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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Zhu, Wen Chen, Yiwen Nie, Shanling Yang, Hai East China University of Science and Technology Department of Computer Science and Engineering Shanghai China Shanghai Key Laboratory of Computer Software Evaluating and Testing Shanghai China National University of Singapore Center for Continuing and Lifelong Education Singapore The University of Sydney Faculty of Engineering Australia

ISBN: (纸本)9798350337488

Cancer survival prediction is pivotal in tailoring individualized treatment strategies and guiding clinician decision-making. Yet, existing methodologies grapple with efficiently harnessing the intricate distribution of medical data spanning various modalities. In response, we present SAMMS, an advanced multi-omics multimodal deep learning framework tailored for survival prediction. SAMMS leverages the robust image segmentation model, "Segment Anything"to adeptly characterize pathological images. This prowess is further enhanced by integrating multi-omics data and clinical insights, facilitating holistic modeling across a diverse modal spectrum. The framework weaves a modality-specific subnetwork with a cross-modality common subnetwork, meticulously capturing intra-modality nuances and inter-modality correlations. SAMMS eclipsed its contemporaries by delivering remarkable performance on TCGA's LGG and KIRC tumor datasets. A battery of analyses underscored SAMMS's unparalleled capability to distill multifaceted insights from multimodal datasets, yielding richer and more integrative multimodal representations. Such strides promise significant advancements in cancer survival analytics, bolstering the precision and efficacy of patient-centric treatments, disease oversight, and clinical decision processes. © 2023 IEEE.

关键词： Multi-omics Data Pathological Images Segment Anything Survival Analysis

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Joint Clustering and Analyze Single Cell Multi-omics Data by scMOGAN

Joint Clustering and Analyze Single Cell Multi-omics Data by...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： An, Congcong Chen, Yiwen Nie, Shanling Yang, Hai East China University of Science and Technology Department of Computer Science and Engineering Shanghai China Shanghai Key Laboratory of Computer Software Evaluating and Testing Shanghai China National University of Singapore Center for Continuing and Lifelong Education Singapore The University of Sydney Faculty of Engineering Australia

ISBN: (纸本)9798350337488

Advancements in single-cell multi-omics sequencing technologies have dramatically transformed the analysis of cellular states at single-cell resolution. Cluster analyses leveraging single-cell transcriptome and epigenome data have enabled the characterization of cellular states and the delineation of transcriptomic regulatory programs associated with cellular heterogeneity. However, the high dimensionality, sparsity, and heterogeneity inherent to multi-omics data present significant challenges to their clustering analysis. In this study, we introduced single-cell Multi-Omics Generative Adversarial Networks (scMOGAN), an unsupervised clustering model specifically tailored for single-cell transcriptome and epigenome data. scMOGAN accomplishes this by efficaciously modeling the omics data and mining potential features through neural networks, ultimately utilizing Gaussian mixture models for cell type identification. To validate and scrutinize the performance of scMOGAN, we performed analyses on two actual multi-omics datasets and one simulated dataset. The results demonstrate that scMOGAN surpasses other existing methods in terms of clustering performance, underscoring its efficacy in navigating the complexities of multi-omics data. © 2023 IEEE.

关键词： clustering generative adversarial networks single cell multi-omics data unsupervised learning

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PMMVar: Leveraging Multi-level Protein Structures for Enhanced Coding Variant Pathogenicity Prediction

PMMVar: Leveraging Multi-level Protein Structures for Enhanc...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Chen, Yijia Chen, Yiwen Nie, Shanling Yang, Hai East China University of Science and Technology Department of Computer Science and Engineering Shanghai China Shanghai Key Laboratory of Computer Software Evaluating and Testing Shanghai China National University of Singapore Center for Continuing and Lifelong Education Singapore The University of Sydney Faculty of Engineering Australia

ISBN: (纸本)9798350337488

Genomic variants, which can disrupt cellular functions, present a challenge in distinguishing deleterious from benign instances. While assessing genome-wide functional impacts, many current algorithms neglect protein tertiary structure of coding region variants due to limitations in protein structural prediction. This study introduces PMMVar, an advanced multimodal deep convolutional network, which adeptly integrates protein tertiary structures with conservation properties from ESM-2, supplemented by other protein structural sequences. PMMVar achieves outstanding performance on the latest clinical variant datasets, NCBI ClinVar (2023), and the Mendelian variant dataset, surpassing existing benchmarks. Ablation analyses validate the significance of protein multi-level structures in enhancing the model's accuracy. Overall, our findings spotlight the essential role of multi-level protein structures in pathogenicity predictions and their potential to discern deleterious genomic variants effectively. © 2023 IEEE.

