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An AutoEncoder-Based Matrix Factorization Approach to Estimating Cell Proportion from Bulk Tumor RNA-seq Data

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An AutoEncoder-Based Matrix Factorization Approach to Estima...

2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

作者： Xu, Yingze Wang, Yan Xie, Xuping Wang, Feilong Chen, Qiong Sun, Huiyan Jilin University College of Computer Science and Technology Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Changchun China Jilin University School of Artificial Intelligence Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Changchun China

ISBN: (纸本)9781665401265

The deconvolution of infiltrating immune cells and stromal cells from complex tumor tissues is significant for studying the impact of these cells on tumor development, as well as assisting cancer therapies. Integrating cell-specific marker genes from several references, we put forward an AutoEncoder-based matrix factorization method to estimate the cell proportion in heterogeneous samples. The proportion predicted by our method achieved over 0.95 Pearson correlation coefficient (PCC) with the ground truth. Moreover, through analyzing association between cell proportion of tumor tissues and clinical information of the tumor patients, we found that the proportion of cancer-associated fibroblast (CAF) gradually increased with the progress of tumor, and the proportion of B cell in tissues was significantly related to the five-year survival rate of tumor patients. © 2021 IEEE.

关键词： RNA

Optimizing Human Pose Estimation Through Focused Human and Joint Regions

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arXiv 2025年

作者： Jiao, Yingying Wang, Zhigang Liu, Zhenguang Fan, Shaojing Wu, Sifan Wu, Zheqi Xu, Zhuoyue College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China College of Computer Science and Technology Zhejiang Gongshang University China The State Key Laboratory of Blockchain and Data Security Zhejiang University China Institute of Blockchain and Data Security China School of Computing National University of Singapore Singapore

Human pose estimation has given rise to a broad spectrum of novel and compelling applications, including action recognition, sports analysis, as well as surveillance. However, accurate video pose estimation remains an open challenge. One aspect that has been overlooked so far is that existing methods learn motion clues from all pixels rather than focusing on the target human body, making them easily misled and disrupted by unimportant information such as background changes or movements of other people. Additionally, while the current Transformer-based pose estimation methods has demonstrated impressive performance with global modeling, they struggle with local context perception and precise positional identification. In this paper, we try to tackle these challenges from three aspects: (1) We propose a bilayer Human-keypoint Mask module that performs coarse-to-fine visual token refinement, which gradually zooms in on the target human body and keypoints while masking out unimportant figure regions. (2) We further introduce a novel deformable cross attention mechanism and a bidirectional separation strategy to adaptively aggregate spatial and temporal motion clues from constrained surrounding contexts. (3) We mathematically formulate the deformable cross attention, constraining that the model focuses solely on the regions centered at the target person body. Empirically, our method achieves state-of-the-art performance on three large-scale benchmark datasets. A remarkable highlight is that our method achieves an 84.8 mean Average Precision (mAP) on the challenging wrist joint, which significantly outperforms the 81.5 mAP achieved by the current state-of-the-art method on the PoseTrack2017 dataset. Copyright © 2025, The Authors. All rights reserved.

关键词： Benchmarking

A Lightweight Api Recommendation Method for App Development Based on Multi-Objective Evolutionary Algorithm

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SSRN

SSRN 2022年

作者： Li, Xun Liu, Lei Liu, Yuzhou Liu, Huaxiao College of Computer Science and Technology Jilin University Jilin130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Changchun Jilin University Jilin130012 China

Context: API is important in daily programming activities during app development, but finding appropriate APIs is time-consuming for developers. To simplify this process, many researchers pay attention to overcoming the task-API knowledge gap using semantic information mined from the large-scale dataset for API recommendation. However, only semantic information is not enough since API descriptions and developer's query may not share similar words, meanwhile, large-scale data mining brings huge time cost and causes knowledge fixed problem (i.e. data cannot be timely updated). This limits the efficiency of existing API commendation methods. Objective: In this work, we aim at proposing a lightweight API recommendation method for app development based on the data in app store. Method: We model API recommendation as a multi-objective optimization problem by considering both structural and semantic information of API, and use the genetic algorithm to gain optimal solutions for overcoming limitations of the small-scale dataset. Specially, we collect APK files of related apps and API descriptions to establish a lightweight dataset, and extract the structural and semantic information of API from them with graph embedding and NLP techniques respectively. Then, we get the recommended APIs satisfying structural and semantic objectives according to the developers’ target functionality with a genetic algorithm. Finally, we give the interpretation of our recommendation information to help developers understand the results easily. Results and Conclusion: We conduct a series of experiments based on apps in Google Play and Q&As in Stack Overflow. The results show that Precision@N of our recommendation can be up to 0.89, MAP@N is up to 0.50, and MRR reaches 0.69, and our method achieves such good performance only utilizing less than 1/19 of the project number of our compared machine learning method. Besides, we conduct a survey and most of the participants confirm the understandabilit

