arXiv subjects

Laura Cantini

Publications and source records attributed to Laura Cantini.

6 recordsLinked to original sources

arXiv2022

Unsupervised Ground Metric Learning using Wasserstein Singular Vectors

Defining meaningful distances between samples in a dataset is a fundamental problem in machine learning. Optimal Transport (OT) lifts a distance between features (the "ground metric") to a geometrically meaningful distance between samples. However, there is usually no straightforward choice of ground metric. Supervised ground metric learning approaches exist but require labeled data. In absence of labels, only ad-hoc ground metrics remain. Unsupervised ground metric learning is thus a fundamental problem to enable data-driven applications of OT. In this paper, we propose for the first time a canonical answer by simultaneously computing an OT distance between samples and between features of a dataset. These distance matrices emerge naturally as positive singular vectors of the function mapping ground metrics to OT distances. We provide criteria to ensure the existence and uniqueness of these singular vectors. We then introduce scalable computational methods to approximate them in high-dimensional settings, using stochastic approximation and entropic regularization. Finally, we showcase Wasserstein Singular Vectors on a single-cell RNA-sequencing dataset.

stat.ML↗

arXiv2019

Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data

After its introduction in 1982, the Hopfield model has been extensively applied for classification and pattern recognition. Recently, its great potential in gene expression patterns retrieval has also been shown. Following this line, we develop Hope4Genes a single-sample class prediction algorithm based on a Hopfield-like model. Differently from previous works, we here tested the performances of the algorithm for class prediction, a task of fundamental importance for precision medicine and therapeutic decision-making. Hope4Genes proved better performances than the state-of-art methodologies in the field independently of the size of the input dataset, its profiling platform, the number of classes and the typical class-imbalance present in biological data. Our results provide encoraging evidence that the Hopfield model, together with the use of its energy for the estimation of the false discoveries, is a particularly promising tool for precision medicine.

q-bio.QM↗

arXiv2018

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer

MicroRNAs play important roles in many biological processes. Their aberrant expression can have oncogenic or tumor suppressor function directly participating to carcinogenesis, malignant transformation, invasiveness and metastasis. Indeed, miRNA profiles can distinguish not only between normal and cancerous tissue but they can also successfully classify different subtypes of a particular cancer. Here, we focus on a particular class of transcripts encoding polycistronic miRNA genes that yields multiple miRNA components. We describe clustered MiRNA Master Regulator Analysis (ClustMMRA), a fully redesigned release of the MMRA computational pipeline (MiRNA Master Regulator Analysis), developed to search for clustered miRNAs potentially driving cancer molecular subtyping. Genomically clustered miRNAs are frequently co-expressed to target different components of pro-tumorigenic signalling pathways. By applying ClustMMRA to breast cancer patient data, we identified key miRNA clusters driving the phenotype of different tumor subgroups. The pipeline was applied to two independent breast cancer datasets, providing statistically concordant results between the two analysis. We validated in cell lines the miR-199/miR-214 as a novel cluster of miRNAs promoting the triple negative subtype phenotype through its control of proliferation and EMT.

q-bio.MN↗

arXiv2015

Detection of gene communities in multi-networks reveals cancer drivers

We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression networks. The rationale behind this choice is that gene co-expression and protein-protein interactions require a tight coregulation of the partners and that such a fine tuned regulation can be obtained only combining both the transcriptional and post-transcriptional layers of regulation. To extract the relevant biological information from the multi-network we studied its partition into communities. To this end we applied a consensus clustering algorithm based on state of art community detection methods. Even if our procedure is valid in principle for any pathology in this work we concentrate on gastric, lung, pancreas and colorectal cancer and identified from the enrichment analysis of the multi-network communities a set of candidate driver cancer genes. Some of them were already known oncogenes while a few are new. The combination of the different layers of information allowed us to extract from the multi-network indications on the regulatory pattern and functional role of both the already known and the new candidate driver genes.

q-bio.MN↗

arXiv2013

Stochastic Turing Patterns for systems with one diffusing species

The problem of pattern formation in a generic two species reaction--diffusion model is studied, under the hypothesis that only one species can diffuse. For such a system, the classical Turing instability cannot take place. At variance, by working in the generalized setting of a stochastic formulation to the inspected problem, Turing like patterns can develop, seeded by finite size corrections. General conditions are given for the stochastic Turing patterns to occur. The predictions of the theory are tested for a specific case study.

cond-mat.stat-mech↗

arXiv2013

Linear noise approximation for stochastic oscillations of intracellular calcium

A stochastic model of intracellular calcium oscillations is analytically studied. The governing master equation is expanded under the linear noise approximation and a closed prediction for the power spectrum of fluctuations analytically derived. A peak in the obtained power spectrum profile signals the presence of stochastic, noise induced, oscillations which extend also outside the region where a deterministic limit cycle is predicted to occur.

cond-mat.stat-mech↗