Simone Spolaor

Bio: Simone Spolaor is an academic researcher from University of Milano-Bicocca. The author has contributed to research in topics: Computational intelligence & Particle swarm optimization. The author has an hindex of 8, co-authored 35 publications receiving 220 citations. Previous affiliations of Simone Spolaor include University of Milan.

Computational Intelligence for Parameter Estimation of Biochemical Systems

Abstract: In the field of Systems Biology, simulating the dynamics of biochemical models represents one of the most effective methodologies to understand the functioning of cellular processes in normal or altered conditions. However, the lack of kinetic rates, necessary to perform accurate simulations, strongly limits the scope of these analyses. Parameter Estimation (PE), which consists in identifying a proper model parameterization, is a non-linear, non-convex and multi-modal optimization problem, typically tackled by means of Computational Intelligence techniques, such as Evolutionary Computation and Swarm Intelligence. In this work, we perform a thorough investigation of the most widespread methods for PE-namely, Artificial Bee Colony (ABC), Covariance Matrix Adaptation Evolution Strategy (CMA-ES), Differential Evolution (DE), Estimation of Distribution Algorithm (EDA), Genetic Algorithms (GAs), Particle Swarm Optimization (PSO), and Fuzzy Self-Tuning PSO (FST-PSO)-comparing their performances on a set of synthetic (yet realistic) biochemical models of increasing size and complexity. Our results show that a variant of the settings-free FST-PSO algorithm can consistently outperform all other methods; ABC and GAs represent the most performing alternatives, while methods based on multivariate normal distributions (e.g., CMA-ES, EDA) struggle to keep pace with the other approaches. Index Terms-Computational Intelligence, Systems Biology, Parameter Estimation, Evolutionary Computation, Swarm Intelligence

GenHap: a novel computational method based on genetic algorithms for haplotype assembly

Abstract: In order to fully characterize the genome of an individual, the reconstruction of the two distinct copies of each chromosome, called haplotypes, is essential. The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. Indeed, the knowledge of complete haplotypes is generally more informative than analyzing single SNPs and plays a fundamental role in many medical applications. To reconstruct the two haplotypes, we addressed the weighted Minimum Error Correction (wMEC) problem, which is a successful approach for haplotype assembly. This NP-hard problem consists in computing the two haplotypes that partition the sequencing reads into two disjoint sub-sets, with the least number of corrections to the SNP values. To this aim, we propose here GenHap, a novel computational method for haplotype assembly based on Genetic Algorithms, yielding optimal solutions by means of a global search process. In order to evaluate the effectiveness of our approach, we run GenHap on two synthetic (yet realistic) datasets, based on the Roche/454 and PacBio RS II sequencing technologies. We compared the performance of GenHap against HapCol, an efficient state-of-the-art algorithm for haplotype phasing. Our results show that GenHap always obtains high accuracy solutions (in terms of haplotype error rate), and is up to 4× faster than HapCol in the case of Roche/454 instances and up to 20× faster when compared on the PacBio RS II dataset. Finally, we assessed the performance of GenHap on two different real datasets. Future-generation sequencing technologies, producing longer reads with higher coverage, can highly benefit from GenHap, thanks to its capability of efficiently solving large instances of the haplotype assembly problem. Moreover, the optimization approach proposed in GenHap can be extended to the study of allele-specific genomic features, such as expression, methylation and chromatin conformation, by exploiting multi-objective optimization techniques. The source code and the full documentation are available at the following GitHub repository: https://github.com/andrea-tango/GenHap .

