Marco Salvatore Nobile

Marco Salvatore Nobile
Università Ca' Foscari Venezia | UNIVE · Department of Environmental Sciences, Informatics and Statistics

PhD in Computer Science

About

108
Publications
23,103
Reads
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1,148
Citations
Introduction
I am Assistant Professor in Artificial Intelligence and Data Analytics at TU/e. My research focuses on the development of novel Computational Intelligence methods (evolutionary computation, swarm intelligence, fuzzy logic, machine learning) applied to complex problems in computational and systems biology. Due to the massive computational requirements of such methods, I also constantly work on the acceleration of my algorithms using high performance architectures, mainly relying on the GPGPU computing paradigm to leverage the huge parallel computational power of modern video cards.
Additional affiliations
August 2019 - present
Eindhoven University of Technology
Position
  • Professor (Assistant)
Education
January 2012 - February 2015
Università degli Studi di Milano-Bicocca
Field of study
  • Computer Science

Publications

Publications (108)
Article
Full-text available
Motivation: The elucidation of dysfunctional cellular processes that can induce the onset of a disease is a challenging issue from both experimental and computational perspectives. Here we introduce a novel computational method based on the coupling between fuzzy logic modeling and a global optimization algorithm, whose aims are to (1) predict the...
Article
Full-text available
The investigation of cell proliferation can provide useful insights for the comprehension of cancer progression, resistance to chemotherapy and relapse. To this aim, computational methods and experimental measurements based on in vivo label-retaining assays can be coupled to explore the dynamic behavior of tumoral cells. ProCell is a software tha...
Preprint
Full-text available
Mathematical models of biochemical networks can largely facilitate the comprehension of the mechanisms at the basis of cellular processes, as well as the formulation of hypotheses that can be tested by means of targeted laboratory experiments. However, two issues might hamper the achievement of fruitful outcomes. On the one hand, detailed mechanist...
Article
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 previou...
Conference Paper
Abstract—In this paper we propose a fuzzy logic-based approach to analyze NHS public administrative data related to pre- and post-pandemic claims filed by patients, analyzing the legal and ethical issues connected to the use of Artificial Intelligence systems, including our own, to take critical decisions having a significant impact on patients, su...
Article
Full-text available
The parameter estimation (PE) of biochemical reactions is one of the most challenging tasks in systems biology given the pivotal role of these kinetic constants in driving the behavior of biochemical systems. PE is a non-convex, multi-modal, and non-separable optimization problem with an unknown fitness landscape; moreover, the quantities of the bi...
Article
Full-text available
Calcium homeostasis and signaling processes in Saccharomyces cerevisiae, as well as in any eukaryotic organism, depend on various transporters and channels located on both the plasma and intracellular membranes. The activity of these proteins is regulated by a number of feedback mechanisms that act through the calmodulin-calcineurin pathway. When e...
Article
Full-text available
Several software tools for the simulation and analysis of biochemical reaction networks have been developed in the last decades; however, assessing and comparing their computational performance in executing the typical tasks of computational systems biology can be limited by the lack of a standardized benchmarking approach. To overcome these limita...
Article
In the crowded environment of bio-inspired population-based metaheuristics, the Salp Swarm Optimization (SSO) algorithm recently appeared and immediately gained a lot of momentum. Inspired by the peculiar spatial arrangement of salp colonies, which are displaced in long chains following a leader, this algorithm seems to provide an interesting optim...
Article
Full-text available
Mathematical models of biochemical networks can largely facilitate the comprehension of the mechanisms at the basis of cellular processes, as well as the formulation of hypotheses that can be tested by means of targeted laboratory experiments. However, two issues might hamper the achievement of fruitful outcomes. On the one hand, detailed mechanist...
Article
Full-text available
Image texture extraction and analysis are fundamental steps in computer vision. In particular, considering the biomedical field, quantitative imaging methods are increasingly gaining importance because they convey scientifically and clinically relevant information for prediction, prognosis, and treatment response assessment. In this context, radiom...
Preprint
Full-text available
Several software tools for the simulation and analysis of biochemical reaction networks have been developed in the last decades; however, assessing and comparing their computational performance in executing the typical tasks of Computational Systems Biology can be limited by the lack of a standardized benchmarking approach. To overcome these limita...
