowledge transfer. This framework generates inputs compatible with RGB frames, enabling event data to effectively reuse pre-trained RGB models and achieve competitive performance with minimal parameter tuning. Within the USKT architecture, we also propose a bidirectional reverse state space model. Unlike conventional bidirectional scanning mechanisms, the proposed Bidirectional Reverse State Space Model (BiR-SSM) leverages a shared weight strategy, which facilitates efficient modeling while conserving computational resources. In terms of effectiveness, integrating USKT with ResNet50 as the backbone improves model performance by 0.95%, 3.57%, and 2.9% on DVS128 Gesture, N-Caltech101, and CIFAR-10-DVS datasets, respectively, underscoring USKT's adaptability and effectiveness. The code will be made available upon acceptance.

cs.CV↗

arXiv2024

SkillTree: Explainable Skill-Based Deep Reinforcement Learning for Long-Horizon Control Tasks

Deep reinforcement learning (DRL) has achieved remarkable success in various research domains. However, its reliance on neural networks results in a lack of transparency, which limits its practical applications. To achieve explainability, decision trees have emerged as a popular and promising alternative to neural networks. Nonetheless, due to their limited expressiveness, traditional decision trees struggle with high-dimensional long-horizon continuous control tasks. In this paper, we proposes SkillTree, a novel framework that reduces complex continuous action spaces into discrete skill spaces. Our hierarchical approach integrates a differentiable decision tree within the high-level policy to generate skill embeddings, which subsequently guide the low-level policy in executing skills. By making skill decisions explainable, we achieve skill-level explainability, enhancing the understanding of the decision-making process in complex tasks. Experimental results demonstrate that our method achieves performance comparable to skill-based neural networks in complex robotic arm control domains. Furthermore, SkillTree offers explanations at the skill level, thereby increasing the transparency of the decision-making process.

cs.LG↗

arXiv2024

From Words to Structured Visuals: A Benchmark and Framework for Text-to-Diagram Generation and Editing

We introduce the task of text-to-diagram generation, which focuses on creating structured visual representations directly from textual descriptions. Existing approaches in text-to-image and text-to-code generation lack the logical organization and flexibility needed to produce accurate, editable diagrams, often resulting in outputs that are either unstructured or difficult to modify. To address this gap, we introduce DiagramGenBenchmark, a comprehensive evaluation framework encompassing eight distinct diagram categories, including flowcharts, model architecture diagrams, and mind maps. Additionally, we present DiagramAgent, an innovative framework with four core modules-Plan Agent, Code Agent, Check Agent, and Diagram-to-Code Agent-designed to facilitate both the generation and refinement of complex diagrams. Our extensive experiments, which combine objective metrics with human evaluations, demonstrate that DiagramAgent significantly outperforms existing baseline models in terms of accuracy, structural coherence, and modifiability. This work not only establishes a foundational benchmark for the text-to-diagram generation task but also introduces a powerful toolset to advance research and applications in this emerging area.

cs.DB↗

arXiv2024

Safe Planner: Empowering Safety Awareness in Large Pre-Trained Models for Robot Task Planning

Robot task planning is an important problem for autonomous robots in long-horizon challenging tasks. As large pre-trained models have demonstrated superior planning ability, recent research investigates utilizing large models to achieve autonomous planning for robots in diverse tasks. However, since the large models are pre-trained with Internet data and lack the knowledge of real task scenes, large models as planners may make unsafe decisions that hurt the robots and the surrounding environments. To solve this challenge, we propose a novel Safe Planner framework, which empowers safety awareness in large pre-trained models to accomplish safe and executable planning. In this framework, we develop a safety prediction module to guide the high-level large model planner, and this safety module trained in a simulator can be effectively transferred to real-world tasks. The proposed Safe Planner framework is evaluated on both simulated environments and real robots. The experiment results demonstrate that Safe Planner not only achieves state-of-the-art task success rates, but also substantially improves safety during task execution. The experiment videos are shown in https://sites.google.com/view/safeplanner .

