Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020)

Name: Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020)
Brand: Springer
Price: 149.79 EUR
Availability: OnlineOnly

Gabriella Panuccio Miguel Rocha Florentino Fdez-Riverola Mohd Saberi Mohamad Roberto Casado-Vara(Herausgeber*in)

Springer (Verlag)

1. Auflage

Erschienen am 22. Juli 2020

XV, 216 Seiten

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978-3-030-54568-0 (ISBN)

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Beschreibung

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Inhalt

Intro
Preface
Organization
General Co-chairs
Program Committee
Organizing Committee
Local Organizing Committee
PACBB 2020 Sponsors
Contents
Identification of Antimicrobial Peptides from Macroalgae with Machine Learning
1 Introduction
2 Methods
2.1 Training and Testing Datasets
2.2 Classifier Configuration
2.3 Incremental Feature Selection
3 Results and Discussion
4 Conclusion
References
A Health-Related Study from Food Online Reviews. The Case of Gluten-Free Foods
1 Introduction
2 Materials and Methods
2.1 Products Reviews Processing
2.2 Corpus Annotation: Named Entity Recognition
2.3 User Characterization: Name Gender Recognition
2.4 Knowledge Inference: Normalized Term Frequency Analysis
3 Results and Discussion
3.1 Temporal Analysis of Positive and Negative Reviews
3.2 Health-Related Trends
3.3 User Gender Analysis
4 Conclusions and Further Research
References
The Activity of Bioinformatics Developers and Users in Stack Overflow
1 Introduction
2 Material and Methods
3 Results
4 Conclusions and Future Works
References
ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning
1 Introduction
2 Package Description and Implementation
3 Application to Case Studies
3.1 Antimicrobial Peptides - AmPEP
3.2 Anticancer Peptides - MLACP
4 Discussion and Conclusions
References
Inferences on Mycobacterium Leprae Host Immune Response Escape and Antibiotic Resistance Using Genomic Data and GenomeFastScreen
1 Introduction
2 Materials and Methods
2.1 Pipeline Implementation
2.2 Data Source and Pre-processing
2.3 Analyses
3 Results
4 Conclusion
References
Compi Hub: A Public Repository for Sharing and Discovering Compi Pipelines
1 Introduction
2 Related Tools
3 Releasing a Compi Pipeline
4 Overview of the Compi Hub Repository
5 Publishing Pipelines at Compi Hub
6 Conclusions and Future Work
References
DeepACPpred: A Novel Hybrid CNN-RNN Architecture for Predicting Anti-Cancer Peptides
1 Introduction
2 Related Work
3 Methods
3.1 Data
3.2 DeepACPpred Model
3.3 Transfer Learning
3.4 Experimental Setup
4 Results and Discussion
4.1 Comparison to MLACP
4.2 Comparison to ACP-DL
4.3 Comparing the Hybrid Model to Individual RNNs and CNNs Models
4.4 Impact of Transfer Learning
5 Conclusions and Future Work
References
Preventing Cardiovascular Disease Development Establishing Cardiac Well-Being Indexes
1 Introduction
2 Limitations of Cardiac Risk Calculators
3 Establishing Cardiac Well-Being Indexes
3.1 Calculating the Indexes
3.2 Analytical System Implementation
4 Analysing the Indexes
5 Conclusions and Future Work
References
Fuzzy Matching for Cellular Signaling Networks in a Choroidal Melanoma Model
1 Introduction
2 Preliminaries
2.1 Rewriting Logic and Maude
2.2 Maude Representation of Pathway Logic Cell Signaling Models
2.3 The Problem Motivating Fuzzy Matching
3 Fuzzy Matching
4 Case Study
5 Implementation
6 Conclusions
References
Towards A More Effective Bidirectional LSTM-Based Learning Model for Human-Bacterium Protein-Protein Interactions
1 Introduction
2 A Comprehensive Re-examination of HPI Study
2.1 Host-Pathogen Protein-Protein Interactions
2.2 Variety of Host-Pathogen Databases
3 Evaluation Design for HB-PPI Dataset
3.1 The HB-PPI Dataset
3.2 Interpreting the Sequence Information
3.3 Machine Learning Based Methods
4 Proposed Bi-LSTM-Based Model and Evaluation
4.1 Our Model
4.2 Evaluation and Discussion