关键词： deep learning multimodal pathogenicity protein structure variant

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Topology entropy: Enhancing graph partitioning for TAD identification and single-cell clustering

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Computational and Structural Biotechnology Journal 2025年 27卷 1864-1886页

作者： Liang, Qiushi Zhao, Shengjie Chen, Lingxi Li, Shuai Cheng School of Computer Science and Technology Tongji University Shanghai201804 China Department of Computer Science City University of Hong Kong 999077 Hong Kong Department of Biomedical Sciences City University of Hong Kong 999077 Hong Kong Engineering Research Center of Key Software Technologies for Smart City Perception and Planning Ministry of Education China

Entropy quantifies the limits of information compression and provides a theoretical foundation for exploring complex structures in large-scale graphs. However, effective metrics are needed to capture the intricate structural details in biological graphs. In this paper, we introduce the topology entropy encoding tree to quantify the complexity of biological graphs and show that minimizing the associated entropy is equivalent to optimal graph partitioning. We develop two methods, TEC-O and TEC-U, for partitioning ordered and unordered biological graphs. TEC-O is applied to identify Topologically Associated Domains (TADs) in Hi-C contact maps, while TEC-U is used for cell clustering in single-cell sequencing data. Results from simulated datasets demonstrate that topology entropy is robust to noise and effectively captures structural information, outperforming existing methods. Experiments on Hi-C data from five cell lines and ten single-cell sequencing datasets show that TEC-O and TEC-U achieve the highest accuracy in TAD detection and cell clustering, respectively, providing biologically meaningful insights. © 2025 The Authors

关键词： Cell culture

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Honeytoken-Detector: A Symbolic Execution-Based Honeypot Token Detection Tool

Honeytoken-Detector: A Symbolic Execution-Based Honeypot Tok...

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software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD-Winter), ACIS International Winter Conference on

作者： Yi Liu Lizhi Cai School of Information Science and Engineering East China University of Science and Technology Shanghai China Shanghai Key Laboratory of Computer Testing & Evaluating Shanghai Development Center of Computer Software Technology Shanghai China

ISBN: (数字)9798350345865

ISBN: (纸本)9798350345872

Smart contracts have emerged as one of the most successful applications in the blockchain domain, playing a significant role in various blockchain ecosystems. Inspired by smart contracts, a multitude of cryptographic assets have been created. To standardize these assets, industry standards such as ERC20 (Ethereum Request for Comments 20), ERC721, and ERC1155 have been proposed. In recent years, smart contracts have frequently fallen victim to attacks. Honeypot contracts, disguised as ERC20-compliant tokens, are widely prevalent on the blockchain, enticing victims to make purchases. Such malicious smart contracts exhibiting deceptive behavior are collectively referred to as honeypot tokens. This paper focuses on ERC20-compliant smart contracts and defines six common types of honeypot issues. Building upon advancements in smart contract vulnerability detection, we propose an enhanced symbolic execution-based detection tool called Honeytoken-Detector. We conduct experiments on both contracts known to have similar issues and actual token contracts from the real world. The experimental results demonstrate the effectiveness of our tool in identifying vulnerabilities.

关键词： Industries Source coding Smart contracts Ecosystems Buildings Blockchains Behavioral sciences

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Object Oriented BDD and Executable Human-Language Module Specification

Object Oriented BDD and Executable Human-Language Module Spe...

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software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD-Winter), ACIS International Winter Conference on

作者： Eric Lee Jiayu Gong Qinghong Cao SE Cloud (Shanghai) Intelligent Technology Co. Ltd. Shanghai China Shanghai Key Laboratory of Computer Software Testing & Evaluation Shanghai Development Center of Computer Software Technology Shanghai China System Operation Department Shanghai Stock Exchange Shanghai China

This paper presents an approach to software development which uses a generative AI Model as compiler to translate human language requirements into high-level programming language. We propose an executable human-language module specification and a tool to support it, which has been used successfully for human-language UI test automation. We anticipate further development of this approach to enable complex software to be programmed in human language, allowing for more intuitive and efficient software development.

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AgileShard: Turning the Sharded Blockchain into a Real-Time Transaction Processing System 44

AgileShard: Turning the Sharded Blockchain into a Real-Time ...

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44th IEEE Real-Time Systems Symposium, RTSS 2023

作者： Shi, Jianfeng Wu, Heng Liu, Wang Gao, Heran Zhang, Wenbo University of Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Nanjing China Software Engineering Technology Research and Development Center Institute of Software Chinese Academy of Sciences Beijing China Nanjing Institute of Software Technology Nanjing China Institute of Software Chinese Academy of Sciences State Key Laboratory of Computer Science Beijing China

ISBN: (纸本)9798350328578

Blockchain, as an emerging transaction processing system, suffers from low throughput and high latency. Sharded blockchains can significantly increase throughput by dividing nodes into groups (i.e., shards) to process disjoint transactions in parallel. However, the diverse latency requirements of transactions in current sharded blockchains are not well met. Three challenges prevent the sharded blockchain from becoming a real-time transaction processing system, namely, the static block size, the first-come-first-served transaction packing strategy, and the load imbalance. Therefore, this paper proposes 3 methods to help turn the sharded blockchain into a real-time transaction processing system. First, we propose an inter-shard dynamic block size negotiation method that enables shards to adaptively determine the globally optimal block size based on the deadlines of pending transactions. Then, we propose a DAG-based transaction packing method for reducing the number of deadline violations and improving parallelism. Finally, we propose a minimum-cost-flow-based shard reconfiguration method to address load imbalance. Under real datasets on Ethereum, experimental results show that AgileShard using the above three methods can effectively improve the transaction deadline satisfaction rate. © 2023 IEEE.

