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A Re-Parametrization-Based Bayesian Differential Analysis Algorithm for Gene Regulatory Networks Modeled with Structural Equation Models

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Computer Modeling in engineering & Sciences 2020年第7期124卷 303-313页

作者： Yan Li Dayou Liu Yungang Zhu Jie Liu College of Computer Science and Technology Jilin UniversityChangchun130012China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin UniversityChangchun130012China

Under different conditions,gene regulatory networks(GRNs)of the same gene set could be similar but *** differential analysis of GRNs under different conditions is important for understanding condition-specific gene regulatory *** a naive approach,existing GRN inference algorithms can be used to separately estimate two GRNs under different conditions and identify the differences between ***,in this way,the similarities between the pairwise GRNs are not taken into *** joint differential analysis algorithms have been proposed recently,which were proved to outperform the naive approach *** this paper,we model the GRNs under different conditions with structural equation models(SEMs)to integrate gene expression data and genetic perturbations,and re-parameterize the pairwise SEMs to form an integrated model that incorporates the differential ***,a Bayesian inference method is used to make joint differential analysis by solving the integrated *** evaluated the performance of the proposed re-parametrization-based Bayesian differential analysis(ReBDA)algorithm by running simulations on synthetic data with different *** performance of the ReBDA algorithm was demonstrated better than another state-of-the-art joint differential analysis algorithm for SEMs ReDNet *** the end,the ReBDA algorithm was applied to make differential analysis on a real human lung gene data set to illustrate its applicability and practicability.

关键词： Gene regulatory networks structural equation models joint

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Todo: Task Offloading Decision Optimizer for the Efficient Provision of Offloading Schemes

SSRN

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SSRN 2023年

作者： Chen, Shilin Wang, Xingwang Sun, Yafeng College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China College of Computer Science and Technology Jilin University Changchun130012 China

As the volume of data stored on local devices increases, users turn to edge devices to help with processing tasks. Developing offloading schemes is challenging due to the varying configurations of edge devices and user preferences. While traditional methods provide schemes for offloading in various scenarios, they face unavoidable challenges, including the requirement to manage device workloads in real-time, significant computational costs, and the difficulty of balancing multi-objectives in offloading schemes. To solve these problems, we propose the Task Offloading Decision Optimizer, which offers efficient multi-objective offloading schemes considering real-time device workload and user preference. The proposed offloading scheme contains three goals: reducing task execution time, decreasing device energy consumption, and lowering rental costs. It comprises two important parts: Scheme Maker and Scheme Assistor. Scheme Maker utilizes deep reinforcement learning, optimizes the internal architecture, and enhances the performance of the operation. It optimizes buffer storage to generate dependable multi-objective offloading schemes considering real-time environmental conditions. Scheme Assistor utilizes the data in the Scheme Maker buffer to enhance efficiency by reducing computational costs. Extensive experiments have proved that the proposed framework efficiently provides offloading schemes considering the real-time conditions of the devices and the users, and it offers offloading schemes that enhance task completion rate by 50%. Compared to the baseline, the task execution time is reduced by 12.1%, and the device energy consumption is reduced by 11.4%. © 2023, The Authors. All rights reserved.

关键词： Reinforcement learning

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Closed Loop Networks for Open-Set Semi-Supervised Learning

SSRN

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SSRN 2023年

作者： Ouyang, Jihong Meng, Qingyi Li, Ximing Zhang, Zhengjie Li, Changchun Wang, Wenting College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University China Department of Computer Science University of Texas Dallas United States

Open-Set Semi-Supervised Learning (OS-SSL) refers to the task of learning classifiers with labeled and unlabeled instances, but the unlabeled data may contain the instances associated with unseen labels, dubbed as Out-Of-Distribution (OOD) instances. The main idea of OS-SSL is to detect and filter out the OOD instances to avoid the negative effects for classifier training. The current methods treat the detection of OOD instances and the classification of seen labels as two specific tasks, and achieve OS-SSL by using a shared backbone with two task-specific heads. However, we found that such way may result in a conflict problem between the two specific heads by observing the gradients of the shared backbone parameters. To solve this problem, we develop a novel OS-SSL method, namely Closed LOop NEtworks (CLONE), which employs two respective networks to detect OOD instances and classify seen labels, but makes a feedback loop between them. We can train CLONE in an end-to-end manner efficiently. We empirically compare CLONE with the existing OS-SSL methods on several benchmark datasets. The experimental results indicate that CLONE can outperform existing baseline methods in most settings. © 2023, The Authors. All rights reserved.

关键词： Cloning

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Task-Oriented Multi-Modal Mutual Learning for Vision-Language Models

Task-Oriented Multi-Modal Mutual Learning for Vision-Languag...

