DeepFrag-k: A Fragment-Based Deep Learning Approach for Protein Fold Recognition

Background: One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment level to improve the accuracy of protein fold recognition. DeepFrag-k is composed of two stages: the first stage employs a multi-modal Deep Belief Network (DBN) to predict the potential structural fragments given a sequence, represented as a fragment vector, and then the second stage uses a deep convolutional neural network (CNN) to classify the fragment vector into the corresponding fold. Results: Our results show that DeepFrag-k yields 92.98% accuracy in predicting the top-100 most popular fragments, which can be used to generate discriminative fragment feature vectors to improve protein fold recognition. Conclusions: There is a set of fragments that can serve as structural “keywords” distinguishing between major protein folds. The deep learning architecture in DeepFrag-k is able to accurately identify these fragments as structure features to improve protein fold recognition

Highly Accurate Fragment Library for Protein Fold Recognition

Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease understanding. Fold recognition is a key step in the protein structure discovery process, especially when traditional computational methods fail to yield convincing structural homologies. In this work, we present a new protein fold recognition approach using machine learning and data mining methodologies. First, we identify a protein structural fragment library (Frag-K) composed of a set of backbone fragments ranging from 4 to 20 residues as the structural “keywords” that can effectively distinguish between major protein folds. We firstly apply randomized spectral clustering and random forest algorithms to construct representative and sensitive protein fragment libraries from a large-scale of high-quality, non-homologous protein structures available in PDB. We analyze the impacts of clustering cut-offs on the performance of the fragment libraries. Then, the Frag-K fragments are employed as structural features to classify protein structures in major protein folds defined by SCOP (Structural Classification of Proteins). Our results show that a structural dictionary with ~400 4- to 20-residue Frag-K fragments is capable of classifying major SCOP folds with high accuracy. Then, based on Frag-k, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features to improve the accuracy of protein fold recognition. DeepFrag-k is composed of two stages: the first stage employs a multimodal Deep Belief Network (DBN) to predict the potential structural fragments given a sequence, represented as a fragment vector, and then the second stage uses a deep convolution neural network (CNN) to classify the fragment vectors into the corresponding folds. Our results show that DeepFrag-k yields 92.98% accuracy in predicting the top-100 most popular fragments, which can be used to generate discriminative fragment feature vectors to improve protein fold recognition

A survey of swarm intelligence for dynamic optimization: algorithms and applications

Swarm intelligence (SI) algorithms, including ant colony optimization, particle swarm optimization, bee-inspired algorithms, bacterial foraging optimization, firefly algorithms, fish swarm optimization and many more, have been proven to be good methods to address difficult optimization problems under stationary environments. Most SI algorithms have been developed to address stationary optimization problems and hence, they can converge on the (near-) optimum solution efficiently. However, many real-world problems have a dynamic environment that changes over time. For such dynamic optimization problems (DOPs), it is difficult for a conventional SI algorithm to track the changing optimum once the algorithm has converged on a solution. In the last two decades, there has been a growing interest of addressing DOPs using SI algorithms due to their adaptation capabilities. This paper presents a broad review on SI dynamic optimization (SIDO) focused on several classes of problems, such as discrete, continuous, constrained, multi-objective and classification problems, and real-world applications. In addition, this paper focuses on the enhancement strategies integrated in SI algorithms to address dynamic changes, the performance measurements and benchmark generators used in SIDO. Finally, some considerations about future directions in the subject are given

VISIO-HAPTIC DEFORMABLE MODEL FOR HAPTIC DOMINANT PALPATION SIMULATOR

Vision and haptic are two most important modalities in a medical simulation. While visual cues assist one to see his actions when performing a medical procedure, haptic cues enable feeling the object being manipulated during the interaction. Despite their importance in a computer simulation, the combination of both modalities has not been adequately assessed, especially that in a haptic dominant environment. Thus, resulting in poor emphasis in resource allocation management in terms of effort spent in rendering the two modalities for simulators with realistic real-time interactions. Addressing this problem requires an investigation on whether a single modality (haptic) or a combination of both visual and haptic could be better for learning skills in a haptic dominant environment such as in a palpation simulator. However, before such an investigation could take place one main technical implementation issue in visio-haptic rendering needs to be addresse

