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DeepHBSP:A Deep Learning Framework for Predicting Human Blood-Secretory Proteins Using Transfer Learning

Journal of Computer Science & Technology 2021年第2期36卷 234-247页

作者： Wei Du Yu Sun Hui-Min Bao Liang Chen Ying Li Yan-Chun Liang Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and TechnologyJilin UniversityChangchun 130012China Department of Computer Science College of EngineeringShantou UniversityShantou 515063China Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Zhuhai College of Jilin University Zhuhai 519041China

The identification of blood-secretory proteins and the detection of protein biomarkers in the blood have an important clinical application *** methods for predicting blood-secretory proteins are mainly based on traditional machine learning algorithms,and heavily rely on annotated protein *** traditional machine learning algorithms,deep learning algorithms can automatically learn better feature representations from raw data,and are expected to be more promising to predict blood-secretory *** present a novel deep learning model(DeepHBSP)combined with transfer learning by integrating a binary classification network and a ranking network to identify blood-secretory proteins from the amino acid sequence information *** loss function of DeepHBSP in the training step is designed to apply descriptive loss and compactness loss to the binary classification network and the ranking network,*** feature extraction subnetwork of DeepHBSP is composed of a multi-lane capsule ***,transfer learning is used to train a highly accurate generalized model with small samples of blood-secretory *** main contributions of this study are as follows:1)a novel deep learning architecture by integrating a binary classification network and a ranking network is proposed,superior to existing traditional machine learning algorithms and other state-of-the-art deep learning architectures for biological sequence analysis;2)the proposed model for blood-secretory protein prediction uses only amino acid sequences,overcoming the heavy dependence of existing methods on annotated protein features;3)the blood-secretory proteins predicted by our model are statistically significant compared with existing blood-based biomarkers of cancer.

关键词： blood-secretory protein deep learning capsule network transfer learning

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Secure and Energy-efficient Unmanned Aerial Vehicle-enabled Visible Light Communication via A Multi-objective Optimization Approach

arXiv

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arXiv 2024年

作者： Liu, Lingling Wang, Aimin Wu, Jing Lu, Jiao Li, Jiahui Sun, Geng College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130012 China

In this research, a unique approach to provide communication service for terrestrial receivers via using unmanned aerial vehicle-enabled visible light communication is investigated. Specifically, we take into account a unmanned aerial vehicle-enabled visible light communication scenario with multiplex transmitters, multiplex receivers, and a single eavesdropper, each of which is equipped with a single photodetector. Then, a unmanned aerial vehicle deployment multi-objective optimization problem is formulated to simultaneously make the optical power received by receiving surface more uniform, minimize the amount of information collected by a eavesdropper, and minimize the energy consumption of unmanned aerial vehicles, while the locations and transmission power of unmanned aerial vehicles are simultaneously optimized under certain constraints. Since the formulated unmanned aerial vehicle deployment multiobjective optimization problem is complex and nonlinear, it is challenging to be tackled by using conventional methods. For the purpose of solving the problem, a multi-objective evolutionary algorithm based on decomposition with chaos initiation and crossover mutation is proposed. Simulation outcomes show that the proposed approach is superior to other approaches, and is efficient at improving the security and energy efficiency of visible light communication system. Copyright © 2024, The Authors. All rights reserved.

关键词： Multiobjective optimization

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arXiv

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arXiv 2025年

作者： Li, Yangning Kang, Hui Li, Jiahui Sun, Geng Sun, Zemin Wang, Jiacheng Zhao, Changyuan Niyato, Dusit 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 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

An expansion of Internet of Things (IoTs) has led to significant challenges in wireless data harvesting, dissemination, and energy management due to the massive volumes of data generated by IoT devices. These challenges are exacerbated by data redundancy arising from spatial and temporal correlations. To address these issues, this paper proposes a novel data-driven collaborative beamforming (CB)-based communication framework for IoT networks. Specifically, the framework integrates CB with an overlap-based multi-hop routing protocol (OMRP) to enhance data transmission efficiency while mitigating energy consumption and addressing hot spot issues in remotely deployed IoT networks. Based on the data aggregation to a specific node by OMRP, we formulate a node selection problem for the CB stage, with the objective of optimizing uplink transmission energy consumption. Given the complexity of the problem, we introduce a softmax-based proximal policy optimization with long-short-term memory (SoftPPO-LSTM) algorithm to intelligently select CB nodes for improving transmission efficiency. Simulation results show that the proposed OMRP improves network lifetime by 17% compared to benchmark routing protocols, while the SoftPPO-LSTM method for CB node selection achieves an 8.3% increase in throughput over benchmark algorithms. The results also reveal that the combined OMRP with the SoftPPO- Copyright © 2025, The Authors. All rights reserved.

关键词： Deep reinforcement learning

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Learning generalizable agents via saliency-guided features decorrelation 23

Learning generalizable agents via saliency-guided features d...