Article
Full-text available
Bayesian Networks have been widely used in the last decades in many _elds, to describe statistical dependencies among random variables. In general, learning the structure of such models is a problem with considerable theoretical interest that poses many challenges. On the one hand, it is a well-known NP-complete problem, practically hardened by the...
Article
Funding Acknowledgements Type of funding sources: None. Introduction The extent of ischemic scar detected by Cardiac Magnetic Resonance (CMR) with late gadolinium enhancement (LGE) is linked with long-term prognosis, but scar quantification is time-consuming. Deep Learning (DL) approaches appear promising in CMR segmentation. Purpose: To train and...
Preprint
Full-text available
In the crowded environment of bio-inspired population-based meta-heuristics, the Salp Swarm Optimization (SSO) algorithm recently appeared and immediately gained a lot of momentum. Inspired by the peculiar spatial arrangement of salp colonies, which are displaced in long chains following a leader, this algorithm seems to provide interesting optimiz...
Article
Full-text available
Background: Tremor severity assessment is an important step for the diagnosis and treatment decision-making of essential tremor (ET) patients. Traditionally, tremor severity is assessed by using questionnaires (e.g., ETRS and QUEST surveys). In this work we assume the possibility of assessing tremor severity using sensor data and computerized anal...
Article
Full-text available
Background Genome-wide reconstructions of metabolism opened the way to thorough investigations of cell metabolism for health care and industrial purposes. However, the predictions offered by Flux Balance Analysis (FBA) can be strongly affected by the choice of flux boundaries, with particular regard to the flux of reactions that sink nutrients into...
Article
Full-text available
Self-assembling processes are ubiquitous phenomena that drive the organization and the hierarchical formation of complex molecular systems. The investigation of assembling dynamics, emerging from the interactions among biomolecules like amino-acids and polypeptides, is fundamental to determine how a mixture of simple objects can yield a complex str...
Article
Full-text available
Combination therapies proved to be a valuable strategy in the fight against cancer, thanks to their increased efficacy in inducing tumor cell death and in reducing tumor growth, metastatic potential, and the risk of developing drug resistance. The identification of effective combinations of drug targets generally relies on costly and time consuming...
Article
Full-text available
Ras oncoproteins play a crucial role in the onset, maintenance, and progression of the most common and deadly human cancers. Despite extensive research efforts, only a few mutant-specific Ras inhibitors have been reported. We show that cmp4-previously identified as a water-soluble Ras inhibitor-targets multiple steps in the activation and downstrea...
Chapter
Acute myeloid leukemia (AML) is a highly frequent hematological malignancy, characterized by clinical and biological diversity, along with high relapse and mortality rates. The inherent functional and genetic intra-tumor heterogeneity in AML is thought to play an important role in disease recurrence and resistance to chemotherapy. Patient-derived x...
Article
Full-text available
Advances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, na...
Article
Several mathematical formalisms can be exploited to model complex systems, in order to capture different features of their dynamic behavior and leverage any available quantitative or qualitative data. Correspondingly, either quantitative models or qualitative models can be defined; bridging the gap between these two worlds would allow us to simulta...
Preprint
Full-text available
Advances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, na...
Chapter
Fuzzy inference systems (FIS) gained popularity and found application in several fields of science over the last years, because they are more transparent and interpretable than other common (black-box) machine learning approaches. However, transparency is not automatically achieved when FIS are estimated from data, thus researchers are actively inv...
Article
Full-text available
Surfing in rough waters is not always as fun as wave riding the “big one”. Similarly, in optimization problems, fitness landscapes with a huge number of local optima make the search for the global optimum a hard and generally annoying game. Computational Intelligence optimization metaheuristics use a set of individuals that “surf” across the fitnes...
Chapter
Mathematical modeling and computational analyses are essential tools to understand and gain novel insights on the functioning of complex biochemical systems. In the specific case of metabolic reaction networks, which are regulated by many other intracellular processes, various challenging problems hinder the definition of compact and fully calibrat...
Chapter
In the latter years, detailed genome-wide metabolic models have been proposed, paving the way to thorough investigations of the connection between genotype and phenotype in human cells. Nevertheless, classic modeling and dynamic simulation approaches—based either on differential equations integration, Markov chains or hybrid methods—are still unfea...
