scholarly journals Capturing Surface Complementarity in Proteins using Unsupervised Learning and Robust Curvature Measure

2021 ◽  
Author(s):  
Abhijit Gupta ◽  
Arnab Mukherjee
Keyword(s):  
Machine Learning ◽  
Biological Function ◽  
Current Approach ◽  
Curvature Measure ◽  
Shape Complementarity ◽  
Binding Partners ◽  
Fitting Method ◽  
Antigen Antibody ◽  
The Relationship ◽  
Sphere Fitting

The structure of a protein plays a pivotal role in determining its function. Often, the protein surface’s shape and curvature dictate its nature of interaction with other proteins and biomolecules. However, marked by corrugations and roughness, a protein’s surface representation poses significant challenges for its curvature-based characterization. In the present study, we employ unsupervised machine learning to segment the protein surface into patches. To measure the surface curvature of a patch, we present an algebraic sphere fitting method that is fast, accurate, and robust. Moreover, we use local curvatures to show the existence of “shape complementarity” in protein-protein, antigen-antibody, and protein-ligand interfaces. We believe that the current approach could help understand the relationship between protein structure and its biological function and can be used to find binding partners of a given protein.

A Survey for Predicting Enzyme Family Classes Using Machine Learning Methods

2019 ◽  
Vol 20 (5) ◽  
pp. 540-550 ◽  
Author(s):  
Jiu-Xin Tan ◽  
Hao Lv ◽  
Fang Wang ◽  
Fu-Ying Dao ◽  
Wei Chen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Catalytic Mechanism ◽  
Biological Function ◽  
Learning Methods ◽  
Biochemical Processes ◽  
Machine Learning Methods ◽  
Enzyme Family ◽  
The Family ◽  
Speed Up ◽  
Family Classification

Enzymes are proteins that act as biological catalysts to speed up cellular biochemical processes. According to their main Enzyme Commission (EC) numbers, enzymes are divided into six categories: EC-1: oxidoreductase; EC-2: transferase; EC-3: hydrolase; EC-4: lyase; EC-5: isomerase and EC-6: synthetase. Different enzymes have different biological functions and acting objects. Therefore, knowing which family an enzyme belongs to can help infer its catalytic mechanism and provide information about the relevant biological function. With the large amount of protein sequences influxing into databanks in the post-genomics age, the annotation of the family for an enzyme is very important. Since the experimental methods are cost ineffective, bioinformatics tool will be a great help for accurately classifying the family of the enzymes. In this review, we summarized the application of machine learning methods in the prediction of enzyme family from different aspects. We hope that this review will provide insights and inspirations for the researches on enzyme family classification.

Delay Prediction of Aircrafts Based on Health Monitoring Data

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
B. A. Dattaram ◽  
N. Madhusudanan
Keyword(s):  
Machine Learning ◽  
Health Monitoring ◽  
Monitoring Data ◽  
Machine Learning Techniques ◽  
Learning Techniques ◽  
Flight Delay ◽  
Delay Prediction ◽  
The Relationship

Flight delay is a major issue faced by airline companies. Delay in the aircraft take off can lead to penalty and extra payment to airport authorities leading to revenue loss. The causes for delays can be weather, traffic queues or component issues. In this paper, we focus on the problem of delays due to component issues in the aircraft. In particular, this paper explores the analysis of aircraft delays based on health monitoring data from the aircraft. This paper analyzes and establishes the relationship between health monitoring data and the delay of the aircrafts using exploratory analytics, stochastic approaches and machine learning techniques.

scholarly journals Advances of ECG Sensors from Hardware, Software and Format Interoperability Perspectives

Electronics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 105
Author(s):  
Khaleel Husain ◽  
Mohd Soperi Mohd Zahid ◽  
Shahab Ul Hassan ◽  
Sumayyah Hasbullah ◽  
Satria Mandala
Keyword(s):  
Machine Learning ◽  
Heart Attack ◽  
Privacy Preservation ◽  
Causes Of Death ◽  
Clinical Settings ◽  
Data Format ◽  
Medical Institutions ◽  
Comprehensive Survey ◽  
Electrocardiogram Ecg ◽  
The Relationship

It is well-known that cardiovascular disease is one of the major causes of death worldwide nowadays. Electrocardiogram (ECG) sensor is one of the tools commonly used by cardiologists to diagnose and detect signs of heart disease with their patients. Since fast, prompt and accurate interpretation and decision is important in saving the life of patients from sudden heart attack or cardiac arrest, many innovations have been made to ECG sensors. However, the use of traditional ECG sensors is still prevalent in the clinical settings of many medical institutions. This article provides a comprehensive survey on ECG sensors from hardware, software and data format interoperability perspectives. The hardware perspective outlines a general hardware architecture of an ECG sensor along with the description of its hardware components. The software perspective describes various techniques (denoising, machine learning, deep learning, and privacy preservation) and other computer paradigms used in the software development and deployment for ECG sensors. Finally, the format interoperability perspective offers a detailed taxonomy of current ECG formats and the relationship among these formats. The intention is to help researchers towards the development of modern ECG sensors that are suitable and approved for adoption in real clinical settings.

