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Science China Life Sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Exploring causal effects of hormone- and radio-treatments in an observational study of breast cancer using copula-based semi-competing risks models

arXiv

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arXiv 2024年

作者： Yu, Tonghui Peng, Mengjiao Cui, Yifan Chen, Elynn Chen, Chixiang School of Physical and Mathematical Sciences Nanyang Technological University Singapore School of Statistics East China Normal University China Center for Data Science Zhejiang University China Stern School of Business New York University New YorkNY United States Division of Biostatistics and Bioinformatics Department of Epidemiology and Public Health University of Maryland School of Medicine BaltimoreMD United States Department of Neurosurgery University of Maryland School of Medicine BaltimoreMD United States

Breast cancer patients may experience relapse or death after surgery during the follow-up period, leading to dependent censoring of relapse. This phenomenon, known as semi-competing risk, imposes challenges in analyzing treatment effects on breast cancer and necessitates advanced statistical tools for unbiased analysis. Despite progress in estimation and inference within semi-competing risks regression, its application to causal inference is still in its early stages. This article aims to propose a frequentist and semi-parametric framework based on copula models that can facilitate valid causal inference, net quantity estimation and interpretation, and sensitivity analysis for unmeasured factors under right-censored semi-competing risks data. We also propose novel procedures to enhance parameter estimation and its applicability in real practice. After that, we apply the proposed framework to a breast cancer study and detect the time-varying causal effects of hormone- and radio-treatments on patients' relapse-free survival and overall survival. Moreover, extensive numerical evaluations demonstrate the method's feasibility, highlighting minimal estimation bias and reliable statistical inference. © 2024, CC BY-NC-ND.

关键词： Sensitivity analysis

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GENERALIZATION IN data-DRIVEN MODELS OF PRIMARY VISUAL CORTEX 9

GENERALIZATION IN DATA-DRIVEN MODELS OF PRIMARY VISUAL CORTE...

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9th International Conference on Learning Representations, ICLR 2021

作者： Lurz, Konstantin-Klemens Bashiri, Mohammad Willeke, Konstantin Jagadish, Akshay K. Wang, Eric Walker, Edgar Y. Cadena, Santiago A. Muhammad, Taliah Cobos, Erick Tolias, Andreas S. Ecker, Alexander S. Sinz, Fabian H. Institute for Bioinformatics and Medical Informatics University of Tübingen Germany International Max Planck Research School for Intelligent Systems Tübingen Germany Bernstein Center for Computational Neuroscience University of Tübingen Germany Department for Neuroscience Baylor College of Medicine HoustonTX United States Center for Neuroscience and Artificial Intelligence Baylor College of Medicine HoustonTX United States Department of Computer Science Campus Institute Data Science University of Göttingen Germany

Deep neural networks (DNN) have set new standards at predicting responses of neural populations to visual input. Most such DNNs consist of a convolutional network (core) shared across all neurons which learns a representation of neural computation in visual cortex and a neuron-specific readout that linearly combines the relevant features in this representation. The goal of this paper is to test whether such a representation is indeed generally characteristic for visual cortex, i.e. generalizes between animals of a species, and what factors contribute to obtaining such a generalizing core. To push all non-linear computations into the core where the generalizing cortical features should be learned, we devise a novel readout that reduces the number of parameters per neuron in the readout by up to two orders of magnitude compared to the previous state-of-the-art. It does so by taking advantage of retinotopy and learns a Gaussian distribution over the neuron's receptive field position. With this new readout we train our network on neural responses from mouse primary visual cortex (V1) and obtain a gain in performance of 7% compared to the previous state-of-the-art network. We then investigate whether the convolutional core indeed captures general cortical features by using the core in transfer learning to a different animal. When transferring a core trained on thousands of neurons from various animals and scans we exceed the performance of training directly on that animal by 12%, and outperform a commonly used VGG16 core pre-trained on imagenet by 33%. In addition, transfer learning with our data-driven core is more data-efficient than direct training, achieving the same performance with only 40% of the data. Our model with its novel readout thus sets a new state-of-the-art for neural response prediction in mouse visual cortex from natural images, generalizes between animals, and captures better characteristic cortical features than current task-driven pre-training appro