Chapter
Prostate cancer is the most common cancer among US men. However, prostate imaging is still challenging despite the advances in multi-parametric magnetic resonance imaging (MRI), which provides both morphologic and functional information pertaining to the pathological regions. Along with whole prostate gland segmentation, distinguishing between the...
Article
Full-text available
Ordinary differential equations (ODEs) are a widespread formalism for the mathematical modeling of natural and engineering systems, whose analysis is generally performed by means of numerical integration methods. However, real-world models are often characterized by stiffness, a circumstance that can lead to prohibitive execution times. In such cas...
Chapter
Image texture extraction and analysis are fundamental steps in Computer Vision. In particular, considering the biomedical field, quantitative imaging methods are increasingly gaining importance since they convey scientifically and clinically relevant information for prediction, prognosis, and treatment response assessment. In this context, radiomic...
Article
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 typ...
Article
Full-text available
Background 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 Si...
Preprint
Full-text available
Prostate cancer is the most common malignant tumors in men but prostate Magnetic Resonance Imaging (MRI) analysis remains challenging. Besides whole prostate gland segmentation, the capability to differentiate between the blurry boundary of the Central Gland (CG) and Peripheral Zone (PZ) can lead to differential diagnosis, since tumor's frequency a...
Article
Background and objectives: Image segmentation represents one of the most challenging issues in medical image analysis to distinguish among different adjacent tissues in a body part. In this context, appropriate image pre-processing tools can improve the result accuracy achieved by computer-assisted segmentation methods. Taking into consideration i...
Preprint
Prostate cancer is the most common cancer among US men. However, prostate imaging is still challenging despite the advances in multi-parametric Magnetic Resonance Imaging (MRI), which provides both morphologic and functional information pertaining to the pathological regions. Along with whole prostate gland segmentation, distinguishing between the...
Chapter
Full-text available
The faithful reproduction and accurate prediction of the phenotypes and emergent behaviors of complex cellular systems are among the most challenging goals in Systems Biology. Although mathematical models that describe the interactions among all biochemical processes in a cell are theoretically feasible, their simulation is generally hard because o...
Article
Full-text available
Motivation Acute myeloid leukemia (AML) is one of the most common hematological malignancies, characterized by high relapse and mortality rates. The inherent intra-tumor heterogeneity in AML is thought to play an important role in disease recurrence and resistance to chemotherapy. Although experimental protocols for cell proliferation studies are w...
Chapter
The computational analysis of complex biological systems can be hindered by two main factors. First, modeling the system so that it can be easily understood and analyzed by non-expert users is not always possible, especially when dealing with systems of Ordinary Differential Equations. Second, when the system is composed of hundreds or thousands of...
Chapter
The reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. In this work, we outline the state-of-the-art on HA approaches and present an in-depth analy...
Preprint
Full-text available
The process of inferring a full haplotype of a cell is known as haplotyping, which consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. In this work, we propose a novel computational method for haplotype assembly based on Genetic Algorithms (GAs), named GenHap. Our approach could effic...
Article
Medical imaging systems often require the application of image enhancement techniques to help physicians in anomaly/abnormality detection and diagnosis, as well as to improve the quality of images that undergo automated image processing. In this work we introduce MedGA, a novel image enhancement method based on Genetic Algorithms that is able to im...
Article
Full-text available
Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is further complicated by many theoretical issues, such as the I-equivalence among different structures. In this work, we focus on a specific subclass of BNs, named Suppes-Bayes Causal Networks (SBCNs), which include specific structural constraints based on Suppes’ probabili...
Conference Paper
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 E...
Preprint
Bayesian Networks have been widely used in the last decades in many fields, to describe statistical dependencies among random variables. In general, learning the structure of such models is a problem with considerable theoretical interest that still poses many challenges. On the one hand, this is a well-known NP-complete problem, which is practical...