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Protein Structure Prediction:Challenges,Advances,and the Shift of Research Paradigms

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 913-925页

作者： Bin Huang Lupeng Kong Chao Wang Fusong Ju Qi Zhang Jianwei Zhu Tiansu Gong Haicang Zhang Chungong Yu Wei-Mou Zheng Dongbo Bu Key Laboratory of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China Changping Laboratory Beijing 102206China Microsoft Research AI4Science Beijing 100080China Huawei Noah’s Ark Lab Wuhan 430206China Zhongke Big Data Academy Zhengzhou 450046China Institute of Theoretical Physics Chinese Academy of SciencesBeijing 100190China

Protein structure prediction is an interdisciplinary research topic that has attracted researchers from multiple fields,including biochemistry,medicine,physics,mathematics,and computer *** researchers adopt various research paradigms to attack the same structure prediction problem:biochemists and physicists attempt to reveal the principles governing protein folding;mathematicians,especially statisticians,usually start from assuming a probability distribution of protein structures given a target sequence and then find the most likely structure,while computer scientists formulate protein structure prediction as an optimization problem-finding the structural conformation with the lowest energy or minimizing the difference between predicted structure and native *** research paradigms fall into the two statistical modeling cultures proposed by Leo Breiman,namely,data modeling and algorithmic ***,we have also witnessed the great success of deep learning in protein structure *** this review,we present a survey of the efforts for protein structure *** compare the research paradigms adopted by researchers from different fields,with an emphasis on the shift of research paradigms in the era of deep *** short,the algorithmic modeling techniques,especially deep neural networks,have considerably improved the accuracy of protein structure prediction;however,theories interpreting the neural networks and knowledge on protein folding are still highly desired.

关键词： Protein folding Protein structure prediction Deep learning Transformer Language model

Concept Prerequisite Relation Prediction by Using Permutation-Equivariant Directed Graph Neural Networks

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arXiv 2023年

作者： Qu, Xiran Shang, Xuequn Zhang, Yupei School of Computer Science Northwestern Polytechnical University Xi’an 710129 China Big data Storage and Management MIIT Lab Xi’an 710129 China

This paper studies the problem of CPRP, concept prerequisite relation prediction, which is a fundamental task in using AI for education. CPRP is usually formulated into a link-prediction task on a relationship graph of concepts and solved by training the graph neural network (GNN) model. However, current directed GNNs fail to manage graph isomorphism which refers to the invariance of non-isomorphic graphs, reducing the expressivity of resulting representations. We present a permutation-equivariant directed GNN model by introducing the Weisfeiler-Leman test into directed GNN learning. Our method is then used for CPRP and evaluated on three public datasets. The experimental results show that our model delivers better prediction performance than the state-of-the-art *** Codes 68T07 © 2023, CC BY-NC-ND.

关键词： Directed graphs

Federated Learning-Outcome Prediction with Multi-layer Privacy Protection

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arXiv 2023年

作者： Zhang, Yupei Li, Yuxin Wang, Yifei Wei, Shuangshuang Xu, Yunan Shang, Xuequn School of Computer Science Northwestern Polytechnical University Xi’an710129 China MIIT Lab of Big Data Storage and Management Xi’an710129 China

Learning-outcome prediction (LOP) is a longstanding and critical problem in educational routes. Many studies have contributed to developing effective models while often suffering from data shortage and weak generalization to various institutions due to the privacy-protection issue. To this end, this study proposes a distributed grade prediction model, dubbed FecMap, by exploiting the federated learning (FL) framework that preserves the private data of local clients and communicates with others through a global generalized model. FecMap considers local subspace learning (LSL), which explicitly learns the local features against the global features, and multi-layer privacy protection (MPP), which hierarchically protects the private features, including model-shareable features and not-allowably shared features, to achieve client-specific classifiers of high performance on LOP per institution. FecMap is then achieved in an iteration manner with all datasets distributed on clients by training a local neural network composed of a global part, a local part, and a classification head in clients and averaging the global parts from clients on the server. To evaluate the FecMap model, we collected three higher-educational datasets of student academic records from engineering majors. Experiment results manifest that FecMap benefits from the proposed LSL and MPP and achieves steady performance on the task of LOP, compared with the state-of-the-art models. This study makes a fresh attempt at the use of federated learning in the learning-analytical task, potentially paving the way to facilitating personalized education with privacy *** Codes 68T07 © 2023, CC BY-NC-ND.

关键词： Forecasting

Optimizing Ethanol Production in Escherichia Coli Using a Hybrid of Particle Swarm Optimization and Artificial Bee Colony 22

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Optimizing Ethanol Production in Escherichia Coli Using a Hy...

