Surrogate-Assisted Artificial Immune Systems for Expensive Optimization Problems

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BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Multi-and many-objective optimization: present and future in de novo drug design

de novo Drug Design (dnDD) aims to create new molecules that satisfy multiple conflicting objectives. Since several desired properties can be considered in the optimization process, dnDD is naturally categorized as a many-objective optimization problem (ManyOOP), where more than three objectives must be simultaneously optimized. However, a large number of objectives typically pose several challenges that affect the choice and the design of optimization methodologies. Herein, we cover the application of multi- and many-objective optimization methods, particularly those based on Evolutionary Computation and Machine Learning techniques, to enlighten their potential application in dnDD. Additionally, we comprehensively analyze how molecular properties used in the optimization process are applied as either objectives or constraints to the problem. Finally, we discuss future research in many-objective optimization for dnDD, highlighting two important possible impacts: i) its integration with the development of multi-target approaches to accelerate the discovery of innovative and more efficacious drug therapies and ii) its role as a catalyst for new developments in more fundamental and general methodological frameworks in the field

The Use of Agent-Based Simulation to Discover Extreme Cases in Immune-Interactions with Early-Stage Cancer Scenarios

Early-stage cancer and its interactions with the immune system are still not fully understood. In order to better understand these processes, researchers employ different methods. Simulation and in particular, agent-based simu-lation (ABS) have been found useful tools for understand-ing it (Look et al., 1981; Castiglione et al., 1999, 2001; Bonabeau, 2002; Figueredo and Aickelin, 2011; Figueredo et al., 2013a,b). In a previous study (Figueredo et al., 2013b) we have built an ABS model to study the interplay of immune cells and early-stage cancer. The model considers interactions be-tween tumour cells and immune effector cells, as well as the immune-stimulatory and suppressive cytokines IL-2 and TGF-. IL-2 molecules mediate the immune response to-wards tumour cells. They interfere on the proliferation o