Simpful: A user-friendly python library for fuzzy logic

Abstract: Many researchers have used fuzzy set theory and fuzzy logic in a variety of applications related to computer science and engineering, given the capability of fuzzy inference systems to deal with uncertainty, represent vague concepts, and connect human language to numerical data. In this work we propose Simpful, a general-purpose and user-friendly Python library designed to facilitate the definition, analysis, and interpretation of fuzzy inference systems. Simpful provides a lightweight Application Programming Interface that allows to intuitively define fuzzy sets and fuzzy rules, and to perform fuzzy inference. Worthy of note, in Simpful the fuzzy rules are specified by means of strings of text written in natural language. We provide here some practical examples to show that Simpful represents a valuable addition to the open-source software that supports fuzzy reasoning.

pyFUME: a Python Package for Fuzzy Model Estimation

Abstract: Living in the era of "data deluge" demands for an increase in the application and development of machine learning methods, both in basic and applied research. Among these methods, in the last decades fuzzy inference systems carved out their own niche as (light) grey box models, which are considered more interpretable and transparent than other commonly employed methods, such as artificial neural networks. Although commercially distributed alternatives are available, software able to assist practitioners and researchers in each step of the estimation of a fuzzy model from data are still limited in scope and applicability. This is especially true when looking at software developed in Python, a programming language that quickly gained popularity among data scientists and it is often considered their language of choice. To fill this gap, we introduce pyFUME, a Python library for automatically estimating fuzzy models from data. pyFUME contains a set of classes and methods to estimate the antecedent sets and the consequent parameters of a Takagi-Sugeno fuzzy model from data, and then create an executable fuzzy model exploiting the Simpful library. pyFUME can be beneficial to practitioners, thanks to its pre-implemented and user-friendly pipelines, but also to researchers that want to fine-tune each step of the estimation process.

Using Mpi Portable Parallel Programming With The Message Passing Interface

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[IEEE IEEE International Conference on Networking, Sensing and Control, 2004 - Taipei, Taiwan (March 21-23, 2004)] IEEE International Conference on Networking, Sensing and Control, 2004 - Particle swarm optimization algorithm and its application to clustering analysis

Abstract: Clustering analysis is applied generally to Pattern Recognition, Color Quantization and Image Classification. It can help the user to distinguish the structure of data and simplify the complexity of data from mass information. The user can understand the implied information behind extracting these data. In real case, the distribution of information can be any size and shape. A particle swarm optimization algorithm-based technique, called PSO-clustering, is proposed in this article. We adopt the particle swarm optimization to search the cluster center in the arbitrary data set automatically. PSO can search the best solution from the probability option of the Social-only model and Cognition-only model[1, 2, 3J. This method is quite simple and valid and it can avoid the minimum local value. Finally, the effectiveness of the PSO-clustering is demonstrated on four artificial data sets.

Fuzzy Self-Tuning PSO: A settings-free algorithm for global optimization

Abstract: Among the existing global optimization algorithms, Particle Swarm Optimization (PSO) is one of the most effective methods for non-linear and complex high-dimensional problems. Since PSO performance strongly depends on the choice of its settings (i.e., inertia, cognitive and social factors, minimum and maximum velocity), Fuzzy Logic (FL) was previously exploited to select these values. So far, FL-based implementations of PSO aimed at the calculation of a unique settings for the whole swarm. In this work we propose a novel self-tuning algorithm—called Fuzzy Self-Tuning PSO (FST-PSO)—which exploits FL to calculate the inertia, cognitive and social factor, minimum and maximum velocity independently for each particle, thus realizing a complete settings-free version of PSO. The novelty and strength of FST-PSO lie in the fact that it does not require any expertise in PSO functioning, since the behavior of every particle is automatically and dynamically adjusted during the optimization. We compare the performance of FST-PSO with standard PSO, Proactive Particles in Swarm Optimization, Artificial Bee Colony, Covariance Matrix Adaptation Evolution Strategy, Differential Evolution and Genetic Algorithms. We empirically show that FST-PSO can basically outperform all tested algorithms with respect to the convergence speed and is competitive concerning the best solutions found, noticeably with a reduced computational effort.

Numerical Optimization Of Computer Models

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Automated basin delineation from digital elevation models using mathermatical morphology

Abstract: Abstract Basin delineation is a major preliminary of hydrologic modeling and watershed management. An efficient method to delineate topographic basins from digital elevation models is presented. It is based upon mathematical morphology and it consists of two major steps. First, remove all the pits within the model by using an original morphological mapping, and second, delineate topographic basins by using morphological thinnings with specific structuring elements. The results are consistent with real terrain features. In a more general way, the proposed methodology illustrates the segmentation approach provided by the morphological watershed mapping.