Proceedings of the 6th International Conference on Advances in Artificial Intelligence

作者： Mohamad Faiz Dzulkalnine Mohd Saberi Mohamad Yee Wen Choon Muhammad Akmal Remli Hany Alashwal Artificial Intelligence and Bioinformatics Research Group Faculty of Computing Universiti Teknologi Malaysia Malaysia Health Data Science Lab Department of Genetics and Genomics College of Medical and Health Sciences United Arab Emirates University UAE and Big Data Analytics Center United Arab Emirates University UAE Institute for Artificial Intelligence and Big Data Universiti Malaysia Kelantan Malaysia and Department of Data Science Universiti Malaysia Kelantan Malaysia Department of Computer Science and Software Engineering College of Information Technology United Arab Emirates University UAE and Big Data Analytics Center United Arab Emirates University UAE

ISBN: (纸本)9781450396943

Metabolic engineering for biomass production using microorganisms’ cell has received considerable attention in recent years. This is due to the biomass products being extensively used in the field of food additives, supplements, pharmaceuticals, and polymer materials. In this paper, ethanol production in Escherichia coli (E. coli) is the desired product. Sugarcane and corn are often used to produce ethanol. However, one of the problems to produce adequate amounts of ethanol is that large areas are needed to plant sugarcane and corn. Furthermore, the amount of time for the process of dry milling and wet milling is high, which are 40 to 50 hours and 24 to 48 hours, respectively. The wet laboratory is also having limitation on the production of ethanol in microorganisms because the amount of the ethanol produced is not satisfying. Hence, a lot of metabolic engineering techniques is introduced to enhance the production of ethanol in E. coli, such as gene knockout strategy, but the production is yet to meet the demand. Therefore, this paper proposes a hybrid algorithm of Particle Swarm Optimization with the Artificial Bee Colony algorithm (PSOABC) to identify the optimal set of gene knockout strategy to improve the ethanol production in E. coli. A list of genes to knockout, production of the desired product, and growth rate are presented in this paper. PSOABC has shown better performance in terms of production, growth rate and accuracy.

关键词： Gene Knockouts Particle Swarm Optimization Artificial Bee Colony Ethanol Flux Balance Analysis

Explore the Mode of big data Talent Training Based on Integration between Industry and Education for IMIS 11

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Explore the Mode of Big Data Talent Training Based on Integr...

11th International Conference on Information Technology in Medicine and Education, ITME 2021

作者： Cuiling, Zhu Chengwei, Yang School of Management Science and Engineering Shandong University of Finance and Economic China Big Data and Artificial Intelligence Lab University of Finance and Economic Shandong China Intelligent Elderly Care and Big Data Engineering Laboratory of ShanDong Province Ji 'Nan China

ISBN: (纸本)9781665406796

With the advent of big data, the construction of new engineering in higher education is urgently required, and the requirements of information management and information system specialty(IMIS for short) in big data analysis and application are also increased. The integration between industry and education is an effective way for IMIS to cultivate new engineering talents needed by the society. It firstly analyzed the current situation of integration between industry, education for IMIS. On this basis, the cultivation mode of big data talents for IMIS based on the deep integration between industry and education is discussed, which are include the construction of application-oriented and innovative talents cultivation system, the curriculum practice system of big data course, and the policy of government financial support. © 2021 IEEE.

关键词： Information management

Malay lexical simplification model for non-native speaker 5

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Malay lexical simplification model for non-native speaker

5th International Conference on Intelligent Systems and Computer Vision, ISCV 2022

作者： Omar, Salehah Bakar, Juhaida Abu Nadzir, Maslinda Mohd Harun, Nor Hazlyna Yusoff, Nooraini Sultan Abdul Halim Mu'adzam Shah Polytechnic Department of Information Technology and Communication Kedah Jitra06000 Malaysia Universiti Utara Malaysia Data Science Research Lab School of Computing Kedah Sintok06010 Malaysia Institute for for Artificial Intelligence and Big Data Universiti Malaysia Kelantan Kelantan Kota Bharu16100 Malaysia

ISBN: (纸本)9781665495585

Vocabulary is an important language skill that can affect a person's understanding of a sentence. Thus, lexical simplification is the task of converting difficult words into simpler words. It is to make it easier for the reader to understand the sentences. The biggest challenge in lexical simplification is to simplify the words needed without changing the meaning of the sentence. Past studies have shown that there are weaknesses in this task, where simple words are also identified as complex words. This issue has led to the simplification of unnecessary words. The purpose of the study is to produce a complex word identification model for the Malay language into words that are more easily understood by nonnative speakers. Experiments was performed on the appropriate features to obtain the required results. Machine learning was used to ensure the results were more accurate. This study is a novelty in text simplification of the Malay language in the field of Natural Language Processing (NLP) and may be used as a preprocessing tool to improve other tasks in NLP. © 2022 IEEE.

