Computational Intelligence for Life Sciences

Computational Intelligence (CI) is a computer science discipline encompassing the theory, design, development and application of biologically and linguistically derived computational paradigms. Traditionally, the main elements of CI are Evolutionary Computation, Swarm Intelligence, Fuzzy Logic, and Neural Networks. CI aims at proposing new algorithms able to solve complex computational problems by taking inspiration from natural phenomena. In an intriguing turn of events, these nature-inspired methods have been widely adopted to investigate a plethora of problems related to nature itself. In this paper we present a variety of CI methods applied to three problems in life sciences, highlighting their effectiveness: we describe how protein folding can be faced by exploiting Genetic Programming, the inference of haplotypes can be tackled using Genetic Algorithms, and the estimation of biochemical kinetic parameters can be performed by means of Swarm Intelligence. We show that CI methods can generate very high quality solutions, providing a sound methodology to solve complex optimization problems in life sciences

Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design

© 2019 Elsevier B.V. Computational Intelligence methods, which include Evolutionary Computation and Swarm Intelligence, can efficiently and effectively identify optimal solutions to complex optimization problems by exploiting the cooperative and competitive interplay among their individuals. The exploration and exploitation capabilities of these meta-heuristics are typically assessed by considering well-known suites of benchmark functions, specifically designed for numerical global optimization purposes. However, their performances could drastically change in the case of real-world optimization problems. In this paper, we investigate this issue by considering the Parameter Estimation (PE) of biochemical systems, a common computational problem in the field of Systems Biology. In order to evaluate the effectiveness of various meta-heuristics in solving the PE problem, we compare their performance by considering a set of benchmark functions and a set of synthetic biochemical models characterized by a search space with an increasing number of dimensions. Our results show that some state-of-the-art optimization methods – able to largely outperform the other meta-heuristics on benchmark functions – are characterized by considerably poor performances when applied to the PE problem. We also show that a limiting factor of these optimization methods concerns the representation of the solutions: indeed, by means of a simple semantic transformation, it is possible to turn these algorithms into competitive alternatives. We corroborate this finding by performing the PE of a model of metabolic pathways in red blood cells. Overall, in this work we state that classic benchmark functions cannot be fully representative of all the features that make real-world optimization problems hard to solve. This is the case, in particular, of the PE of biochemical systems. We also show that optimization problems must be carefully analyzed to select an appropriate representation, in order to actually obtain the performance promised by benchmark results

Enhanced segment particle swarm optimization for large-scale kinetic parameter estimation of escherichia coli network model

The development of a large-scale metabolic model of Escherichia coli (E. coli) is very crucial to identify the potential solution of industrially viable productions. However, the large-scale kinetic parameters estimation using optimization algorithms is still not applied to the main metabolic pathway of the E. coli model, and they’re a lack of accuracy result been reported for current parameters estimation using this approach. Thus, this research aimed to estimate large-scale kinetic parameters of the main metabolic pathway of the E. coli model. In this regard, a Local Sensitivity Analysis, Segment Particle Swarm Optimization (Se-PSO) algorithm, and the Enhanced Segment Particle Swarm Optimization (ESe-PSO) algorithm was adapted and proposed to estimate the parameters. Initially, PSO algorithm was adapted to find the globally optimal result based on unorganized particle movement in the search space toward the optimal solution. This development then introduces the Se-PSO algorithm in which the particles are segmented to find a local optimal solution at the beginning and later sought by the PSO algorithm. Additionally, the study proposed an Enhance Se-PSO algorithm to improve the linear value of inertia weigh