关键词： Blockchain

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Dual Path Transformer with Partition Attention

arXiv

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arXiv 2023年

作者： Jiang, Zhengkai Liu, Liang Zhang, Jiangning Wang, Yabiao Chen, Mingang Wang, Chengjie Tencent Youtu Lab China Shanghai Development Center of Computer Software Technolog China

This paper introduces a novel attention mechanism, called dual attention, which is both efficient and effective. The dual attention mechanism consists of two parallel components: local attention generated by Convolutional Neural Networks (CNNs) and long-range attention generated by Vision Transformers (ViTs). To address the high computational complexity and memory footprint of vanilla Multi-Head Self-Attention (MHSA), we introduce a novel Multi-Head Partition-wise Attention (MHPA) mechanism. The partition-wise attention approach models both intra-partition and inter-partition attention simultaneously. Building on the dual attention block and partition-wise attention mechanism, we present a hierarchical vision backbone called DualFormer. We evaluate the effectiveness of our model on several computer vision tasks, including image classification on ImageNet, object detection on COCO, and semantic segmentation on Cityscapes. Specifically, the proposed DualFormer-XS achieves 81.5% top-1 accuracy on ImageNet, outperforming the recent state-of-the-art MPViT-XS by 0.6% top-1 accuracy with much higher throughput. Copyright © 2023, The Authors. All rights reserved.

关键词： Object detection

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LoSS: Local Structural Separation Hypergraph Convolutional Neural Network 26

LoSS: Local Structural Separation Hypergraph Convolutional N...

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26th European Conference on Artificial Intelligence, ECAI 2023

作者： Hu, Bingde Gao, Yang Feng, Zunlei Song, Mingli Wang, Xinyu Li, Ying College of Computer Science and Technology Zhejiang University China College of Software Technology Zhejiang University China ZJU-Bangsun Joint Research Center China Shanghai Institute for Advanced Study Zhejiang University China Bangsun Technology

ISBN: (纸本)9781643684369

Graph classification is a classic problem with practical applications in many real-life scenes. Existing graph neural networks, including GCN, GAT, and GIN, are proposed to extract useful features from complex graph structures. However, most existing methods' feature extraction and aggregation inevitably mix the useful and redundant features, which will disturb the final classification performance. In this paper, to handle the above drawback, we put forward the Local Structural Separation Hypergraph Convolutional Neural Network (LoSS) based on two discoveries: most graph classification tasks only focus on a few groups of adjacent nodes, and different categories have their specific high response bits in graph embeddings. In LoSS, we first decouple the original graph into different hypergraphs and aggregate the features in each substructure, which aims to find useful features for the final classification. Next, the low-correlation feature suppression strategy is devised to suppress the irrelevant node-level and bit-level features in the forward inference process, effectively reducing the disturbance of redundant features. Experiments on five datasets show that the proposed LoSS can effectively locate and aggregate useful hypergraph features and achieve SOTA performance compared with existing methods. © 2023 The Authors.

关键词： Aggregates

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A Multi-Agent Spatial Logic for Scenario-Based Decision Modeling and Verification in Platoon Systems

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Journal of computer Science & technology 2021年第6期36卷 1231-1247页

作者： Jingwen Xu Yanhong Huang Jianqi Shi Shengchao Qin National Trusted Embedded Software Engineering Technology Research Center East China Normal University Shanghai 200062China College of Computer Science and Software Engineering Shenzhen UniversityShenzhen 518061China

To cater for the scenario of coordinated transportation of multiple trucks on the highway,a platoon system for autonomous driving has been extensively explored in the *** such a platoon is deployed,it is necessary to ensure the safety of its driving behavior,whereby each vehicle’s behavior is commanded by the decision-making function whose decision is based on the observed driving ***,there is currently a lack of verification methods to ensure the reliability of the scenario-based decision-making process in the platoon *** this paper,we focus on the platoon driving scenario,whereby the platoon is composed of intelligent heavy trucks driving on cross-sea *** propose a formal modeling and verification approach to provide safety assurance for platoon vehicles’cooperative driving *** existing Multi-Lane Spatial Logic(MLSL)with a dedicated abstract model can express driving scene spatial properties and prove the safety of multi-lane traffic maneuvers under the single-vehicle *** cater for the platoon system’s multi-vehicle perspective,we modify the existing abstract model and propose a Multi-Agent Spatial Logic(MASL)that extends MLSL by relative orientation and multi-agent *** then utilize a timed automata type supporting MASL formulas to model vehicles’decision controllers for platoon *** the behavior of a human-driven vehicle(HDV)joining the platoon as a case study,we have implemented the model and verified safety properties on the UPPAAL tool to illustrate the viability of our framework.

关键词： autonomous driving decision-making model platoon system safety verification timed automaton

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