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Proceedings of the 37th International Conference on Neural Information Processing Systems

作者： Sili Huang Yanchao Sun Jifeng Hu Siyuan Guo Hechang Chen Yi Chang Lichao Sun Bo Yang Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education and School of Artificial Intelligence Jilin University China Department of Computer Science University of Maryland College Park School of Artificial Intelligence Jilin University China Lehigh University Bethlehem Pennsylvania Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education

In visual-based Reinforcement Learning (RL), agents often struggle to generalize well to environmental variations in the state space that were not observed during training. The variations can arise in both task-irrelevant features, such as background noise, and task-relevant features, such as robot configurations, that are related to the optimal decisions. To achieve generalization in both situations, agents are required to accurately understand the impact of changed features on the decisions, i.e., establishing the true associations between changed features and decisions in the policy model. However, due to the inherent correlations among features in the state space, the associations between features and decisions become entangled, making it difficult for the policy to distinguish them. To this end, we propose Saliency-Guided Features Decorrelation (SGFD) to eliminate these correlations through sample reweighting. Concretely, SGFD consists of two core techniques: Random Fourier Functions (RFF) and the saliency map. RFF is utilized to estimate the complex non-linear correlations in high-dimensional images, while the saliency map is designed to identify the changed features. Under the guidance of the saliency map, SGFD employs sample reweighting to minimize the estimated correlations related to changed features, thereby achieving decorrelation in visual RL tasks. Our experimental results demonstrate that SGFD can generalize well on a wide range of test environments and significantly outperforms state-of-the-art methods in handling both task-irrelevant variations and task-relevant variations.

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BA-LORA: BIAS-ALLEVIATING LOW-RANK ADAPTATION TO MITIGATE CATASTROPHIC INHERITANCE IN LARGE LANGUAGE MODELS

arXiv

引用

arXiv 2024年

作者： Chang, Yupeng Chang, Yi Wu, Yuan School of Artificial Intelligence Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University China International Center of Future Science Jilin University China

Large language models (LLMs) have demonstrated remarkable proficiency across various natural language processing (NLP) tasks. However, adapting LLMs to downstream applications requires computationally intensive and memory-demanding fine-tuning procedures. To alleviate these burdens, parameter-efficient fine-tuning (PEFT) techniques have emerged as a promising approach to tailor LLMs with minimal computational overhead. While PEFT methods offer substantial advantages, they do not fully address the pervasive issue of bias propagation from pre-training data. This work introduces Bias-Alleviating Low-Rank Adaptation (BA-LoRA), a novel PEFT method designed to counteract bias inheritance. BA-LoRA incorporates three distinct regularization terms: (1) a consistency regularizer, (2) a diversity regularizer, and (3) a singular value decomposition regularizer. These regularizers aim to enhance the models’ consistency, diversity, and generalization capabilities during fine-tuning. We conduct extensive experiments on natural language understanding (NLU) and natural language generation (NLG) tasks using prominent LLMs such as LLaMA, Mistral, and Gemma. The results demonstrate that BA-LoRA outperforms LoRA and its state-of-the-art variants. Moreover, the extended experiments demonstrate that our method effectively mitigates the adverse effects of pre-training bias, leading to more reliable and robust model outputs. The code is available at https://***/cyp-jlu-ai/BA-LoRA. Copyright © 2024, The Authors. All rights reserved.

关键词： Natural language processing systems

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Large Language Model Evaluation via Matrix Nuclear-Norm

arXiv

引用

arXiv 2024年

作者： Li, Yahan Xia, Tingyu Chang, Yi Wu, Yuan School of Artificial Intelligence Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University China International Center of Future Science Jilin University China

As large language models (LLMs) continue to evolve, efficient evaluation metrics are vital for assessing their ability to compress information and reduce redundancy. While traditional metrics like Matrix Entropy offer valuable insights, they are computationally intensive for large-scale models due to their O(n3) time complexity with Singular Value Decomposition (SVD). To mitigate this issue, we introduce the Matrix Nuclear-Norm, which not only serves as a metric to quantify the data compression proficiency of LLM but also provides a convex approximation of matrix rank to capture both predictive discriminability and diversity. By employing the L1,2-norm to further approximate the nuclear norm, we can effectively assess the model’s information compression capabilities. This approach reduces the time complexity to O(n2) and eliminates the need for SVD computation. Consequently, the Matrix Nuclear-Norm achieves speeds 8 to 24 times faster than Matrix Entropy for the CEREBRAS-GPT model as sizes increase from 111M to 6.7B. This performance gap becomes more pronounced with larger models, as validated in tests with other models like Pythia. Additionally, evaluations on benchmarks and model responses confirm that our proposed Matrix Nuclear-Norm is a reliable, scalable, and efficient tool for assessing LLMs’ performance, striking a balance between accuracy and computational efficiency. The code is available at https://***/MLGroupJLU/MatrixNuclearNorm. Copyright © 2024, The Authors. All rights reserved.