关键词： Multiobjective optimization

PNESR-DDI: An Effective Drug-Drug Interaction Prediction Model Based on Pretraining Method and Enhanced Subgraph Reconstruction

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PNESR-DDI: An Effective Drug-Drug Interaction Prediction Mod...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Ke Chen Xiaosong Han Xiaoran Li Yanchun Liang Dong Xu Renchu Guan Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Software Jilin University Changchun China Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Jilin University Changchun China Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education School of Computer Science Zhuhai College of Science and Technology Zhuhai China Department of Electrical Engineering and Computer Science Christopher S. Bond Life Sciences Center University of Missouri Columbia USA

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Drug-Drug Interaction (DDI) task plays a crucial role in clinical treatment and drug development. Recently, deep learning methods have been successfully applied for DDI prediction. However, training deep learning models always need large amount of data, while known DDIs are scarce. To address this challenge, a graph neural network-based DDI prediction model named PNESR-DDI is proposed, which compensates for the lack of DDIs by enriching drug representations. First, to obtain initial node representations that incorporate rich semantic information from the biomedical knowledge graph (KG), a link prediction pre-training method on external KG is proposed in the node embedding pre-training module. Then, considering the large scale of the KG, subgraph extraction for the target drug pairs is introduced to reduce noise and decrease computational complexity in the subgraph anchoring module. After that, the subgraph is updated, and node similarities are propagated in the subgraph reconstruction module. Based on the node similarity scores, the subgraph is pruned and reconstructed, which adjusts node representations to be more conducive to DDI prediction. Finally, the drug embeddings, subgraph representations, and drug fingerprint features are concatenated to predict DDIs. PNESRDDI is evaluated on two benchmark DDI datasets: DrugBank and TWOSIDES. Experiment results show that PNESR-DDI achieves better performance than baselines. Ablation results validate the effectiveness of the pre-training method and the adaptive subgraph reconstruction strategy.

关键词： Drugs Deep learning Adaptation models Visualization Biological system modeling Noise knowledge graphs Predictive models Fingerprint recognition Transformers

Hybrid Parameter Update: Alleviating Imbalance Impacts for Distributed Deep Learning

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Hybrid Parameter Update: Alleviating Imbalance Impacts for D...

IEEE International Conference on High Performance Computing and Communications (HPCC)

作者： Hongliang Li Dong Xu Zhewen Xu Xiang Li College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education Changchun China

Nowadays, data parallelism has been widely applied to train large datasets on distributed deep learning clusters, but it has suffered from costly global parameter updates at batch barriers. Performance imbalance among worker instances, introduced by uneven workload partitioning or biased resource allocation, can cause straggly workers, which can lead to severe impacts on both training speed and result accuracy. This paper studies the issue focusing on the tradeoff between training speed and result accuracy. We propose Cooperate Grouping Parallel (CGP), a hybrid parameter update solution that allows the flexibility of both synchronous and asynchronous update schemes. We introduce a novel Cooperate Worker Grouping Problem (CWGP) that seeks a task grouping configuration that leads to maximum model accuracy and holds customized training speed guarantees. We propose an evolution-based Pareto local searching algorithm to compute efficient worker grouping configurations. Comprehensive evaluation results are presented to demonstrate the effectiveness of CGP under both persistent and fluctuant imbalances. The proposed method alleviates the imbalance impacts without introducing extra adjustment over-heads.

关键词： Training Deep learning computational modeling Focusing Distributed databases Parallel processing Resource management

Convergence-Aware Optimal Checkpointing for Exploratory Deep Learning Training Jobs

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SSRN

SSRN 2024年

作者： Li, Hongliang Wang, Zichen Zhao, Hairui Zhang, Meng Li, Xiang Xu, Haixiao College of Computer Science and Technology Jilin University Qianjin street 2699 Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering The Ministry of Education Qianjin street 2699 Jilin Changchun130012 China High Performance Computing Center Qianjin street 2699 Jilin Changchun130012 China

Training Deep Learning (DL) models are becoming more time-consuming, thus interruptions to the training processes are inevitable. Existing fault-tolerant work adopted checkpoint/recovery mechanism from traditional HPC platforms that makes periodical persistent copies of model states to save execution progress. These checkpoints have fixed time intervals that they are evenly placed across the training. We can obtain an optimal checkpointing interval for an HPC job with the precondition that the progress of a job is proportional to its execution time. Unfortunately, it is not the case in DL model training where a DL training job yields diminishing returns across its lifetime. It makes the early progress of a DL training job more valuable than the later ones. Even placement of checkpoints would either increase the risks in the early stages or waste resources overprotecting the latter stages. Meanwhile, the issue can get amplified for exploratory training jobs, where early terminations are common. Moreover, in data parallelism, the state-of-art quality-driven scheduling strategies allocate more resources for the early stages of a job than the later ones to accelerate the training progress which further amplifies the issue. This paper introduces a novel checkpointing interval problem for exploratory DL training jobs based on model convergence progress. We present COCI, an approach to compute optimal checkpointing configuration for a DL training job, minimizing the fault-tolerant overhead, including checkpointing cost and recovery cost. We implement COCI based on state-of-art iteration-level checkpointing mechanism, as a pluggable module compatible with PyTorch. COCI requires no extra user input. We conduct comprehensive evaluations with real DL application setups. The experimental results show that COCI reduces up to 40.18% fault-tolerant overhead compared to existing state-of-the-art DL fault-tolerant methods in serial scenario, 57.26% in data parallel scenario and 63.8