关键词： Neurons

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ProHap Explorer: Visualizing Haplotypes in Proteogenomic datasets

arXiv

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arXiv 2025年

作者： Vašíček, Jakub Skiadopoulou, Dafni Kuznetsova, Ksenia G. Käll, Lukas Vaudel, Marc Bruckner, Stefan Mohn Center for Diabetes Precision Medicine Department of Clinical Science University of Bergen Bergen Norway Computational Biology Unit Department of Informatics University of Bergen Bergen Norway Metabolism Program Broad Institute of MIT and Harvard CambridgeMA United States Science for Life Laboratory Department of Gene Technology KTH - Royal Institute of Technology Stockholm Sweden Department of Genetics and Bioinformatics Health Data and Digitalization Norwegian Institute of Public Health Oslo Norway Institute for Visual and Analytic Computing University of Rostock Rostock Germany

In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently introduced ProHap, a tool for generating customized protein haplotype databases. Here, we present ProHap Explorer, a visualization interface designed to investigate the influence of common haplotypes on the human proteome. It enables users to explore haplotypes, their effects on protein sequences, and the identification of non-canonical peptides in public mass spectrometry datasets. The design builds on well-established representations in biological sequence analysis, ensuring familiarity for domain experts while integrating novel interactive elements tailored to proteogenomic data exploration. User interviews with proteomics experts confirmed the tool's utility, highlighting its ability to reveal whether haplotypes affect proteins of interest. By facilitating the intuitive exploration of proteogenomic variation, ProHap Explorer supports research in personalized medicine and the development of targeted therapies. © 2025, CC BY.

关键词： Proteomics

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Treatment outcomes of HIV patients with hepatitis B and C virus co-infections in Southwest China:an observational cohort study

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Infectious Diseases of Poverty 2022年第1期11卷 27-33页

作者： Jingya Jia Qiuying Zhu Luojia Deng Guanghua Lan Andrew Johnson Huanhuan Chen Zhiyong Shen Jianjun Li Hui Xing Yuhua Ruan Jing Li Hui Lu Sten H.Vermund Jinhui Zhu Han-Zhu Qian SJTU-Yale Joint Center for Biostatistics and Data Science Shanghai Jiao Tong UniversityShanghaiChina Department of Bioinformatics and Biostatistics School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response Guangxi Center for Disease Control and PreventionNanningChina Groton School GrotonMAUSA State Key Laboratory of Infectious Disease Prevention and Control(SKLID) Chinese Center for Disease Control and Prevention(China CDC)Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesBeijingChina School of Public Health Yale UniversityNew HavenCTUSA

Background:Antiretroviral therapy(ART)has reduced mortality among people living with HIV(PLWH)in China,but co-infections of hepatitis B virus(HBV)and hepatitis C virus(HCV)may individually or jointly reduce the effect of *** study aimed to evaluate the impacts of HBV/HCV coinfections on treatment drop-out and mortality among PLWH on ***:A retrospective cohort study analysis of 58,239 people living with HIV(PLWH)who initiated antiretroviral therapy(ART)during 2010-2018 was conducted in Guangxi Province,*** were from the observational database of the National Free Antiretroviral Treatment *** proportional hazard models were fitted to evaluate the effects of baseline infection of HBV or HCV or both on death and treatment attrition among ***:Our study showed high prevalence of HBV(11.5%),HCV(6.6%)and HBV-HCV(1.5%)*** overall mortality rate and treatment attrition rate was 2.95[95%confidence interval(CI):2.88-3.02]and 5.92(95%CI:5.82-6.01)per 100 person-years,*** with HIV-only patients,HBV-co-infected patients had 42%higher mortality[adjusted hazard ratio(a HR)=1.42;95%CI 1.32-1.54],HCV-co-infected patients had 65%higher mortality(a HR=1.65;95%CI:1.47-1.86),and patients with both HCV and HBV co-infections had 123%higher mortality(a HR=2.23;95%CI:1.87-2.66).Conclusions:HBV and HCV coinfection may have an additive effect on increasing the risk of all-cause death among PLWH who are on *** is suggested that there is need for primary prevention and access to effective hepatitis treatment for PLWH.