关键词： Singular value decomposition

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From Incomplete Coarse-Grained to Complete Fine-Grained: A Two-Stage Framework for Spatiotemporal Data Reconstruction

arXiv

引用

arXiv 2024年

作者： Sun, Ziyu Su, Haoyang Wang, En Yang, Funing Yang, Yongjian Liu, Wenbin The College of Computer Science and Technology Jilin University Changchun130012 China The Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China

With the rapid development of various sensing devices, spatiotemporal data is becoming increasingly important nowadays. However, due to sensing costs and privacy concerns, the collected data is often incomplete and coarse-grained, limiting its application to specific tasks. To address this, we propose a new task called spatiotemporal data reconstruction, which aims to infer complete and fine-grained data from sparse and coarse-grained observations. To achieve this, we introduce a two-stage data inference framework, DiffRecon, grounded in the Denoising Diffusion Probabilistic Model (DDPM). In the first stage, we present Diffusion-C, a diffusion model augmented by ST-PointFormer, a powerful encoder designed to leverage the spatial correlations between sparse data points. Following this, the second stage introduces Diffusion-F, which incorporates the proposed T-PatternNet to capture the temporal pattern within sequential data. Together, these two stages form an end-to-end framework capable of inferring complete, fine-grained data from incomplete and coarse-grained observations. We conducted experiments on multiple real-world datasets to demonstrate the superiority of our method. © 2024, CC BY.

关键词： Spatio-temporal data

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Reusable Generator Data-Free knowledge Distillation with Hard Loss Simulation for Image Classification

SSRN

引用

SSRN 2024年

作者： Sun, Yafeng Wang, Xingwang Huang, Junhong Chen, Shilin Hou, Minghui 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

In many image classification scenarios where knowledge distillation (KD) is applied, multiple users need to train various student models that conform to the device's computational limitations at different times. However, due to security concerns, existing data-free KD (DFKD) methods discard the trained generator after completing a task, preventing its reuse in training subsequent students and resulting in wasted resources. Furthermore, the unlabeled nature of fake images eliminates the hard loss that plays a crucial role in data-driven KD. This paper introduces the reusable generator DFKD with hard loss simulation (RG-HLS) to address these challenges. RG-HLS employs a generator consisting of two generative networks and a decoder. The decoder and one of the generative networks can be reused in subsequent tasks. The adversarial example attack is also introduced to mimic the behavior of the teacher model in predicting real images, ensuring that DFKD exhibits a hard loss similar to that of data-driven KD. Extensive experiments across CIFAR-10, CIFAR-100, and Tiny-ImageNet datasets validate the proposed method's superior performance. The reusable generator accelerates convergence without compromising security, and integrating the hard loss further boosts accuracy. Code is available at https://***/sunyafeng-jlu/RG-HLS. © 2024, The Authors. All rights reserved.

关键词： Image classification

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AWEQ: Post-Training Quantization with Activation-Weight Equalization for Large Language Models

arXiv

引用

arXiv 2023年

作者： Li, Baisong Wang, Xingwang Xu, Haixiao School of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University China

Large language models(LLMs) excellent performance across a variety of tasks, but they come with significant computational and storage costs. Quantizing these models is an effective way to alleviate this issue. However, existing methods struggle to strike a balance between model accuracy and hardware efficiency. This is where we introduce AWEQ, a post-training method that requires no additional training overhead. AWEQ excels in both ultra-low-bit quantization and 8-bit weight and activation (W8A8) quantization. There is an observation that weight quantization is less challenging than activation quantization. AWEQ transfers the difficulty of activation quantization to weights using channel equalization, achieving a balance between the quantization difficulties of both, and thereby maximizing performance. We have further refined the equalization method to mitigate quantization bias error, ensuring the robustness of the model. Extensive experiments on popular models such as LLaMA and OPT demonstrate that AWEQ outperforms all existing post-training quantization methods for large models. Copyright © 2023, The Authors. All rights reserved.

关键词： Chemical activation

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Toward Time-Continuous Data Inference in Sparse Urban CrowdSensing

arXiv

引用

arXiv 2024年

作者： Sun, Ziyu Su, Haoyang Sun, Hanqi Wang, En Liu, Wenbin The College of Computer Science and Technology Jilin University Changchun130012 China The Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China

Mobile Crowd Sensing (MCS) is a promising paradigm that leverages mobile users and their smart portable devices to perform various real-world tasks. However, due to budget constraints and the inaccessibility of certain areas, Sparse MCS has emerged as a more practical alternative, collecting data from a limited number of target subareas and utilizing inference algorithms to complete the full sensing map. While existing approaches typically assume a time-discrete setting with data remaining constant within each sensing cycle, this simplification can introduce significant errors, especially when dealing with long cycles, as real-world sensing data often changes continuously. In this paper, we go from fine-grained completion, i.e., the subdivision of sensing cycles into minimal time units, towards a more accurate, time-continuous completion. We first introduce Deep Matrix Factorization (DMF) as a neural network-enabled framework and enhance it with a Recurrent Neural Network (RNN-DMF) to capture temporal correlations in these finer time slices. To further deal with the continuous data, we propose TIME-DMF, which captures temporal information across unequal intervals, enabling time-continuous completion. Additionally, we present the Query-Generate (Q-G) strategy within TIME-DMF to model the infinite states of continuous data. Extensive experiments across five types of sensing tasks demonstrate the effectiveness of our models and the advantages of time-continuous completion. Copyright © 2024, The Authors. All rights reserved.

关键词： Budget control

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