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International Conference on Computer Vision (ICCV)

作者： Sifan Long Zhen Zhao Junkun Yuan Zichang Tan Jiangjiang Liu Luping Zhou Shengsheng Wang Jingdong Wang College of Computer Science and Technology Jilin University Jilin China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin China Baidu VIS University of Sydney Zhejiang University

Prompt learning has become one of the most efficient paradigms for adapting large pre-trained vision-language models to downstream tasks. Current state-of-the-art methods, like CoOp and ProDA, tend to adopt soft prompts to learn an appropriate prompt for each specific task. Recent CoCoOp further boosts the base-to-new generalization performance via an image-conditional prompt. However, it directly fuses identical image semantics to prompts of different labels and significantly weakens the discrimination among different classes as shown in our experiments. Motivated by this observation, we first propose a class-aware text prompt (CTP) to enrich generated prompts with label-related image information. Unlike CoCoOp, CTP can effectively involve image semantics and avoid introducing extra ambiguities into different prompts. On the other hand, instead of reserving the complete image representations, we propose text-guided feature tuning (TFT) to make the image branch attend to class-related representation. A contrastive loss is employed to align such augmented text and image representations on downstream tasks. In this way, the image-to-text CTP and text-to-image TFT can be mutually promoted to enhance the adaptation of VLMs for downstream tasks. Extensive experiments demonstrate that our method outperforms the existing methods by a significant margin. Especially, compared to CoCoOp, we achieve an average improvement of 4.03% on new classes and 3.19% on harmonic-mean over eleven classification benchmarks.

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Learning with Partial Labels from Semi-supervised Perspective

arXiv

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arXiv 2022年

作者： Li, Ximing Jiang, Yuanzhi Li, Changchun Wang, Yiyuan Ouyang, Jihong College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of MOE Jilin University China College of Information Science and Technology Northeast Normal University China Key Laboratory of Applied Statistics of MOE Northeast Normal University China

Partial Label (PL) learning refers to the task of learning from the partially labeled data, where each training instance is ambiguously equipped with a set of candidate labels but only one is valid. Advances in the recent deep PL learning literature have shown that the deep learning paradigms, e.g., self-training, contrastive learning, or class activate values, can achieve promising performance. Inspired by the impressive success of deep Semi-Supervised (SS) learning, we transform the PL learning problem into the SS learning problem, and propose a novel PL learning method, namely Partial Label learning with Semi-supervised Perspective (PLSP). Specifically, we first form the pseudo-labeled dataset by selecting a small number of reliable pseudo-labeled instances with high-confidence prediction scores and treating the remaining instances as pseudo-unlabeled ones. Then we design a SS learning objective, consisting of a supervised loss for pseudo-labeled instances and a semantic consistency regularization for pseudo-unlabeled instances. We further introduce a complementary regularization for those non-candidate labels to constrain the model predictions on them to be as small as possible. Empirical results demonstrate that PLSP significantly outperforms the existing PL baseline methods, especially on high ambiguity levels. Code available: https://***/changchunli/PLSP. Copyright © 2022, The Authors. All rights reserved.

关键词： Deep learning

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IoT Device Identification via A Bio-Inspired Feature Selection Approach

IoT Device Identification via A Bio-Inspired Feature Selecti...

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IEEE International Conference on Communications (ICC)

作者： Boxiong Wang Hui Kang Geng Sun Jiahui Li College of Software Jilin University Changchun China College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China

The rapid development of the Internet-of-Things (IoT) also brings security and other problems. Device identification is a crucial tool for IoT security issues, which can detect and prevent cyber-attacks. Feature selection is an effective data preprocessing technique in IoT device identification, which can improve the performance of classification and reduce computational complexity. In this paper, we propose a novel wrapper feature selection approach based on the improved binary honey badger algorithm (IBHBA) to select features in IoT traffic. Four improved factors are employed in IBHBA to expand the search scope, balance the exploration and exploitation phases, and enhance the search capability. Moreover, a binary mechanism is adopted to make the algorithm more suitable for feature selection in IoT device identification. The experimental results on several real IoT traffic datasets denote that IBHBA outperforms some classical and latest comparison algorithms in the feature selection of IoT device identification.

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Energy Efficient UAV-assisted Communications via Collaborative Beamforming

Energy Efficient UAV-assisted Communications via Collaborati...

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IEEE International Symposium on Personal, Indoor and Mobile Radio Communications (PIMRC)

作者： Tingting Zheng Yanheng Liu Geng Sun Mushu Li Conghao Zhou Xuemin Sherman Shen College of Computer Science and Technology Jilin University Changchun China Department of Electrical and Computer Engineering University of Waterloo Waterloo ON Canada Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China

In this paper, we propose collaborative beamforming (CB) in unmanned aerial vehicle (UAV)-assisted communication networks to improve transmission data rate with minimum energy consumption. Specifically, CB allows a group of UAVs forming a virtual element antenna array (VEAA) and transmitting data collaboratively in a synchronous manner through a high-gain mainlobe (ML) beam. The goal is to optimize the deployment locations of UAVs in the VEAA and excitation current weights for performing CB transmissions considering the energy cost for UAV deployment. Accordingly, we formulate an Energy-Efficient Communication Multi-objective Optimization Problem (EECMOP) to jointly maximize the transmission rate and minimize the maximum sidelobe level (SLL) as well as UAV energy consumption. Then, we propose an Enhanced Multi Objective Ant Lion Optimizer (EMOALO) algorithm which incorporates a chaos theory to develop chaotic initialization and adjustable mode operators for solving the problem. Simulation results demonstrate the effectiveness of the EMOALO algorithm in improving energy efficiency for UAV-assisted communication networks.

