Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics最新文献

A Comparison of Supervised Classification Methods for Classifying Biological Cell Types 生物细胞类型的监督分类方法比较

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512456

Yuning Chen, Abhishek Hemlani, Song Zheng

引用次数: 0

Emergent Properties of Blood Flow in Arteries using Cellular Automata 利用细胞自动机研究动脉血流的紧急特性

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512463

Siva Manohar Reddy Kesu, Hariharan Ramasangu

引用次数: 0

Phylogenetic Analysis of aaRS Reveals the Kinship of Amino Acids aaRS的系统发育分析揭示氨基酸亲缘关系

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512459

Ming-Rui Li, Meng Su

引用次数: 0

Automated Cell Recognition using Single-cell RNA Sequencing with Machine Learning 使用单细胞RNA测序和机器学习的自动细胞识别

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512455

Chengqi Xu, Yuetian Chen, Yiyang Cao

{"title":"Automated Cell Recognition using Single-cell RNA Sequencing with Machine Learning","authors":"Chengqi Xu, Yuetian Chen, Yiyang Cao","doi":"10.1145/3512452.3512455","DOIUrl":"https://doi.org/10.1145/3512452.3512455","url":null,"abstract":"This paper investigates the superiority and limitations of different dimensionality reduction schemes and classification methods in specific single-cell RNA sequencing (scRNA-seq) data sets. With systematic analysis as well as variables-controlled experiments, a pipeline was constructed from rpkm data to final cell type recognition and multiple dimension reduction methods are applied (including PCA, AutoEncoder, ISOMAP, and the combination algorithm of PCA+t-SNE) and multiple classifiers (Random Forest and Support Vector Machine, etc.) to obtain the accuracy difference of multiple solutions. By comparing the variation of different models and parameters on the final classification accuracy, this paper summarizes and outlook the information loss and classification effects of different processing schemes on the data set and seeks to find the best combination from them. Using the combination of PCA+SVM, this work obtained 53.13% global maximum accuracy and based on this result to further explore the possibility of improving accuracy and model transfer learning in a wider range of applications.","PeriodicalId":120446,"journal":{"name":"Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125836732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IT Solutions for Preventing and Monitoring Adverse Drug Reactions: A Systematic Literature Review 预防和监测药物不良反应的IT解决方案:系统的文献综述

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512460

A. Khalil, Ford Lumban Gaol, Boy Subirosa Sabarguna, Harjanto Prabowo

{"title":"IT Solutions for Preventing and Monitoring Adverse Drug Reactions: A Systematic Literature Review","authors":"A. Khalil, Ford Lumban Gaol, Boy Subirosa Sabarguna, Harjanto Prabowo","doi":"10.1145/3512452.3512460","DOIUrl":"https://doi.org/10.1145/3512452.3512460","url":null,"abstract":"∗ Patient safety is one of the most crucial aspects in the healthcare industry. Minimizing adverse drug reactions (ADR) and medical errors are the focus for improving patient’s quality of life. However, it is undeniable that no drug is free from side effects. In fact, ADR caused 2.3% to 21.2% of hospital admissions, and ADR cases are also hard to trace because less than 5% of cases were reported directly by the patient. An increasing amount of research has been conducted to see the potential of information technology (IT) for preventing and monitoring ADR. However, we rarely find a comprehensive article review to discuss IT solutions for preventing and monitoring ADR. Therefore, this paper conducted a systematic review of papers published in 2016-2021 to see the current IT solutions for preventing and monitoring ADR. This paper focuses on clinical decision support system (CDSS) as the solutions for preventing ADR, and Patient Health Monitoring (PHM) software for monitoring ADR. Our study found most previous research conducted by developed countries with cardiology and endocrinology as the most prevalent disease domain. In relation to prior research on CDSS, the use of knowledge-based CDSS still dominates the previous research. At the same time, mobile is the most used platform for monitoring ADR. We also attempted to categorize the features based on the approaches to give drug recommendations and report ADR.","PeriodicalId":120446,"journal":{"name":"Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics","volume":"469 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131121955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Predicting Anatomical Therapeutic Chemical Drug Classes from 17 molecules’ Properties of Drugs by Multi-Label Binary Relevance Approach with MLSMOTE 基于MLSMOTE的多标签二值关联方法从17种药物分子性质预测解剖治疗化学药物类别

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512453

Pranab Das, Dilwar Hussain Mazumder

{"title":"Predicting Anatomical Therapeutic Chemical Drug Classes from 17 molecules’ Properties of Drugs by Multi-Label Binary Relevance Approach with MLSMOTE","authors":"Pranab Das, Dilwar Hussain Mazumder","doi":"10.1145/3512452.3512453","DOIUrl":"https://doi.org/10.1145/3512452.3512453","url":null,"abstract":"Anatomical Therapeutic Chemical (ATC) classes prediction is one of the prominent activities in the costly and tedious pipeline of drug discovery where machine learning plays an important role by minimizing the cost and time of prediction. Most of the existing research have been done to predict ATC classes from the chemical-chemical association, side-effects, target proteins, gene expressions, chemical structures, drug targets, and textual information of drugs. However, the capability of 17 molecules’ properties have not yet been explored to predict drug ATC classes. The current work proposes a methodology for predicting the drug ATC classes using the 17 molecules’ properties. ATC classes prediction is a multi-label classification task and therefore, a binary relevance strategy has been employed to solve this issue with four basic machine learning classifiers, namely K-Nearest Neighbour (KNN), Extra Tree Classifier (ETC), Random Forest (RF), and Decision Tree (DT). The common problem of multi-label datasets is class imbalance which is addressed using the MLSMOTE (Multi-Label Synthetic Minority Over-Sampling Technique). The proposed methodology exhibits promising results, and it achieved the accuracy ranging from 96.90% to 98.06%, which indicates that 17 molecules’ properties are good enough in efficient prediction of ATC classes.","PeriodicalId":120446,"journal":{"name":"Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124661929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