关键词： Hepatitis C virus Hepatitis B virus HIV Antiretroviral therapy Mortality Retrospective cohort

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Molecular docking and molecular dynamics simulation studies of inhibitor candidates against Anopheles gambiae 3-hydroxykynurenine transaminase and implications on vector control

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Heliyon 2025年第1期11卷 e41633页

作者： Adedeji, Eunice O. Ogunlana, Olubanke O. Oduselu, Gbolahan O. Koenig, Rainer Adebiyi, Ezekiel Soremekun, Opeyemi S. Fatumo, Segun Covenant University Bioinformatics Research (CUBRe) Covenant University Ogun State Ota Nigeria Department of Biochemistry Covenant University Ogun State Ota Nigeria Department of Biology University of York York United Kingdom Covenant Applied Informatics and Communication Africa Centre of Excellence Covenant University Ota Nigeria Institute for Infectious Diseases and Infection Control (IIMK RG Systems Biology) Jena University Hospital Am Klinikum 1 Jena 07747 Germany African Center of Excellence in Bioinformatics & Data Intensive Science Makerere University Kampala 10218 Uganda Division of Applied Bioinformatics German Cancer Research Center (DKFZ) G200 Im Neuenheimer Feld 280 Heidelberg 69120 Germany The African Computational Genomics (TACG) Research Group MRC/UVRI and LSHTM Entebbe Uganda Precision Healthcare University Research Institute Queen Mary University of London United Kingdom Department of Non-Communicable Disease Epidemiology London School of Hygiene & Tropical Medicine United Kingdom

Isoxazole and oxadiazole derivatives inhibiting 3-hydroxykynurenine transaminase (3HKT) are potential larvicidal candidates. This study aims to identify more suited potential inhibitors of Anopheles gambiae 3HKT (Ag3HKT) through molecular docking and molecular dynamics simulation. A total of 958 compounds were docked against Anopheles gambiae 3HKT (PDB ID: 2CH2) using Autodock vina and Autodock4. The top three identified hits were subjected to 300 ns molecular dynamics simulation using AMBER 18 and ADMET analysis using SWISSADME predictor and ADMETSAR. Replacement of alkyl attachment on C5 of isoxazole or oxadiazole derivative with a cycloalkyl group yielded compounds with lower binding energy than their straight chain counterparts. The top three compounds were brominated compounds, 2‐[3‐(4‐bromophenyl)‐1,2‐oxazol‐5‐yl]cyclopentane‐1‐carboxylic acid, 2-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]cyclopentane-1-carboxylic acid, 3-[3-(4-bromo-2-methylphenyl)-1,2,4-oxadiazol-5-yl]cyclopentane-1-carboxylic acid, and they had binding energies of −8.58, −8.25, and −8.18 kcal/mol in virtual screening against 2CH2 protein target, respectively. These compounds were predicted to be less toxic than temephos, a standard larvicide and more biodegradable than previously reported inhibitors. The three compounds exhibited a greater stabilizing effect on 2CH2 protein target than 4-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid, a previously reported inhibitor candidate with good larvicidal activity on Aedes aegypti. Further thermodynamic calculations revealed that the top three compounds possessed total binding energies (ΔG_bind) of −26.64 kcal/mol, −24.26 kcal/mol and −14.11 kcal/mol, respectively, as compared to −12.02 kcal/mol for 4-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid. These compounds could be better larvicides than previously reported isoxazole or oxadiazole derivatives and safer than temephos. © 2025 The Authors

