Biocomputing 2021 - Proceedings Of The Pacific Symposium.

• Author: Altman, Russ B.
• TeilnehmendeR: Dunker, A. Keith 1943-; Hunter, Lawrence, 1961-; Ritchie, Marylyn D.; Murray, Tiffany A.; Klein, Teri E.
• Place / Publishing House: Singapore : : World Scientific Publishing Company,, 2020.; ©2021.
• Year of Publication: 2020
• Language: English
• Physical Description: 1 online resource (372 pages)

The Pacific Symposium on Biocomputing (PSB) 2021 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are...

Table of Contents

• Intro
• Contents
• Preface
• ACHIEVING TRUSTWORTHY BIOMEDICAL DATA
• Session Introduction: Achieving Trustworthy Biomedical Data Solutions
• 1. Introduction
• 2. Preserving Privacy and Explaining Decisions of Artificial Intelligence
• 3. Sharing Genomic and Health Records
• 4. Deploying Digital Health Solutions
• 5. Crowdsourcing Healthcare
• 6. Considering the Bioethics
• 7. Anticipating the Future
• References
• Selection of Trustworthy Crowd Workers for Telemedical Diagnosis of Pediatric Autism Spectrum Disorder
• 1. Introduction
• 2. Methods
• 2.1. Clinically representative videos
• 2.2. Crowdsourcing task for Microworkers
• 2.3. Classifier to evaluate performance
• 2.4. Metrics evaluated
• 2.5. Prediction of crowd worker performance from metrics
• 3. Results
• 3.1. Correlation between metrics and probability of the correct class
• 3.2. Regression prediction of the mean probability of the correct class
• 4. Discussion and Future Work
• 5. Conclusion
• 6. Acknowledgments
• References
• Differential Privacy Protection Against Membership Inference Attack on Machine Learning for Genomic Data
• 1. Introduction
• 2. Related Work
• 3. Methods
• 3.1. Membership inference attack (MIA)
• 3.2. Di erential privacy (DP)
• 4. Experimental Setup
• 4.1. Dataset
• 4.2. Implementation of target models
• 4.3. Implementation of DP
• 4.4. Implementation of MIA
• 4.5. Evaluation metrics
• 5. Results
• 5.1. Vulnerability of target model against MIA without DP protection
• 5.2. Impact of privacy budget on the target model accuracy
• 5.3. E ectiveness of DP against MIA
• 5.4. E ect of model sparsity
• 6. Conclusion
• References
• Making Compassionate Use More Useful: Using Real-World Data, Real-World Evidence and Digital Twins to Supplement or Supplant Randomized Controlled Trials
• 1. Introduction.
• 1.1 Compassionate use
• 1.2 Compassionate use during the pandemic
• 1.3 What is an RCT?
• 1.3 EA data and NDAs
• 2. Real-World Information
• 2.1 Real-world data in trials
• 2.2 Real-world data and real-world evidence
• 2.2 Real-world limitations
• 3.0 Making RWD Work
• 3.1 Digital twins
• 4.0 Conclusions
• References
• ADVANCED METHODS FOR BIG DATA ANALYTICS IN WOMEN'S HEALTH
• Session Introduction: Advanced Methods for Big Data Analytics in Women's Health
• 1. Introduction
• 2. Session Summary
• 2.1. Full-length papers
• 3. Discussion
• References
• Intimate Partner Violence and Injury Prediction from Radiology Reports
• 1. Introduction
• 2. Related Work
• 2.1. Intimate partner violence
• 2.2. Clinical prediction
• 2.3. Natural language processing
• 3. Dataset
• 3.1. IPV patient selection
• 3.2. Control group selection
• 3.3. Injury labels
• 3.4. Data cleaning
• 3.5. Demographic data
• 4. Methodology
• 4.1. Experiment setup
• 4.2. Models
• 4.3. Evaluation
• 4.3.1. Prediction and predictive features
• 4.3.2. Error analysis
• 4.3.3. Report-program date gap
• 5. Results
• 5.1. IPV and injury prediction and predictive features
• 5.2. Error analysis
• 5.3. Report-program date gap
• 6. Discussion and conclusion
• References
• Not All C-sections Are the Same: Investigating Emergency vs. Elective C-section deliveries as an Adverse Pregnancy Outcome
• 1. Background and Significance
• 2. Methods
• 2.1. Dataset characteristics
• 2.2. Identification of delivery outcomes
• 2.2.1. Cesarean section deliveries
• 2.2.2. Preterm birth, stillbirth, and multiple birth deliveries
• 2.3. Integration of data from encounter records
• 2.4. Generalized regression models
• 3. Results
• 3.1. Utilization of cesarean section codes
• 3.2. Admission types recorded in encounter records.
• 3.3. Age distribution by delivery admit type
• 3.4. Number of deliveries by weekday and admit type
• 4. Generalized regression model
• 4.1. Surgical Incision Type for C-section and Effect on Emergency Admission
• 5. Discussion
• References
• Co-occurrence Patterns of Intimate Partner Violence
• 1. Introduction
• 2. Materials and Methods
• 2.1. Description of Data and Pre-Processing
• 2.2. Co-Occurrence of Violence Types
• 2.3. Co-Occurrence Network of Individual Violence Items
• 2.4. Radial Visualization
• 2.5. Clustering of Survivors and Identification of Subgroups
• 2.6. Health Problems and Trauma Symptoms
• 3. Results
• 4. Discussion
• 5. Acknowledgments
