Allostery in Its Many Disguises: From Theory to Applications.

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts

A Survey on Evolutionary Computation for Computer Vision and Image Analysis: Past, Present, and Future Trends

Computer vision (CV) is a big and important field in artificial intelligence covering a wide range of applications. Image analysis is a major task in CV aiming to extract, analyse and understand the visual content of images. However, imagerelated tasks are very challenging due to many factors, e.g., high variations across images, high dimensionality, domain expertise requirement, and image distortions. Evolutionary computation (EC) approaches have been widely used for image analysis with significant achievement. However, there is no comprehensive survey of existing EC approaches to image analysis. To fill this gap, this paper provides a comprehensive survey covering all essential EC approaches to important image analysis tasks including edge detection, image segmentation, image feature analysis, image classification, object detection, and others. This survey aims to provide a better understanding of evolutionary computer vision (ECV) by discussing the contributions of different approaches and exploring how and why EC is used for CV and image analysis. The applications, challenges, issues, and trends associated to this research field are also discussed and summarised to provide further guidelines and opportunities for future research

Compositional evolution: interdisciplinary investigations in evolvability, modularity, and symbiosis

Conventionally, evolution by natural selection is almost inseparable from the notion of accumulating successive slight variations. Although it has been suggested that symbiotic mechanisms that combine together existing entities provide an alternative to gradual, or 'accretive', evolutionary change, there has been disagreement about what impact these mechanisms have on our understanding of evolutionary processes. Meanwhile, in artificial evolution methods used in computer science, it has been suggested that the composition of genetic material under sexual recombination may provide adaptation that is not available under mutational variation, but there has been considerable difficulty in demonstrating this formally. Thus far, it has been unclear what types of systems, if any, can be evolved by such 'compositional' mechanisms that cannot be evolved by accretive mechanisms. This dissertation takes an interdisciplinary approach to this question by building abstract computational simulations of accretive and compositional mechanisms. We identify a class of complex systems possessing 'modular interdependency', incorporating highly epistatic but modular substructure. This class typifies characteristics that are pathological for accretive evolution - the corresponding fitness landscape is highly rugged, has many local optima creating broad fitness saddles, and includes 'irreducibly complex' adaptations that cannot be reached by a succession of gradually changing proto-systems. Nonetheless, we provide simulations to show that this class of system is easily evolvable under sexual recombination or a mechanism of 'symbiotic encapsulation'. Our simulations and analytic results help us to understand the fundamental differences in the adaptive capacities of these mechanisms, and the conditions under which they provide an adaptive advantage. These models exemplify how certain kinds of complex systems, considered unevolvable under normal accretive change, are, in principle, easily evolvable under compositional evolution

Novel approaches to cooperative coevolution of heterogeneous multiagent systems

Tese de doutoramento, Informática (Engenharia Informática), Universidade de Lisboa, Faculdade de Ciências, 2017Heterogeneous multirobot systems are characterised by the morphological and/or behavioural heterogeneity of their constituent robots. These systems have a number of advantages over the more common homogeneous multirobot systems: they can leverage specialisation for increased efficiency, and they can solve tasks that are beyond the reach of any single type of robot, by combining the capabilities of different robots. Manually designing control for heterogeneous systems is a challenging endeavour, since the desired system behaviour has to be decomposed into behavioural rules for the individual robots, in such a way that the team as a whole cooperates and takes advantage of specialisation. Evolutionary robotics is a promising alternative that can be used to automate the synthesis of controllers for multirobot systems, but so far, research in the field has been mostly focused on homogeneous systems, such as swarm robotics systems. Cooperative coevolutionary algorithms (CCEAs) are a type of evolutionary algorithm that facilitate the evolution of control for heterogeneous systems, by working over a decomposition of the problem. In a typical CCEA application, each agent evolves in a separate population, with the evaluation of each agent depending on the cooperation with agents from the other coevolving populations. A CCEA is thus capable of projecting the large search space into multiple smaller, and more manageable, search spaces. Unfortunately, the use of cooperative coevolutionary algorithms is associated with a number of challenges. Previous works have shown that CCEAs are not necessarily attracted to the global optimum, but often converge to mediocre stable states; they can be inefficient when applied to large teams; and they have not yet been demonstrated in real robotic systems, nor in morphologically heterogeneous multirobot systems. In this thesis, we propose novel methods for overcoming the fundamental challenges in cooperative coevolutionary algorithms mentioned above, and study them in multirobot domains: we propose novelty-driven cooperative coevolution, in which premature convergence is avoided by encouraging behavioural novelty; and we propose Hyb-CCEA, an extension of CCEAs that places the team heterogeneity under evolutionary control, significantly improving its scalability with respect to the team size. These two approaches have in common that they take into account the exploration of the behaviour space by the evolutionary process. Besides relying on the fitness function for the evaluation of the candidate solutions, the evolutionary process analyses the behaviour of the evolving agents to improve the effectiveness of the evolutionary search. The ultimate goal of our research is to achieve general methods that can effectively synthesise controllers for heterogeneous multirobot systems, and therefore help to realise the full potential of this type of systems. To this end, we demonstrate the proposed approaches in a variety of multirobot domains used in previous works, and we study the application of CCEAs to new robotics domains, including a morphological heterogeneous system and a real robotic system.Fundação para a Ciência e a Tecnologia (FCT, PEst-OE/EEI/LA0008/2011

Computational Challenges in Cooperative Intelligent Urban Transport

This report documents the talks and group work of Dagstuhl Seminar 16091 “Computational Challenges in Cooperative Intelligent Urban Transport”. This interdisciplinary seminar brought researchers together from many fields including computer science, transportation, operations research, mathematics, machine learning and artificial intelligence. The seminar included two formats of talks: several minute research statements and longer overview talks. The talks given are documented here with abstracts. Furthermore, this seminar consisted of significant amounts of group work that is also documented with short abstracts detailing group discussions and planned outcomes