关键词： 1,2,4-Oxadiazole 3HKT Isoxazoles Larvicide Mosquito Vector control

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Chemically inspired Erdős-Rényi oriented hypergraphs

arXiv

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arXiv 2023年

作者： Garcia-Chung, Angel Bermúdez-Montaña, Marisol Stadler, Peter F. Jost, Jürgen Restrepo, Guillermo Tecnológico de Monterrey Escuela de Ingeniería y Ciencias Estado de México52926 Mexico Max Planck Institute for Mathematics in the Sciences Leipzig Germany Interdisciplinary Center for Bioinformatics Universität Leipzig Leipzig Germany Bioinformatics Group Department of Computer Science Universität Leipzig Leipzig Germany Institute for Theoretical Chemistry University of Vienna Vienna Austria The Santa Fe Institute Santa FeNM United States Facultad de Ciencias Universidad Nacional de Colombia Bogotá Colombia Center for Scalable Data Analytics and Artificial Intelligence Universität Leipzig Leipzig Germany School of Applied Sciences and Engineering EAFIT University Medellín Colombia

High-order structures have been recognised as suitable models for systems going beyond the binary relationships for which graph models are appropriate. Despite their importance and surge in research on these structures, their random cases have been only recently become subjects of interest. One of these high-order structures is the oriented hypergraph, which relates couples of subsets of an arbitrary number of vertices. Here we develop the Erdős-Rényi model for oriented hypergraphs, which corresponds to the random realisation of oriented hyperedges of the complete oriented hypergraph. A particular feature of random oriented hypergraphs is that the ratio between their expected number of oriented hyperedges and their expected degree or size is 3/2 for large number of vertices. We highlight the suitability of oriented hypergraphs for modelling large collections of chemical reactions and the importance of random oriented hypergraphs to analyse the unfolding of chemistry. © 2023, CC BY-SA.

关键词： Graph theory

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ROSE: Robust Selective Fine-tuning for Pre-trained Language Models

arXiv

引用

arXiv 2022年

作者： Jiang, Lan Zhou, Hao Lin, Yankai Li, Peng Zhou, Jie Jiang, Rui Ministry of Education Key Laboratory of Bioinformatics Center for Synthetic and Systems Biology Department of Automation BNRist Tsinghua University China Pattern Recognition Center WeChat AI Tencent Inc. China Gaoling School of Artificial Intelligence Renmin University of China Beijing China Beijing Key Laboratory of Big Data Management and Analysis Methods Beijing China Tsinghua University China

Even though the large-scale language models have achieved excellent performances, they suffer from various adversarial attacks. A large body of defense methods has been proposed. However, they are still limited due to redundant attack search spaces and the inability to defend against various types of attacks. In this work, we present a novel fine-tuning approach called RObust SEletive fine-tuning (ROSE) to address this issue. ROSE conducts selective updates when adapting pretrained models to downstream tasks, filtering out invaluable and unrobust updates of parameters. Specifically, we propose two strategies: the first-order and second-order ROSE for selecting target robust parameters. The experimental results show that ROSE achieves significant improvements in adversarial robustness on various downstream NLP tasks, and the ensemble method even surpasses both variants above. Furthermore, ROSE can be easily incorporated into existing fine-tuning methods to improve their adversarial robustness further. The empirical analysis confirms that ROSE eliminates unrobust spurious updates during fine-tuning, leading to solutions corresponding to flatter and wider optima than the conventional method. Code is available at https://***/jiangllan/ROSE. © 2022, CC BY.

关键词： Computational linguistics

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FedMonitor: An Implementation Architecture for Monitoring of Resources and Events'Notifications on Federated Cloud Computing Infrastructures

FedMonitor: An Implementation Architecture for Monitoring of...