• References
• BIOCOMPUTING AND AI FOR INFECTIOUS DISEASE MODELLING AND THERAPEUTICS
• Session Introduction: AI for Infectious Disease Modelling and Therapeutics
• 1. Background
• 2. Introduction
• 3. Social Media and COVID-19
• 4. Biomedical literature and COVID-19 plus neglected tropical diseases
• 5. Genomics and HCV
• 6. Protein intrinsically disordered regions and SARS-CoV-2
• 7. Protein-protein interactions and SARS-CoV-2
• References
• Characterization of Anonymous Physician Perspectives on COVID-19 Using Social Media Data
• 1. Introduction
• 2. Methods
• 2.1. Data Collection
• 2.2. N-gram Frequency Measures
• 2.3. Sentiment Analysis
• 3. Results
• 3.1. Frequency of terms and n-grams
• 3.2. Sentiment analysis
• 3.3. Sentiments of tweets containing specific terms
• 4. Discussion and Conclusion
• 5. Acknowledgments
• References
• Semantic Changepoint Detection for Finding Potentially Novel Research Publications
• 1. Introduction
• 2. Methods
• 2.1. Data collection and general procedures
• 2.2. Title and abstract entropies
• 2.3. Bayesian changepoint analysis
• 2.4. Differential word clouds
• 2.5. Title and abstract embeddings.
• 2.6. Semantic novelty
• 2.6.1. Strategy T1: Novel paper detection based on semantic distance
• 2.6.2. Strategy T2: Detection of novel papers that may constitute a trend
• 2.6.3. Strategy Y1: Detection of a group of novel papers based on their mean vector
• 2.6.4. Strategy Y2: Proportion of novel papers
• 3. Results and Discussion
• 4. Conclusions
• 5. Supplementary Information
• 6. Acknowledgements
• References
• TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference
• 1. Background
• 2. Methods
• 2.1. Minimizing inter-host transmissions
• 2.2. Description of TreeFix-TP
• 2.3. Evaluation using simulated data sets
• 2.3.1. Data set generation
• 2.3.2. Evaluating reconstruction accuracy
• 3. Results
• 3.1. Phylogenetic error correction results
• 3.2. Source recovery in HCV outbreaks
• 3.3. Running time and scalability
• 4. Discussion and Conclusions
• Acknowledgments
• Authors' Contributions
• Supplementary Material
• References
• SARS-CoV-2 Drug Discovery based on Intrinsically Disordered Regions
• 1. Introduction
• 2. Methods
• 2.1. Molecular docking
• 2.1.1. Data collection
• 2.1.2. Data preprocessing
• 2.1.3. Target file generation
• 2.1.4. Flexible docking
• 2.1.5. Ensemble docking
• 2.2. Statistical model
• 2.2.1. Chemprop
• 2.2.2. Data and training
• 3. Results
• 3.1. Interaction modelling
• 3.2. Activity prediction
• 4. Conclusion
• 5. Acknowledgements
• References
• Feasibility of the Vaccine Development for SARS-CoV-2 and Other Viruses Using the Shell Disorder Analysis
• 1. Introduction
• 1.1. SARS-COV-2 Vaccine
• 1.2. Shell disorder analysis of HIV and other viruses
• 1.3. Spinoff projects including coronaviruses: Shell disorder and modes of transmission
• 1.4. Yet another spinoff: Correlations between the inner shell disorder and virulence.
• 2. Results
• 2.1. Clustering of CoV based mainly on NPID
• 2.2 Outer shell disorder is an indicator for the presence or absence of effective vaccines
• 2.3. A disordered outer shell provides an immune evasion tactic: Viral shapeshifting
• 2.4. SARS-CoV-2: Exceptionally hard shell (low MPID) associated with burrowing animals and buried feces
• 2.5. Behavior of the animal hosts matters in the evolutions of the viruses: EIAV vs. HIV
• 2.6. Feasibility of developing attenuated vaccine strains for SARS-CoV-2
• 3. Discussion
• 3.1. Links between respiratory transmission, N (Inner shell) disorder, and virulence: Viral load in body fluids vs. vital organs
• 3.2. Greater disorder in the inner shell proteins provide means for the more efficient replication of viral particles
• 3.3 Two modes of immune evasion: "Trojan Horse" (inner shell disorder) and "viral shapeshifting" (outer shell disorder)
• 3.4. FIV, HIV-1 and HIV-2: Similarities and differences
• 3.5. FIV vaccine enigma: Questionable efficacy
• 4. Conclusions
• 4.1. Development of the SARS-CoV-2 vaccine is feasible and vaccine strains can be found in nature
• 5. Materials and Methods
• References
• Protein Sequence Models for Prediction and Comparative Analysis of the SARS-CoV-2−Human Interactome
• 1. Introduction
• 2. Methods
• 2.1. Generalized Additive Models with interactions (GA2M)
• 3. Gold Standard Interaction Datasets
• 3.1. Dealing with the lack of negative examples
• 3.2. Features
• 4. Experiments
• 4.1. TAPE: Transformer based model for protein sequences
• 5. Results
• 5.1. Prediction performance and validation of predicted interactions
• 5.2. Enrichment analysis of predicted human binding partners
• 6. Discussion
• 6.1. Visualizing the virus-human interactions
• 6.2. Highly ranked sequence features
• 6.3. Structural analysis
• 7. Prior Work
• 8. Conclusion.
• 9. Acknowledgements.