Combining motion planning with social reward sources for collaborative human-robot navigation task design

Across the human history, teamwork is one of the main pillars sustaining civilizations and technology development. In consequence, as the world embraces omatization, human-robot collaboration arises naturally as a cornerstone. This applies to a huge spectrum of tasks, most of them involving navigation. As a result, tackling pure collaborative navigation tasks can be a good first foothold for roboticists in this enterprise. In this thesis, we define a useful framework for knowledge representation in human-robot collaborative navigation tasks and propose a first solution to the human-robot collaborative search task. After validating the model, two derived projects tackling its main weakness are introduced: the compilation of a human search dataset and the implementation of a multi-agent planner for human-robot navigatio

XFlow: Benchmarking Flow Behaviors over Graphs

The occurrence of diffusion on a graph is a prevalent and significant phenomenon, as evidenced by the spread of rumors, influenza-like viruses, smart grid failures, and similar events. Comprehending the behaviors of flow is a formidable task, due to the intricate interplay between the distribution of seeds that initiate flow propagation, the propagation model, and the topology of the graph. The study of networks encompasses a diverse range of academic disciplines, including mathematics, physics, social science, and computer science. This interdisciplinary nature of network research is characterized by a high degree of specialization and compartmentalization, and the cooperation facilitated by them is inadequate. From a machine learning standpoint, there is a deficiency in a cohesive platform for assessing algorithms across various domains. One of the primary obstacles to current research in this field is the absence of a comprehensive curated benchmark suite to study the flow behaviors under network scenarios. To address this disparity, we propose the implementation of a novel benchmark suite that encompasses a variety of tasks, baseline models, graph datasets, and evaluation tools. In addition, we present a comprehensive analytical framework that offers a generalized approach to numerous flow-related tasks across diverse domains, serving as a blueprint and roadmap. Drawing upon the outcomes of our empirical investigation, we analyze the advantages and disadvantages of current foundational models, and we underscore potential avenues for further study. The datasets, code, and baseline models have been made available for the public at: https://github.com/XGraphing/XFlo

Cooperative Success Under Shared Cognitive States and Valuations

A mental model of the another person’s state of mind including their thoughts, feelings, and beliefs, otherwise known as Theory of Mind (ToM), can be created to better predict their behavior and optimize our own decisions. These representations can be explicitly modeled during both the development and presence of stable cooperation via communication outcomes, allowing us to understand the sophistication or depth of mental coordination, involved in an individual’s social perception and reasoning. Almost all current scientific studies of ToM take a spectatorial approach, relying on observation followed by evaluation (e.g., the Sally-Anne Task). However given evidence that social cognition fundamentally shifts during valuationally significant social encounters with others, this study adopts a second-person approach. Each participant’s actions under dynamic uncertainty influence the joint reward probabilities of both, favoring cooperation and coordination. Only Teachers have knowledge of the correct action-reward contingencies, while Learners must ascertain the Teacher’s directive and correctly adjust their actions to obtain the optimal reward. The complexity of cooperative behaviors cannot be captured with simple reinforcement learning models, however a similarity in valuation exists, probing further investigation

Computational investigations of structure probing experiments for RNA structure prediction

Ribonucleic acids (RNA) transcripts, and in particular non-coding RNAs, play fundamental roles in cellular metabolism, as they are involved in protein synthesis, catalysis, and regulation of gene expression. In some cases, an RNA\u2019s biological function is mostly dependent on a specific active conformation, making the identification of this single stable structure crucial to identify the role of the RNA and the relationships between its mutations and diseases. On the other hand, RNAs are often found in a dynamic equilibrium of multiple interconverting conformations, that is necessary to regulate their functional activity. In these cases it becomes fundamental to gain knowledge of RNA\u2019s structural ensembles, in order to fully determine its mechanism of action. The current structure determination techniques, both for single-state models such as X-ray crystallography, and for multi-state models such as nuclear magnetic resonance and single-molecule methods, despite proving accurate and reliable in many cases, are extremely slow and costly. In contrast, chemical probing is a class of experimental techniques that provide structural information at single-nucleotide resolution at significantly lower costs in terms of time and required infrastructures. In particular, selective 2\u2032 hydroxyl acylation analyzed via primer extension (SHAPE) has proved a valid chemical mapping technique to probe RNA structure even in vivo. This thesis reports a systematic investi- gation of chemical probing experiments based on two different approaches. The first approach, presented in Chapter 2, relies on machine-learning techniques to optimize a model for mapping experimental data into structural information. The model relies also on co-evolutionary data, in the form of direct coupling analysis (DCA) couplings. The inclusion of this kind of data is chosen in the same spirit of reducing the costs of structure probing, as co-evolutionary analysis relies only on sequencing techniques. The resulting model is proposed as a candidate standard tool for prediction of RNA secondary structure, and some insight in the mechanism of chemical probing is gained by interpreting back its features. Importantly, this work has been developed in the per- spective of building a framework for future refinement and improvement. In this spirit, all the used data and scripts are available at https://github.com/bussilab/shape-dca-data, and the model can be easily retrained and adapted to incorporate arbitrary experimental informa- tion. As the interpretation of the model features suggests the possible emergence of cooperative effects involving RNA nucleotides interacting with SHAPE reagents, a second approach based on Molecular Dynamics simulations is proposed to investigate this hypothesis. The results, along with an originally developed methodology to analyse Molecular Dynamics simulations at variable number of particles, are presented in Chapter 3