A Meta-Analysis on the Relationship Between Derivatization and Cytotoxicity of Chalcone Compound 查尔酮衍生物化与细胞毒性关系的meta分析

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512465

Rui-qiang Su

{"title":"A Meta-Analysis on the Relationship Between Derivatization and Cytotoxicity of Chalcone Compound","authors":"Rui-qiang Su","doi":"10.1145/3512452.3512465","DOIUrl":"https://doi.org/10.1145/3512452.3512465","url":null,"abstract":"Cancer is a worldwide leading cause of death. The development of an effective anti-cancer drug is with pressing need. Chalcone and its derivatives have been considered as general anti-cancer compounds. Because of its easy synthesis and good biological activity, Chalcones has attracted extensive attention. However, the potency of Chalcones to various cancer types and the ideal modification site on Chalcones has not been well documented. Herein, we systematically retrieved multiple pieces of literature from the Web-Of-Science search engine and examined chalcone derivatization literature from 2017 to 2022. Through meta-analysis, we found significant heterogeny between the cytotoxicity effects of chalcone compounds between normal cells and cancer cells (P <0.05). Chalcone derivatives indicate different potency to glioma (mean 0.46 μM), skin cancer (mean 6.63 μM), colon cancer (mean 7.87 μM), colorectal cancer (mean 8.12 μM), and brain cancer (mean 9.53 μM). Moreover, the modification site also statistically correlates to the potency of Chalcone derivatives. Among fluorine, bromine, chloride modifications, ortho chlorine substitution shows the optimal potency as indicated by the minimum overall mean IC50 values.","PeriodicalId":120446,"journal":{"name":"Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129918965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA-methylation based Machine-learning Model for Impaired Liver Function Prediction

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512454

Jitong Xian

{"title":"DNA-methylation based Machine-learning Model for Impaired Liver Function Prediction","authors":"Jitong Xian","doi":"10.1145/3512452.3512454","DOIUrl":"https://doi.org/10.1145/3512452.3512454","url":null,"abstract":"Liver diseases include any medical disorders that negatively impact the normal functions of liver. They pose a great threat to public health due to their high prevalence. The early diagnosis of liver diseases is important for successful treatment but is hindered by the fact that liver diseases tend to show few symptoms in their early stages. In this project, I collected DNA methylation data from normal liver samples (n = 191) as well as data generated from early and late stage of liver diseases (n = 756) and identified 258 loci that were differentially methylated between all studied disease groups and the normal group. Using these CpGs as features, I trained a predictive SVM (support vector machine) model to discriminate whether a liver is diseased, and then used the 10-fold cross-validations to evaluate the model's predictive skills. The SVM model achieved outstanding classification power for impaired and normal livers, with AUROC (Area Under the Receiver Operating Characteristic curve) = 0.95, precision = 0.93, and recall = 0.96. The DNA methylation markers discovered in this study promise early diagnosis of liver diseases and pave the way for the future development of preventive and therapeutic epigenetic agents.","PeriodicalId":120446,"journal":{"name":"Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics","volume":"464 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125852390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Design of a High-Resolution Ultrasonic Temperature Meter for Soft Tissue-Mimicking Phantoms based on a PSoC Module 基于PSoC模块的高分辨率模拟软组织超声温度计设计

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512461

Pedro Jesus Acevedo-Contla, Demetrio Fabian Garcia-Nocetti, M. Fuentes-Cruz, Adalberto Joel Duran-Ortega

{"title":"Design of a High-Resolution Ultrasonic Temperature Meter for Soft Tissue-Mimicking Phantoms based on a PSoC Module","authors":"Pedro Jesus Acevedo-Contla, Demetrio Fabian Garcia-Nocetti, M. Fuentes-Cruz, Adalberto Joel Duran-Ortega","doi":"10.1145/3512452.3512461","DOIUrl":"https://doi.org/10.1145/3512452.3512461","url":null,"abstract":"The measurement of temperature using non-invasive ultrasonic methods is based on changes in the ultrasonic velocity due to the temperature variation in the medium. This article describes an electronic device for measuring temperature in soft tissue-mimicking phantoms using a PSoC-5LP module, PVDF ultrasonic transducers (LDT1-028K), and an External Circuit Module. Control signals, signal acquisition and display of the temperature value are programmed using a PSoC module. The External Circuit Module was implemented with a PVDF transducer driver, an RF amplifier and a pulse voltage converter. In the experimental implementation, a distance was set between the PVDF transducers and then an operating temperature interval was selected. Considering these specifications, the flight time of the ultrasonic wave at the initial temperature is detected, which is compared with the flight time of the temperature to be measured. The difference between flight times produces a narrow pulse being converted to DC voltage, which is proportional to the temperature change. The device for measuring temperature in soft tissue-mimicking phantoms was designed to work at an operating frequency of 1MHz and a temperature measurement interval from 350C to 400C with a 0.10C resolution. The experiment was carried out using a temperature controlled water tank (bath); the device has a sampling rate of 100 samples per second, calculates the average and display the result with a refresh rate of one second. The device developed was found to be useful to measure temperature in soft tissue-mimicking phantoms due to the selected temperature interval and the resolution obtained.","PeriodicalId":120446,"journal":{"name":"Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129316859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Tissue and Drug Specificity of Drug Sensitivities in Different Cancer Cell Lines 不同肿瘤细胞系药物敏感性的组织和药物特异性

Proceedings of the 2021 5th International Conference on Computational Biology and Bioinformatics Pub Date : 2021-12-26 DOI: 10.1145/3512452.3512462

Yan Wang

引用次数: 0