cs.RO↗

arXiv2024

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction

Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their specific types is therefore essential for elucidating protein function and understanding disease mechanisms. Existing computational approaches predominantly focus on protein sequences to predict PTM sites, driven by the recognition of sequence-dependent motifs. However, these approaches often overlook protein structural contexts. In this work, we first compile a large-scale sequence-structure PTM dataset, which serves as the foundation for fair comparison. We introduce the MeToken model, which tokenizes the micro-environment of each amino acid, integrating both sequence and structural information into unified discrete tokens. This model not only captures the typical sequence motifs associated with PTMs but also leverages the spatial arrangements dictated by protein tertiary structures, thus providing a holistic view of the factors influencing PTM sites. Designed to address the long-tail distribution of PTM types, MeToken employs uniform sub-codebooks that ensure even the rarest PTMs are adequately represented and distinguished. We validate the effectiveness and generalizability of MeToken across multiple datasets, demonstrating its superior performance in accurately identifying PTM types. The results underscore the importance of incorporating structural data and highlight MeToken's potential in facilitating accurate and comprehensive PTM predictions, which could significantly impact proteomics research. The code and datasets are available at https://github.com/A4Bio/MeToken.

cs.LG↗

arXiv2024

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative heterogeneous graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements various cutting-edge methods. Secondly, a single task on \textit{de novo} molecule generation can hardly reflect their capabilities. To broaden the scope, we have adapted these models to a range of tasks essential in drug design, which are considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of \textit{de novo} molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide the pre-trained versions of the state-of-the-art models and deep insights with analysis from empirical studies. The codebase for CBGBench is publicly accessible at \url{https://github.com/Edapinenut/CBGBench}.

cs.LG↗

arXiv2024

Unveiling the Backbone-Optimizer Coupling Bias in Visual Representation Learning

This paper delves into the interplay between vision backbones and optimizers, unvealing an inter-dependent phenomenon termed \textit{\textbf{b}ackbone-\textbf{o}ptimizer \textbf{c}oupling \textbf{b}ias} (BOCB). We observe that canonical CNNs, such as VGG and ResNet, exhibit a marked co-dependency with SGD families, while recent architectures like ViTs and ConvNeXt share a tight coupling with the adaptive learning rate ones. We further show that BOCB can be introduced by both optimizers and certain backbone designs and may significantly impact the pre-training and downstream fine-tuning of vision models. Through in-depth empirical analysis, we summarize takeaways on recommended optimizers and insights into robust vision backbone architectures. We hope this work can inspire the community to question long-held assumptions on backbones and optimizers, stimulate further explorations, and thereby contribute to more robust vision systems. The source code and models are publicly available at https://bocb-ai.github.io/.

cs.CV↗

arXiv2024

OpenMixup: Open Mixup Toolbox and Benchmark for Visual Representation Learning

Mixup augmentation has emerged as a widely used technique for improving the generalization ability of deep neural networks (DNNs). However, the lack of standardized implementations and benchmarks has impeded recent progress, resulting in poor reproducibility, unfair comparisons, and conflicting insights. In this paper, we introduce OpenMixup, the first mixup augmentation codebase, and benchmark for visual representation learning. Specifically, we train 18 representative mixup baselines from scratch and rigorously evaluate them across 11 image datasets of varying scales and granularity, ranging from fine-grained scenarios to complex non-iconic scenes. We also open-source our modular codebase, including a collection of popular vision backbones, optimization strategies, and analysis toolkits, which not only supports the benchmarking but enables broader mixup applications beyond classification, such as self-supervised learning and regression tasks. Through experiments and empirical analysis, we gain observations and insights on mixup performance-efficiency trade-offs, generalization, and optimization behaviors, and thereby identify preferred choices for different needs. To the best of our knowledge, OpenMixup has facilitated several recent studies. We believe this work can further advance reproducible mixup augmentation research and thereby lay a solid ground for future progress in the community. The source code and user documents are available at \url{https://github.com/Westlake-AI/openmixup}.