Scalarized Preferences in Multi-objective Optimization

Multikriterielle Optimierungsprobleme verfügen über keine Lösung, die optimal in jeder Zielfunktion ist. Die Schwierigkeit solcher Probleme liegt darin eine Kompromisslösung zu finden, die den Präferenzen des Entscheiders genügen, der den Kompromiss implementiert. Skalarisierung – die Abbildung des Vektors der Zielfunktionswerte auf eine reelle Zahl – identifiziert eine einzige Lösung als globales Präferenzenoptimum um diese Probleme zu lösen. Allerdings generieren Skalarisierungsmethoden keine zusätzlichen Informationen über andere Kompromisslösungen, die die Präferenzen des Entscheiders bezüglich des globalen Optimums verändern könnten. Um dieses Problem anzugehen stellt diese Dissertation eine theoretische und algorithmische Analyse skalarisierter Präferenzen bereit. Die theoretische Analyse besteht aus der Entwicklung eines Ordnungsrahmens, der Präferenzen als Problemtransformationen charakterisiert, die präferierte Untermengen der Paretofront definieren. Skalarisierung wird als Transformation der Zielmenge in diesem Ordnungsrahmen dargestellt. Des Weiteren werden Axiome vorgeschlagen, die wünschenswerte Eigenschaften von Skalarisierungsfunktionen darstellen. Es wird gezeigt unter welchen Bedingungen existierende Skalarisierungsfunktionen diese Axiome erfüllen. Die algorithmische Analyse kennzeichnet Präferenzen anhand des Resultats, das ein Optimierungsalgorithmus generiert. Zwei neue Paradigmen werden innerhalb dieser Analyse identifiziert. Für beide Paradigmen werden Algorithmen entworfen, die skalarisierte Präferenzeninformationen verwenden: Präferenzen-verzerrte Paretofrontapproximationen verteilen Punkte über die gesamte Paretofront, fokussieren aber mehr Punkte in Regionen mit besseren Skalarisierungswerten; multimodale Präferenzenoptima sind Punkte, die lokale Skalarisierungsoptima im Zielraum darstellen. Ein Drei-Stufen-Algorith\-mus wird entwickelt, der lokale Skalarisierungsoptima approximiert und verschiedene Methoden werden für die unterschiedlichen Stufen evaluiert. Zwei Realweltprobleme werden vorgestellt, die die Nützlichkeit der beiden Algorithmen illustrieren. Das erste Problem besteht darin Fahrpläne für ein Blockheizkraftwerk zu finden, die die erzeugte Elektrizität und Wärme maximieren und den Kraftstoffverbrauch minimiert. Präferenzen-verzerrte Approximationen generieren mehr Energie-effiziente Lösungen, unter denen der Entscheider seine favorisierte Lösung auswählen kann, indem er die Konflikte zwischen den drei Zielen abwägt. Das zweite Problem beschäftigt sich mit der Erstellung von Fahrplänen für Geräte in einem Wohngebäude, so dass Energiekosten, Kohlenstoffdioxidemissionen und thermisches Unbehagen minimiert werden. Es wird gezeigt, dass lokale Skalarisierungsoptima Fahrpläne darstellen, die eine gute Balance zwischen den drei Zielen bieten. Die Analyse und die Experimente, die in dieser Arbeit vorgestellt werden, ermöglichen es Entscheidern bessere Entscheidungen zu treffen indem Methoden angewendet werden, die mehr Optionen generieren, die mit den Präferenzen der Entscheider übereinstimmen

Computer vision and optimization methods applied to the measurements of in-plane deformations

fi=vertaisarvioitu|en=peerReviewed

Algorithm Engineering for Realistic Journey Planning in Transportation Networks

Diese Dissertation beschäftigt sich mit der Routenplanung in Transportnetzen. Es werden neue, effiziente algorithmische Ansätze zur Berechnung optimaler Verbindungen in öffentlichen Verkehrsnetzen, Straßennetzen und multimodalen Netzen, die verschiedene Transportmodi miteinander verknüpfen, eingeführt. Im Fokus der Arbeit steht dabei die Praktikabilität der Ansätze, was durch eine ausführliche experimentelle Evaluation belegt wird

Dispatching and Rescheduling Tasks and Their Interactions with Travel Demand and the Energy Domain: Models and Algorithms

Abstract The paper aims to provide an overview of the key factors to consider when performing reliable modelling of rail services. Given our underlying belief that to build a robust simulation environment a rail service cannot be considered an isolated system, also the connected systems, which influence and, in turn, are influenced by such services, must be properly modelled. For this purpose, an extensive overview of the rail simulation and optimisation models proposed in the literature is first provided. Rail simulation models are classified according to the level of detail implemented (microscopic, mesoscopic and macroscopic), the variables involved (deterministic and stochastic) and the processing techniques adopted (synchronous and asynchronous). By contrast, within rail optimisation models, both planning (timetabling) and management (rescheduling) phases are discussed. The main issues concerning the interaction of rail services with travel demand flows and the energy domain are also described. Finally, in an attempt to provide a comprehensive framework an overview of the main metaheuristic resolution techniques used in the planning and management phases is shown

Numerical and Evolutionary Optimization 2020

This book was established after the 8th International Workshop on Numerical and Evolutionary Optimization (NEO), representing a collection of papers on the intersection of the two research areas covered at this workshop: numerical optimization and evolutionary search techniques. While focusing on the design of fast and reliable methods lying across these two paradigms, the resulting techniques are strongly applicable to a broad class of real-world problems, such as pattern recognition, routing, energy, lines of production, prediction, and modeling, among others. This volume is intended to serve as a useful reference for mathematicians, engineers, and computer scientists to explore current issues and solutions emerging from these mathematical and computational methods and their applications

Evolution through reputation: noise-resistant selection in evolutionary multi-agent systems

Little attention has been paid, in depth, to the relationship between fitness evaluation in evolutionary algorithms and reputation mechanisms in multi-agent systems, but if these could be related it opens the way for implementation of distributed evolutionary systems via multi-agent architectures. Our investigation concentrates on the effectiveness with which social selection, in the form of reputation, can replace direct fitness observation as the selection bias in an evolutionary multi-agent system. We do this in two stages: In the first, we implement a peer-to-peer, adaptive Genetic Algorithm (GA), in which agents act as individual GAs that, in turn, evolve dynamically themselves in real-time, using the traditional evolutionary operators of fitness-based selection, crossover and mutation. In the second stage, we replace the fitness-based selection operator with a reputation-based one, in which agents choose their mates based on the collective past experiences of themselves and their peers. Our investigation shows that this simple model of distributed reputation can be successful as the evolutionary drive in such a system, exhibiting practically identical performance and scalability to direct fitness observation. Further, we discuss the effect of noise (in the form of “defective” agents) in both models. We show that the reputation-based model is significantly better at identifying the defective agents, thus showing an increased level of resistance to noise