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Semi-supervised multi-label learning with balanced binary angular margin loss 24

Semi-supervised multi-label learning with balanced binary an...

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Proceedings of the 38th International Conference on Neural Information Processing Systems

作者： Ximing Li Silong Liang Changchun Li Pengfei Wang Fangming Gu College of Computer Science and Technology Jilin University China and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China Computer Network Information Center Chinese Academy of Sciences China and University of Chinese Academy of Sciences Chinese Academy of Sciences China

ISBN: (纸本)9798331314385

Semi-supervised multi-label learning (SSMLL) refers to inducing classifiers using a small number of samples with multiple labels and many unlabeled samples. The prevalent solution of SSMLL involves forming pseudo-labels for unlabeled samples and inducing classifiers using both labeled and pseudo-labeled samples in a self-training manner. Unfortunately, with the commonly used binary type of loss and negative sampling, we have empirically found that learning with labeled and pseudo-labeled samples can result in the variance bias problem between the feature distributions of positive and negative samples for each label. To alleviate this problem, we aim to balance the variance bias between positive and negative samples from the perspective of the feature angle distribution for each label. Specifically, we extend the traditional binary angular margin loss to a balanced extension with feature angle distribution transformations under the Gaussian assumption, where the distributions are iteratively updated during classifier training. We also suggest an efficient prototype-based negative sampling method to maintain high-quality negative samples for each label. With this insight, we propose a novel SSMLL method, namely Semi-Supervised Multi-Label Learning with Balanced Binary Angular Margin loss (S2ML2-BBAM). To evaluate the effectiveness of S2ML2-BBAM, we compare it with existing competitors on benchmark datasets. The experimental results validate that S2ML2-BBAM can achieve very competitive performance.

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Sfmfold: A Multi-Modal Contrast Learning Model for Rna Secondary Structure Prediction

SSRN

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SSRN 2025年

作者： Li, Ang Liu, Yuanning Zhang, Zhaoyang Li, Shuwang Dong, Hao Lv, Meng 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 Software Jilin University Changchun130012 China College of Information Engineering Chang’an University Xi’an710064 China

The secondary structure of RNA can regulate the interaction between RNA and protein and perform various biological tasks through specific folding shapes, which plays an important role in revealing biomolecular mechanisms and developing new vaccines and therapeutic drugs. However, existing RNA secondary structure prediction methods based on thermodynamics and traditional neural network models usually lack the ability to model long-distance dependencies of RNA molecules and cannot handle complex non-nested structures in RNA molecules. In this paper, we propose a multi-modal contrastive learning method SFMFold based on state space model, which captures long-distance interactions in RNA sequences through RNA sequence representation learning part, and models the structure of RNA molecules through RNA structure representation learning part. Finally, the features of the two modalities are aligned and deeply fused to obtain the final RNA molecule prediction map. We test SFMFold on several datasets, and the experiments show that our proposed model shows excellent performance in cross-family prediction and long sequence prediction tasks. In addition, SFMFold can also effectively predict non-nested structures such as pseudoknot with better accuracy than the SOTA methods. © 2025, The Authors. All rights reserved.

关键词： Prediction models

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Why Misinformation is Created? Detecting them by Integrating Intent Features

arXiv

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arXiv 2024年

作者： Wang, Bing Fu, Bo Li, Ximing Pei, Songwen Li, Changchun Wang, Shengsheng College of Computer Science and Technology Jilin University Changchun Jilin China Liaoning Normal University Liaoning Dalian China University of Shanghai for Science and Technology Shanghai China Key Laboratory of Symbolic Computation and Knowledge Engineering The Ministry of Education Jilin University China

Various social media platforms, e.g., Twitter and Reddit, allow people to disseminate a plethora of information more efficiently and conveniently. However, they are inevitably full of misinformation, causing damage to diverse aspects of our daily lives. To reduce the negative impact, timely identification of misinformation, namely Misinformation Detection (MD), has become an active research topic receiving widespread attention. As a complex phenomenon, the veracity of an article is influenced by various aspects. In this paper, we are inspired by the opposition of intents between misinformation and real information. Accordingly, we propose to reason the intent of articles and form the corresponding intent features to promote the veracity discrimination of article features. To achieve this, we build a hierarchy of a set of intents for both misinformation and real information by referring to the existing psychological theories, and we apply it to reason the intent of articles by progressively generating binary answers with an encoder-decoder structure. We form the corresponding intent features and integrate it with the token features to achieve more discriminative article features for MD. Upon these ideas, we suggest a novel MD method, namely Detecting Misinformation by Integrating Intent featuRes (Dm-inter). To evaluate the performance of Dm-inter, we conduct extensive experiments on benchmark MD datasets. The experimental results validate that Dm-inter can outperform the existing baseline MD methods. Copyright © 2024, The Authors. All rights reserved.

关键词： Data mining

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