Science News for Theological Study: Machine Learning Unravels the Protein Folding Knot

2021 ◽  
pp. 1-3
Author(s):  
Andrew Davison
2018 ◽  
Author(s):  
Sebastian Bittrich ◽  
Marika Kaden ◽  
Christoph Leberecht ◽  
Florian Kaiser ◽  
Thomas Villmann ◽  
...  

AbstractBackgroundMachine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Meanwhile, algorithms improve in performance, but also gain complexity, and tend to neglect interpretability and comprehensiveness of the resulting models.ResultsGeneralized Matrix Learning Vector Quantization (GMLVQ) is a supervised, prototype-based machine learning method and provides comprehensive visualization capabilities not present in other classifiers which allow for a fine-grained interpretation of the data. In contrast to commonly used machine learning strategies, GMLVQ is well-suited for imbalanced classification problems which are frequent in life sciences. We present a Weka plug-in implementing GMLVQ. The feasibility of GMLVQ is demonstrated on a dataset of Early Folding Residues (EFR) that have been shown to initiate and guide the protein folding process. Using 27 features, an area under the receiver operating characteristic of 76.6% was achieved which is comparable to other state-of-the-art classifiers.ConclusionsThe application on EFR prediction demonstrates how an easy interpretation of classification models can promote the comprehension of biological mechanisms. The results shed light on the special features of EFR which were reported as most influential for the classification: EFR are embedded in ordered secondary structure elements and they participate in networks of hydrophobic residues. Visualization capabilities of GMLVQ are presented as we demonstrate how to interpret the results.


PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0143166 ◽  
Author(s):  
Marc Corrales ◽  
Pol Cuscó ◽  
Dinara R. Usmanova ◽  
Heng-Chang Chen ◽  
Natalya S. Bogatyreva ◽  
...  

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 250
Author(s):  
Dmitry N. Ivankov ◽  
Alexei V. Finkelstein

“How do proteins fold?” Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is how protein can find the global free energy minimum in a biologically reasonable time, without exhaustive enumeration of all possible conformations, the so-called “Levinthal’s paradox.” Less conceptual but still critical are aspects about factors defining folding times of particular proteins and about perspectives of machine learning for their prediction. We will discuss in this review the key ideas and discoveries leading to the current understanding of folding kinetics, including the solution of Levinthal’s paradox, as well as the current state of the art in the prediction of protein folding times.


2020 ◽  
Vol 60 ◽  
pp. 77-84 ◽  
Author(s):  
Frank Noé ◽  
Gianni De Fabritiis ◽  
Cecilia Clementi

2019 ◽  
Vol 28 (2) ◽  
pp. 121-134 ◽  
Author(s):  
ANDREAS HOLZINGER ◽  
MARKUS PLASS ◽  
KATHARINA HOLZINGER ◽  
GLORIA CERASELA CRIS¸AN ◽  
CAMELIA-M. PINTEA ◽  
...  

The ultimate goal of the Machine Learning (ML) community is to develop algorithms that can automatically learn from data, to extract knowledge and to make decisions without any human intervention. Specifically, automatic Machine Learning (aML) approaches show impressive success, e.g. in speech/image recognition or autonomous drive and smart car industry. Recent results even demonstrate intriguingly that deep learning applied for automatic classification of skin lesions is on par with the performance of dermatologists, yet outperforms the average human efficiency. As human perception is inherently limited to 3D environments, such approaches can discover patterns, e.g. that two objects are similar, in arbitrarily high-dimensional spaces what no human is able to do. Humans can deal simultaneously only with limited amounts of data, whilst “big data” is not only beneficial but necessary for aML. However, in health informatics, there are few data sets; aML approaches often suffer from insufficient training samples. Many problems are computationally hard, e.g. subspace clustering, k-anonymization, or protein folding. Here, interactive machine learning (iML) could be successfully used, as a human-in-the-loop contributes to reduce a huge search space through heuristic selection of suitable samples. This can reduce the complexity of NP-hard problems through the knowledge brought in by a human agent involved into the learning algorithm. A huge motivation for iML is that standard black-box approaches lack transparency, hence do not foster trust and acceptance of ML among end-users. Most of all, rising legal and privacy aspects, e.g. the European General Data Protection Regulations (GDPR) make black-box approaches difficult to use, because they often are not able to explain why a decision has been made, e.g. why two objects are similar. All these reasons motivate the idea to open the black-box to a glass-box. In this paper, we present some experiments to demonstrate the effectiveness of the iML human-in-the-loop model, in particular when using a glass-box instead of a black-box model and thus enabling a human directly to interact with a learning algorithm. We selected the Ant Colony System (ACS) algorithm, and applied it on the Traveling Salesman Problem (TSP). The TSP-problem is a good example, because it is of high relevance for health informatics as for example on protein folding problem, thus of enormous importance for fostering cancer research. Finally, from studies of learning from observation, i.e. of how humans extract so much from so little data, fundamental ML-research also may benefit.


2021 ◽  
Vol 19 (1) ◽  
pp. 5-6
Author(s):  
Andrew Davison

2020 ◽  
Vol 43 ◽  
Author(s):  
Myrthe Faber

Abstract Gilead et al. state that abstraction supports mental travel, and that mental travel critically relies on abstraction. I propose an important addition to this theoretical framework, namely that mental travel might also support abstraction. Specifically, I argue that spontaneous mental travel (mind wandering), much like data augmentation in machine learning, provides variability in mental content and context necessary for abstraction.


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