A comparative analysis of algorithms for satellite operations scheduling

Scheduling is employed in everyday life, ranging from meetings to manufacturing and operations among other activities. One instance of scheduling in a complex real-life setting is space mission operations scheduling, i.e. instructing a satellite to perform fitting tasks during predefined time periods with a varied frequency to achieve its mission goals. Mission operations scheduling is pivotal to the success of any space mission, choreographing every task carefully, accounting for technological and environmental limitations and constraints along with mission goals.;It remains standard practice to this day, to generate operations schedules manually ,i.e. to collect requirements from individual stakeholders, collate them into a timeline, compare against feasibility and available satellite resources, and find potential conflicts. Conflict resolution is done by hand, checked by a simulator and uplinked to the satellite weekly. This process is time consuming, bears risks and can be considered sub-optimal.;A pertinent question arises: can we automate the process of satellite mission operations scheduling? And if we can, what method should be used to generate the schedules? In an attempt to address this question, a comparison of algorithms was deemed suitable in order to explore their suitability for this particular application.;The problem of mission operations scheduling was initially studied through literature and numerous interviews with experts. A framework was developed to approximate a generic Low Earth Orbit satellite, its environment and its mission requirements. Optimisation algorithms were chosen from different categories such as single-point stochastic without memory (Simulated Annealing, Random Search), multi-point stochastic with memory (Genetic Algorithm, Ant Colony System, Differential Evolution) and were run both with and without Local Search.;The aforementioned algorithmic set was initially tuned using a single 89-minute Low Earth Orbit of a scientific mission to Mars. It was then applied to scheduling operations during one high altitude Low Earth Orbit (2.4hrs) of an experimental mission.;It was then applied to a realistic test-case inspired by the European Space Agency PROBA-2 mission, comprising a 1 day schedule and subsequently a 7 day schedule - equal to a Short Term Plan as defined by the European Space Agency.;The schedule fitness - corresponding to the Hamming distance between mission requirements and generated schedule - are presented along with the execution time of each run. Algorithmic performance is discussed and put at the disposal of mission operations experts for consideration.Scheduling is employed in everyday life, ranging from meetings to manufacturing and operations among other activities. One instance of scheduling in a complex real-life setting is space mission operations scheduling, i.e. instructing a satellite to perform fitting tasks during predefined time periods with a varied frequency to achieve its mission goals. Mission operations scheduling is pivotal to the success of any space mission, choreographing every task carefully, accounting for technological and environmental limitations and constraints along with mission goals.;It remains standard practice to this day, to generate operations schedules manually ,i.e. to collect requirements from individual stakeholders, collate them into a timeline, compare against feasibility and available satellite resources, and find potential conflicts. Conflict resolution is done by hand, checked by a simulator and uplinked to the satellite weekly. This process is time consuming, bears risks and can be considered sub-optimal.;A pertinent question arises: can we automate the process of satellite mission operations scheduling? And if we can, what method should be used to generate the schedules? In an attempt to address this question, a comparison of algorithms was deemed suitable in order to explore their suitability for this particular application.;The problem of mission operations scheduling was initially studied through literature and numerous interviews with experts. A framework was developed to approximate a generic Low Earth Orbit satellite, its environment and its mission requirements. Optimisation algorithms were chosen from different categories such as single-point stochastic without memory (Simulated Annealing, Random Search), multi-point stochastic with memory (Genetic Algorithm, Ant Colony System, Differential Evolution) and were run both with and without Local Search.;The aforementioned algorithmic set was initially tuned using a single 89-minute Low Earth Orbit of a scientific mission to Mars. It was then applied to scheduling operations during one high altitude Low Earth Orbit (2.4hrs) of an experimental mission.;It was then applied to a realistic test-case inspired by the European Space Agency PROBA-2 mission, comprising a 1 day schedule and subsequently a 7 day schedule - equal to a Short Term Plan as defined by the European Space Agency.;The schedule fitness - corresponding to the Hamming distance between mission requirements and generated schedule - are presented along with the execution time of each run. Algorithmic performance is discussed and put at the disposal of mission operations experts for consideration

Architectures and GPU-Based Parallelization for Online Bayesian Computational Statistics and Dynamic Modeling