Assessment of Machine Learning-Based Audiovisual Quality Predictors

2021 ◽  
Vol 17 (2) ◽  
pp. 1-22
Author(s):  
Mythili K. ◽  
Manish Narwaria
Keyword(s):  
Machine Learning ◽  
Signal Processing ◽  
Quality Assessment ◽  
Computational Models ◽  
Model Development ◽  
Multimedia Communication ◽  
Current Approach ◽  
Learning Ability ◽  
Data Uncertainty ◽  
Attractive Alternative

Quality assessment of audiovisual (AV) signals is important from the perspective of system design, optimization, and management of a modern multimedia communication system. However, automatic prediction of AV quality via the use of computational models remains challenging. In this context, machine learning (ML) appears to be an attractive alternative to the traditional approaches. This is especially when such assessment needs to be made in no-reference (i.e., the original signal is unavailable) fashion. While development of ML-based quality predictors is desirable, we argue that proper assessment and validation of such predictors is also crucial before they can be deployed in practice. To this end, we raise some fundamental questions about the current approach of ML-based model development for AV quality assessment and signal processing for multimedia communication in general. We also identify specific limitations associated with the current validation strategy which have implications on analysis and comparison of ML-based quality predictors. These include a lack of consideration of: (a) data uncertainty, (b) domain knowledge, (c) explicit learning ability of the trained model, and (d) interpretability of the resultant model. Therefore, the primary goal of this article is to shed some light into mentioned factors. Our analysis and proposed recommendations are of particular importance in the light of significant interests in ML methods for multimedia signal processing (specifically in cases where human-labeled data is used), and a lack of discussion of mentioned issues in existing literature.

scholarly journals The relationship between trust in AI and trustworthy machine learning technologies

2020 ◽  
Author(s):  
Ehsan Toreini ◽  
Mhairi Aitken ◽  
Kovila Coopamootoo ◽  
Karen Elliott ◽  
Carlos Gonzalez Zelaya ◽  
...  
Keyword(s):  
Machine Learning ◽  
Learning Technologies ◽  
The Relationship

scholarly journals Algorithmic and human prediction of success in human collaboration from visual features

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Martin Saveski ◽  
Edmond Awad ◽  
Iyad Rahwan ◽  
Manuel Cebrian
Keyword(s):  
Machine Learning ◽  
Visual Cues ◽  
Success Factors ◽  
Group Performance ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Adventure Game ◽  
Group Success ◽  
The Relationship ◽  
Better Than

AbstractAs groups are increasingly taking over individual experts in many tasks, it is ever more important to understand the determinants of group success. In this paper, we study the patterns of group success in Escape The Room, a physical adventure game in which a group is tasked with escaping a maze by collectively solving a series of puzzles. We investigate (1) the characteristics of successful groups, and (2) how accurately humans and machines can spot them from a group photo. The relationship between these two questions is based on the hypothesis that the characteristics of successful groups are encoded by features that can be spotted in their photo. We analyze >43K group photos (one photo per group) taken after groups have completed the game—from which all explicit performance-signaling information has been removed. First, we find that groups that are larger, older and more gender but less age diverse are significantly more likely to escape. Second, we compare humans and off-the-shelf machine learning algorithms at predicting whether a group escaped or not based on the completion photo. We find that individual guesses by humans achieve 58.3% accuracy, better than random, but worse than machines which display 71.6% accuracy. When humans are trained to guess by observing only four labeled photos, their accuracy increases to 64%. However, training humans on more labeled examples (eight or twelve) leads to a slight, but statistically insignificant improvement in accuracy (67.4%). Humans in the best training condition perform on par with two, but worse than three out of the five machine learning algorithms we evaluated. Our work illustrates the potentials and the limitations of machine learning systems in evaluating group performance and identifying success factors based on sparse visual cues.

A Machine Learning Approach to Analyzing the Relationship Between Temperatures and Multi-Proxy Tree-Ring Records

2018 ◽  
Vol 74 (2) ◽  
pp. 210-224 ◽  
Author(s):  
Jernej Jevšenak ◽  
Sašo Džeroski ◽  
Saša Zavadlav ◽  
Tom Levanič
Keyword(s):  
Machine Learning ◽  
Tree Ring ◽  
Learning Approach ◽  
Machine Learning Approach ◽  
The Relationship

Studying how genetic variants affect mechanism in biological systems

2018 ◽  
Vol 62 (4) ◽  
pp. 575-582
Author(s):  
Francesco Raimondi ◽  
Robert B. Russell
Keyword(s):  
Genetic Variation ◽  
Molecular Mechanism ◽  
Genetic Variants ◽  
Biological Function ◽  
Biological Systems ◽  
Protein Structures ◽  
Clinical Applications ◽  
Biological Pathways ◽  
The Relationship

Genetic variants are currently a major component of system-wide investigations into biological function or disease. Approaches to select variants (often out of thousands of candidates) that are responsible for a particular phenomenon have many clinical applications and can help illuminate differences between individuals. Selecting meaningful variants is greatly aided by integration with information about molecular mechanism, whether known from protein structures or interactions or biological pathways. In this review we discuss the nature of genetic variants, and recent studies highlighting what is currently known about the relationship between genetic variation, biomolecular function, and disease.

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