cs.CV↗

arXiv2024

Switch EMA: A Free Lunch for Better Flatness and Sharpness

Exponential Moving Average (EMA) is a widely used weight averaging (WA) regularization to learn flat optima for better generalizations without extra cost in deep neural network (DNN) optimization. Despite achieving better flatness, existing WA methods might fall into worse final performances or require extra test-time computations. This work unveils the full potential of EMA with a single line of modification, i.e., switching the EMA parameters to the original model after each epoch, dubbed as Switch EMA (SEMA). From both theoretical and empirical aspects, we demonstrate that SEMA can help DNNs to reach generalization optima that better trade-off between flatness and sharpness. To verify the effectiveness of SEMA, we conduct comparison experiments with discriminative, generative, and regression tasks on vision and language datasets, including image classification, self-supervised learning, object detection and segmentation, image generation, video prediction, attribute regression, and language modeling. Comprehensive results with popular optimizers and networks show that SEMA is a free lunch for DNN training by improving performances and boosting convergence speeds.

cs.LG↗

arXiv2024

Samba: Synchronized Set-of-Sequences Modeling for Multiple Object Tracking

Multiple object tracking in complex scenarios - such as coordinated dance performances, team sports, or dynamic animal groups - presents unique challenges. In these settings, objects frequently move in coordinated patterns, occlude each other, and exhibit long-term dependencies in their trajectories. However, it remains a key open research question on how to model long-range dependencies within tracklets, interdependencies among tracklets, and the associated temporal occlusions. To this end, we introduce Samba, a novel linear-time set-of-sequences model designed to jointly process multiple tracklets by synchronizing the multiple selective state-spaces used to model each tracklet. Samba autoregressively predicts the future track query for each sequence while maintaining synchronized long-term memory representations across tracklets. By integrating Samba into a tracking-by-propagation framework, we propose SambaMOTR, the first tracker effectively addressing the aforementioned issues, including long-range dependencies, tracklet interdependencies, and temporal occlusions. Additionally, we introduce an effective technique for dealing with uncertain observations (MaskObs) and an efficient training recipe to scale SambaMOTR to longer sequences. By modeling long-range dependencies and interactions among tracked objects, SambaMOTR implicitly learns to track objects accurately through occlusions without any hand-crafted heuristics. Our approach significantly surpasses prior state-of-the-art on the DanceTrack, BFT, and SportsMOT datasets.

cs.CV↗

arXiv2024

Walker: Self-supervised Multiple Object Tracking by Walking on Temporal Appearance Graphs

The supervision of state-of-the-art multiple object tracking (MOT) methods requires enormous annotation efforts to provide bounding boxes for all frames of all videos, and instance IDs to associate them through time. To this end, we introduce Walker, the first self-supervised tracker that learns from videos with sparse bounding box annotations, and no tracking labels. First, we design a quasi-dense temporal object appearance graph, and propose a novel multi-positive contrastive objective to optimize random walks on the graph and learn instance similarities. Then, we introduce an algorithm to enforce mutually-exclusive connective properties across instances in the graph, optimizing the learned topology for MOT. At inference time, we propose to associate detected instances to tracklets based on the max-likelihood transition state under motion-constrained bi-directional walks. Walker is the first self-supervised tracker to achieve competitive performance on MOT17, DanceTrack, and BDD100K. Remarkably, our proposal outperforms the previous self-supervised trackers even when drastically reducing the annotation requirements by up to 400x.

cs.CV↗

arXiv2024

SLAck: Semantic, Location, and Appearance Aware Open-Vocabulary Tracking

Open-vocabulary Multiple Object Tracking (MOT) aims to generalize trackers to novel categories not in the training set. Currently, the best-performing methods are mainly based on pure appearance matching. Due to the complexity of motion patterns in the large-vocabulary scenarios and unstable classification of the novel objects, the motion and semantics cues are either ignored or applied based on heuristics in the final matching steps by existing methods. In this paper, we present a unified framework SLAck that jointly considers semantics, location, and appearance priors in the early steps of association and learns how to integrate all valuable information through a lightweight spatial and temporal object graph. Our method eliminates complex post-processing heuristics for fusing different cues and boosts the association performance significantly for large-scale open-vocabulary tracking. Without bells and whistles, we outperform previous state-of-the-art methods for novel classes tracking on the open-vocabulary MOT and TAO TETA benchmarks. Our code is available at \href{https://github.com/siyuanliii/SLAck}{github.com/siyuanliii/SLAck}.

cs.CV↗