关键词： Iterative methods

UAV-assisted Joint Mobile Edge Computing and Data Collection via Matching-enabled Deep Reinforcement Learning

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arXiv 2025年

作者： Wang, Boxiong Kang, Hui Li, Jiahui Sun, Geng Sun, Zemin Wang, Jiacheng Niyato, Dusit College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China College of Computing and Data Science Nanyang Technological University 639798 Singapore College of Computing and Data Science Nanyang Technological University Singapore

Unmanned aerial vehicle (UAV)-assisted mobile edge computing (MEC) and data collection (DC) have been popular research issues. Different from existing works that consider MEC and DC scenarios separately, this paper investigates a multi-UAV-assisted joint MEC-DC system. Specifically, we formulate a joint optimization problem to minimize the MEC latency and maximize the collected data volume. This problem can be classified as a non-convex mixed integer programming problem that exhibits long-term optimization and dynamics. Thus, we propose a deep reinforcement learning-based approach that jointly optimizes the UAV movement, user transmit power, and user association in real time to solve the problem efficiently. Specifically, we reformulate the optimization problem into an action space-reduced Markov decision process (MDP) and optimize the user association by using a two-phase matching-based association (TMA) strategy. Subsequently, we propose a soft actor-critic (SAC)-based approach that integrates the proposed TMA strategy (SAC-TMA) to solve the formulated joint optimization problem collaboratively. Simulation results demonstrate that the proposed SAC-TMA is able to coordinate the two subsystems and can effectively reduce the system latency and improve the data collection volume compared with other benchmark algorithms. Copyright © 2025, The Authors. All rights reserved.

关键词： Unmanned aerial vehicles (UAV)

SpatioTemporal Learning for Human Pose Estimation in Sparsely-Labeled Videos

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arXiv 2025年

作者： Jiao, Yingying Wang, Zhigang Wu, Sifan Fan, Shaojing Liu, Zhenguang Xu, Zhuoyue Wu, Zheqi College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China College of Computer Science and Technology Zhejiang Gongshang University China School of Computing National University of Singapore Singapore The State Key Laboratory of Blockchain and Data Security Zhejiang University China Institute of Blockchain and Data Security China

Human pose estimation in videos remains a challenge, largely due to the reliance on extensive manual annotation of large datasets, which is expensive and labor-intensive. Furthermore, existing approaches often struggle to capture long-range temporal dependencies and overlook the complementary relationship between temporal pose heatmaps and visual features. To address these limitations, we introduce STDPose, a novel framework that enhances human pose estimation by learning spatiotemporal dynamics in sparsely-labeled videos. STDPose incorporates two key innovations: 1) A novel Dynamic-Aware Mask to capture long-range motion context, allowing for a nuanced understanding of pose changes. 2) A system for encoding and aggregating spatiotemporal representations and motion dynamics to effectively model spatiotemporal relationships, improving the accuracy and robustness of pose estimation. STDPose establishes a new performance benchmark for both video pose propagation (i.e., propagating pose annotations from labeled frames to unlabeled frames) and pose estimation tasks, across three large-scale evaluation datasets. Additionally, utilizing pseudo-labels generated by pose propagation, STDPose achieves competitive performance with only 26.7% labeled data. Copyright © 2025, The Authors. All rights reserved.

关键词： Large datasets

ON A NOVEL UCP RESULT AND ITS APPLICATION TO INVERSE CONDUCTIVE SCATTERING

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arXiv 2024年

作者： Diao, Huaian Fei, Xiaoxu Liu, Hongyu School of Mathematics Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130012 China School of Mathematics and Statistics Central South University Changsha410083 China Department of Mathematics City University of Hong Kong Kowloon Hong Kong

In this paper, we derive a novel Unique Continuation Principle (UCP) for a system of second-order elliptic PDEs and apply it to investigate inverse problems in conductive scattering. The UCP relaxes the typical assumptions imposed on the domain or boundary with certain interior transmission conditions. This is motivated by the study of the associated inverse scattering problem and enables us to establish several novel unique identifiability results for the determination of generalized conductive scatterers using a single far-field pattern, significantly extending the results in [15, 21]. A key technical advancement in our work is the combination of Complex Geometric Optics (CGO) techniques from [15, 21] with the Fourier expansion method to microlocally analyze corner singularities and their implications for inverse problems. We believe that the methods developed can have broader applications in other contexts. © 2024, CC BY.

关键词： Inverse problems