关键词： Learning algorithms

VProChart: Answering Chart Question Through Visual Perception Alignment Agent and Programmatic Solution Reasoning 39

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VProChart: Answering Chart Question Through Visual Perceptio...

39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Huang, Muye Zhang, Lingling Han, Lai Wu, Wenjun Zhang, Xinyu Liu, Jun School of Computer Science and Technology Xi’an Jiaotong University China MOE KLINNS Lab Xi’an Jiaotong University China Shaanxi Province Key Laboratory of Big Data Knowledge Engineering China

ISBN: (纸本)157735897X

Charts are widely used for data visualization across various fields, including education, research, and business. Chart Question Answering (CQA) is an emerging task focused on the automatic interpretation and reasoning of data presented in charts. However, chart images are inherently difficult to interpret, and chart-related questions often involve complex logical and numerical reasoning, which hinders the performance of existing models. This paper introduces VProChart, a novel framework designed to address these challenges in CQA by integrating a lightweight Visual Perception Alignment Agent (VPAgent) and a Programmatic Solution Reasoning approach. VPAgent aligns and models chart elements based on principles of human visual perception, enhancing the understanding of chart context. The Programmatic Solution Reasoning approach leverages large language models (LLMs) to transform natural language reasoning questions into structured solution programs, facilitating precise numerical and logical reasoning. Extensive experiments on benchmark datasets such as ChartQA and PlotQA demonstrate that VProChart significantly outperforms existing methods, highlighting its ability to understand and reason with charts. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

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OUTLIER SYNTHESIS VIA HAMILTONIAN MONTE CARLO FOR OUT-OF-DISTRIBUTION DETECTION

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arXiv 2025年

作者： Li, Hengzhuang Zhang, Teng National Engineering Research Center for Big Data Technology and System Service Computing Technology and Systems Laboratory Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China

Out-of-distribution (OOD) detection is crucial for developing trustworthy and reliable machine learning systems. Recent advances in training with auxiliary OOD data demonstrate efficacy in enhancing detection capabilities. Nonetheless, these methods heavily rely on acquiring a large pool of high-quality natural outliers. Some prior methods try to alleviate this problem by synthesizing virtual outliers but suffer from either poor quality or high cost due to the monotonous sampling strategy and the heavy-parameterized generative models. In this paper, we overcome all these problems by proposing the Hamiltonian Monte Carlo Outlier Synthesis (HamOS) framework, which views the synthesis process as sampling from Markov chains. Based solely on the in-distribution data, the Markov chains can extensively traverse the feature space and generate diverse and representative outliers, hence exposing the model to miscellaneous potential OOD scenarios. The Hamiltonian Monte Carlo with sampling acceptance rate almost close to 1 also makes our framework enjoy great efficiency. By empirically competing with SOTA baselines on both standard and large-scale benchmarks, we verify the efficacy and efficiency of our proposed HamOS. Our code is available at: https://***/Fir-lat/HamOS_OOD. © 2025, CC BY.

关键词： Markov chains

HYPERBOLIC HYPERGRAPH NEURAL NETWORKS FOR MULTI-RELATIONAL KNOWLEDGE HYPERGRAPH REPRESENTATION

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arXiv 2024年

作者： Li, Mengfan Shi, Xuanhua Qiao, Chenqi Zhang, Teng Jin, Hai National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan430074 China

Knowledge hypergraphs generalize knowledge graphs using hyperedges to connect multiple entities and depict complicated relations. Existing methods either transform hyperedges into an easier-to-handle set of binary relations or view hyperedges as isolated and ignore their adjacencies. Both approaches have information loss and may potentially lead to the creation of sub-optimal models. To fix these issues, we propose the Hyperbolic Hypergraph Neural Network (H2GNN), whose essential component is the hyper-star message passing, a novel scheme motivated by a lossless expansion of hyperedges into hierarchies. It implements a direct embedding that consciously incorporates adjacent entities, hyper-relations, and entity position-aware information. As the name suggests, H2GNN operates in the hyperbolic space, which is more adept at capturing the tree-like hierarchy. We compare H2GNN with 15 baselines on knowledge hypergraphs, and it outperforms state-of-the-art approaches in both node classification and link prediction tasks. Copyright © 2024, The Authors. All rights reserved.

关键词： Knowledge graph