Recent work demonstrates that coupling Bayesian computational statistics methods with dynamic models can facilitate the analysis of complex systems associated with diverse time series, including those involving social and behavioural dynamics. Particle Markov Chain Monte Carlo (PMCMC) methods constitute a particularly powerful class of Bayesian methods combining aspects of batch Markov Chain Monte Carlo (MCMC) and the sequential Monte Carlo method of Particle Filtering (PF). PMCMC can flexibly combine theory-capturing dynamic models with diverse empirical data. Online machine learning is a subcategory of machine learning algorithms characterized by sequential, incremental execution as new data arrives, which can give updated results and predictions with growing sequences of available incoming data. While many machine learning and statistical methods are adapted to online algorithms, PMCMC is one example of the many methods whose compatibility with and adaption to online learning remains unclear. In this thesis, I proposed a data-streaming solution supporting PF and PMCMC methods with dynamic epidemiological models and demonstrated several successful applications. By constructing an automated, easy-to-use streaming system, analytic applications and simulation models gain access to arriving real-time data to shorten the time gap between data and resulting model-supported insight. The well-defined architecture design emerging from the thesis would substantially expand traditional simulation models' potential by allowing such models to be offered as continually updated services. Contingent on sufficiently fast execution time, simulation models within this framework can consume the incoming empirical data in real-time and generate informative predictions on an ongoing basis as new data points arrive. In a second line of work, I investigated the platform's flexibility and capability by extending this system to support the use of a powerful class of PMCMC algorithms with dynamic models while ameliorating such algorithms' traditionally stiff performance limitations. Specifically, this work designed and implemented a GPU-enabled parallel version of a PMCMC method with dynamic simulation models. The resulting codebase readily has enabled researchers to adapt their models to the state-of-art statistical inference methods, and ensure that the computation-heavy PMCMC method can perform significant sampling between the successive arrival of each new data point. Investigating this method's impact with several realistic PMCMC application examples showed that GPU-based acceleration allows for up to 160x speedup compared to a corresponding CPU-based version not exploiting parallelism. The GPU accelerated PMCMC and the streaming processing system can complement each other, jointly providing researchers with a powerful toolset to greatly accelerate learning and securing additional insight from the high-velocity data increasingly prevalent within social and behavioural spheres. The design philosophy applied supported a platform with broad generalizability and potential for ready future extensions. The thesis discusses common barriers and difficulties in designing and implementing such systems and offers solutions to solve or mitigate them

A Review of Resonant Converter Control Techniques and The Performances

paper first discusses each control technique and then gives experimental results and/or performance to highlights their merits. The resonant converter used as a case study is not specified to just single topology instead it used few topologies such as series-parallel resonant converter (SPRC), LCC resonant converter and parallel resonant converter (PRC). On the other hand, the control techniques presented in this paper are self-sustained phase shift modulation (SSPSM) control, self-oscillating power factor control, magnetic control and the H-∞ robust control technique

A Review of Resonant Converter Control Techniques and The Performances

paper first discusses each control technique and then gives experimental results and/or performance to highlights their merits. The resonant converter used as a case study is not specified to just single topology instead it used few topologies such as series-parallel resonant converter (SPRC), LCC resonant converter and parallel resonant converter (PRC). On the other hand, the control techniques presented in this paper are self-sustained phase shift modulation (SSPSM) control, self-oscillating power factor control, magnetic control and the H-∞ robust control technique

OBSERVER-BASED-CONTROLLER FOR INVERTED PENDULUM MODEL

This paper presents a state space control technique for inverted pendulum system. The system is a common classical control problem that has been widely used to test multiple control algorithms because of its nonlinear and unstable behavior. Full state feedback based on pole placement and optimal control is applied to the inverted pendulum system to achieve desired design specification which are 4 seconds settling time and 5% overshoot. The simulation and optimization of the full state feedback controller based on pole placement and optimal control techniques as well as the performance comparison between these techniques is described comprehensively. The comparison is made to choose the most suitable technique for the system that have the best trade-off between settling time and overshoot. Besides that, the observer design is analyzed to see the effect of pole location and noise present in the system

State-Feedback Controller Based on Pole Placement Technique for Inverted Pendulum System

This paper presents a state space control technique for inverted pendulum system using simulation and real experiment via MATLAB/SIMULINK software. The inverted pendulum is difficult system to control in the field of control engineering. It is also one of the most important classical control system problems because of its nonlinear characteristics and unstable system. It has three main problems that always appear in control application which are nonlinear system, unstable and non-minimumbehavior phase system. This project will apply state feedback controller based on pole placement technique which is capable in stabilizing the practical based inverted pendulum at vertical position. Desired design specifications which are 4 seconds settling time and 5 % overshoot is needed to apply in full state feedback controller based on pole placement technique. First of all, the mathematical model of an inverted pendulum system is derived to obtain the state space representation of the system. Then, the design phase of the State-Feedback Controller can be conducted after linearization technique is performed to the nonlinear equation with the aid of mathematical aided software such as Mathcad. After that, the design is simulated using MATLAB/Simulink software. The controller design of the inverted pendulum system is verified using simulation and experiment test. Finally the controller design is compared with PID controller for benchmarking purpose