5 Conclusion
References
Machine Learning for Depression Screening in Online Communities
1 Introduction
2 Background
3 Methodology
3.1 Corpus Description
3.2 Text Preprocessing
3.3 Psycholinguistic Features
3.4 Binary Classification
4 Results
5 Discussion
6 Conclusions
References
Towards Triclustering-Based Classification of Three-Way Clinical Data: A Case Study on Predicting Non-invasive Ventilation in ALS
1 Introduction
2 Methods
2.1 Triclustering Three-Way Clinical Data
2.2 Triclustering-Based Random Forest
3 Results and Discussion
3.1 Data
3.2 Data Preprocessing
3.3 Model Evaluation
3.4 Baseline Results Using Random Forests and Original Features
3.5 Results Using Random Forests and Triclusters as Features
4 Conclusions
References
Searching RNA Substructures with Arbitrary Pseudoknots
1 Introduction
2 Background and Problem Definition
3 Relations Between Loops on Arc Diagram
4 Structural Matching
5 Conclusions and Future Work
A Appendix
References
An Application of Ontological Engineering for Design and Specification of Ontocancro
1 Introduction
2 Methodologies and Tools Used for the Ontological Engineering Development
2.1 NeOn Methodology
2.2 Biological Pathway Exchange (BioPAX)
2.3 Ontocancro
3 Design and Specification of Ontocancro Based on Ontological Engineering
4 Results and Final Considerations
References
Evaluation of the Effect of Cell Parameters on the Number of Microtubule Merotelic Attachments in Metaphase Using a Three-Dimensional Computer Model
1 Introduction
2 Similar Works
3 Computer Model
4 Numerical Experiments Technique
5 Results and Discussion
References
Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis
1 Introduction
2 Materials and Methods
3 Results and Discussion
3.1 Network Topology and Analysis
3.2 Overview of Global Regulatory Mechanisms and Main Biological Processes
3.3 Balance of the Reconstructed Transcriptional Regulatory Networks
4 Conclusion
References
A Hybrid of Bat Algorithm and Minimization of Metabolic Adjustment for Succinate and Lactate Production
1 Introduction
2 A Hybrid Algorithm of Bat Algorithm and Minimization of Metabolic Adjustment (BATMOMA)
2.1 Bat Representation of Metabolic Genotype
2.2 Initialization Population Phase
2.3 Fitness Evaluation Using MOMA
2.4 Global Solution Generation Phase
2.5 Local Solution Generation Phase
2.6 New Solution Searching Phase
3 Result and Discussion
3.1 Comparative Results for Succinate and Lactate
4 Conclusion and Future Works
References
Robustness of Pathway Enrichment Analysis to Transcriptome-Wide Gene Expression Platform
1 Introduction
2 Materials and Methods
2.1 Data Acquisition and Pre-processing
2.2 Enrichment Methods
2.3 Performance Evaluation
3 Results
4 Conclusions
References
Hypoglycemia Prevention Using an Embedded Model Control with a Safety Scheme: In-silico Test
1 Introduction
2 The Colmegna Model
3 Continuous Time Embedded Model Extracted from Colmegna Model
4 The Embedded Model Control
4.1 The State Predictor
4.2 Disturbance Rejection Matrices and Feedback Control
5 Safety Scheme
5.1 Insulin on Board Estimation
5.2 Safety Layer
6 Results
6.1 Test Scenario
6.2 Performance Obtained
7 Conclusion
References
Bidirectional-Pass Algorithm for Interictal Event Detection
1 Introduction
2 Data Sets and Methodology
2.1 Data Acquisition
2.2 Methodology
3 Implementation and Case Study
3.1 Event Modelling
3.2 Forward-Pass
3.3 Backward-Pass
4 Conclusion
References
Towards the Reconstruction of the Genome-Scale Metabolic Model of Lactobacillus acidophilus La-14
1 Introduction
2 Results and Discussion
2.1 Biomass Composition
2.2 Carbohydrate Uptake
2.3 Model Validation
2.4 Model Summary
3 Materials and Methods
3.1 Tools and Online Resources
3.2 Genome Annotation
3.3 Network Assembly and Curation
3.4 Conversion of the Network into a Stoichiometric Model
3.5 Validation of the Metabolic Model
References
Author Index

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