Blog

Simone Spolaor recipient of EUSFLAT 2020 best PhD thesis award

My former PhD student, Simone Spolaor, was awarded by EUSFLAT for the best 2020 PhD thesis on fuzzy logic. Prof. Daniela Besozzi (Simone’s main advisor) and me are incredibly proud of this achievement. Simone’s thesis, titled “Fuzzy Logic for the modeling and simulation of complex systems”, is an investigation about moving back and forth from …

New paper on PLOS Computational Biology

GPUs are basically multi-core co-processors performing vectorial computation applying the so-called SIMD paradigm, i.e., the very same computation (implemented as a kernel) is performed across different data. The computation can be, for instance, a biochemical simulation. In this case, the simulation is defined coarse-grained and it is the case of cupSODA or cuTauLeaping. However, the …

New paper on Scientific Reports

Self-assembling peptides can be useful for clinical applications, for instance as scaffolds based on beta-sheets motifs. The dynamic evolution and self-assemly of peptide systems can be investigated in silico by using molecular dynamics. In particular, coarse-grained simulation exploiting MARTINI force fields can strongly reduce the overall running time and still provide useful information. In a …

New paper: unsupervised learning for medical images analysis

We recently published a new paper on Journal of Supercomputing. The article focuses on an approach that combines automatic feature extraction and unsupervised learning for the analysis of medical images. The idea is to extract (long) vectors of Haralick features for each pixel, and use that information to train a Self-Organizing Map: similar pixels will …

PhD position on explainable AI systems for biomedical decision support

Some weeks ago I have been awarded with an EAISI Startup Package, a grant provided by the Eindhoven Artificial Intelligence Systems Institute funding a PhD student position. The project that was funded — and that will be the topic of the PhD student — revolves around the data-driven development of decision support systems in biomedical …

New protocol published

The new book “Leukemia Stem Cells: Methods and Protocols” — part of Springer’s Methods in Molecular Biology book series (volume 2185, edited by César Cobaleda and Isidro Sánchez-García) — contains a chapter describing the experimental and computational protocol that we developed for the investigation of cell proliferation in human Acute Myeloid Leukemia xenografts. The protocol …

Simpful’s paper accepted

Simpful is now mature enough to have an official paper associated to the project. Our manuscript — describing both Simpful functionalities and inner machinery — was accepted for publication on the International Journal of Computational Intelligence Systems. In the meanwhile, the development of Simpful continues. We will introduce support for additional reasoning systems and, in …

Simpful v 2.1.5

We recently published the Release 2.1.5 of Simpful, our python tool for fuzzy modeling and reasoning. The new release supports the following improvements: Mamdani reasoning (which implies the support for output fuzzy sets); new pre-baked fuzzy sets (Triangular, Trapezoid) which integrate the already existing objects (e.g., Sigmoid, Gaussian). Of course, Simpful still supports the design …

Two new journal papers

Recently, we got two papers accepted for pubblication. The first one was the followup of our CIBCB 2019 paper, published on IEEE Journal of Biomedical and Health Informatics. The paper describes the last developments of our ProCell tool for cell proliferation analysis, whose GUI was completely overhauled by designer Luca Zanini and whose simulation core …

A new role: Topic Editor for MDPI’s Entropy

Today, I officially became Topic Editor of MDPI’s journal Entropy. Entropy is an international, interdisciplinary, peer-reviewed, monthly, open access journal about… entropy and information studies. Entropy is characterized by an impressive acceptance-to-publication speed (median: 2.7 days); the current impact factor of 2.5, and it is on the rise. This is my first experience as editor. …