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International Conference on Emerging Trends in Networks and Computer Communications (ETNCC)

作者： Emmanuel Adetiba Uche Nnaji John S. Wejin Festus Ojesanmi Matthew B. Akanle Priscilla O. Ajayi Faith O. Sweetwiliams Surendra C. Thakur Ezekiel F. Adebiyi Department of Electrical and Information Engineering and Covenant Applied Informatics & Communication African Center of Excellene(CApIC-ACE) Covenant University Ota Nigeria HRA Institute for Systems Science Durban University of Technology Durban South Africa Department of Computer and Information Science & CApIC-ACE Covenant University Ota Nigeria Department of Electrical and Information Engineering & CApIC-ACE Covenant University Jalingo Nigeria Department of Computer Science Tareba State University Jalingo Nigeria Covenant Applied Informatics & Communication African Center of Excellene(CApIC-ACE) Covenant University Ota Nigeria Department of Electrical and Information Engineering Covenant University & CApIC-ACE Covenant University Ota Nigeria Center for Systems and Information Services & CApIC-ACE Covenant University Ota Nigeria Department of Information Technology and KZN e-Skills Co-Laboratory Durban University of Technology Durban South Africa Covenant University Bioinformatics Research (CUBRe) Covenant University Ota Ogun State Nigeria African Center of Excellence in Bioinformatics & Data Intensive Science Makerere University Kampala Uganda

ISBN: (数字)9798350353266

ISBN: (纸本)9798350353273

In the evolving landscape of cloud computing, federated cloud infrastructures present unique challenges and opportunities for resource and application monitoring. Monitoring the diverse array of cloud resources and applications within a federated cloud environment is crucial for delivering consistent Quality of Service (QoS) and continuous oversight across various cloud applications and infrastructure. Despite the various successes documented in the literature on multi-cloud monitoring, existing frameworks have not fully explored or provided enough insights into centralized monitoring of resources, applications, and network devices in a federated cloud environment. This paper introduces FedMonitor, an implementation architecture designed to enhance the monitoring and notification capabilities in federated cloud environments by building on the theoretical ideals in our earlier work (i.e. FEDARGOS-V1). FedMonitor leverages Prometheus and Grafana to crawl, manage and visualize metrics from diverse software services, hardware resources, and network devices within a federated cloud environment. The results demonstrate hat FedMonitor improves the effectiveness of resource and application monitoring in federated cloud environments.

关键词： Measurement Cloud computing Visualization Computer architecture Quality of service Production Software Real-time systems Stakeholders Monitoring

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Web Development of Direct-to-consumer Genetics Testing

Web Development of Direct-to-consumer Genetics Testing

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Kians Azizatikarna Deby Erina Parung Dian Amirullah Alam Ahmad Hidayat Tjeng Wawan Cenggoro Arif Budiarto Simon Bens Pardamean Genetics Indonesia Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9781665453967

As the cost of genetic testing becomes more affordable each year, direct-to-customer (DTC) genetic testing services witness rapid market growth. This has encouraged the development of an easy-to-use website application to optimize potential customers to obtain informed choice regarding the offered DTC genetic testing as well as purchasing information. We present a wireframing process as a part of the agile software development process to build a web portal prototype for an Indonesia-based genetic testing service called DNAku. The approach in building the prototype used in this case is a part of the Agile Software Development Method. In brief, the wireframing stage resulted in this work consists of three main important outcomes. The first one is the use case diagram as a blueprint of this web-based system. A site map is then proposed as an extended version of the use case diagram which visualizes the whole pages with the links. Finally, based on this site map a series of page mock-ups are designed using Hyper Text Marking Language (HTML) and Cascading Style Sheets (CSS). The result of the prototype can be used as the basis for the next development stage, which is the coding stage based on the collected feedback from users. Considering the continuous application development via the wireframing method by taking into account the cycle of feedbacks from involved parties, this approach can strengthen the infrastructure to sustain DTC genetic business model, which has a niche market in Indonesia.

关键词： Visualization Costs Buildings Prototypes Agile software development Genetics Encoding

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