An integrated computational pipeline for machine learning-driven diagnosis based on Raman spectra of saliva samples.

Raman Spectroscopy promises the ability to encode in spectral data the significant differences between biological samples belonging to patients affected by a disease and samples of healthy patients (controls). However, the decoding and interpretation of the Raman spectral fingerprint is still a difficult and time-consuming procedure even for domain experts. In this work, we test an end-to-end deep-learning diagnostic pipeline able to classify spectral data from saliva samples. The pipeline has been validated against the SARS-COV-2 Infection and for the screening of neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. The proposed system can be used for the fast prototyping of promising non-invasive, cost and time-efficient diagnostic screening tests.

Identification of the Raman Salivary Fingerprint of Parkinson's Disease Through the Spectroscopic- Computational Combinatory Approach.

Despite the wide range of proposed biomarkers for Parkinson's disease (PD), there are no specific molecules or signals able to early and uniquely identify the pathology onset, progression and stratification. Saliva is a complex biofluid, containing a wide range of biological molecules shared with blood and cerebrospinal fluid. By means of an optimized Raman spectroscopy procedure, the salivary Raman signature of PD can be characterized and used to create a classification model. Raman analysis was applied to collect the global signal from the saliva of 23 PD patients and related pathological and healthy controls. The acquired spectra were computed using machine and deep learning approaches. The Raman database was used to create a classification model able to discriminate each spectrum to the correct belonging group, with accuracy, specificity, and sensitivity of more than 97% for the single spectra attribution. Similarly, each patient was correctly assigned with discriminatory power of more than 90%. Moreover, the extracted data were significantly correlated with clinical data used nowadays for the PD diagnosis and monitoring. The preliminary data reported highlight the potentialities of the proposed methodology that, once validated in larger cohorts and with multi-centered studies, could represent an innovative minimally invasive and accurate procedure to determine the PD onset, progression and to monitor therapies and rehabilitation efficacy.

Efficient Kernel-Based Subsequence Search for Enabling Health Monitoring Services in IoT-Based Home Setting.

This paper presents an efficient approach for subsequence search in data streams. The problem consists of identifying coherent repetitions of a given reference time-series, also in the multivariate case, within a longer data stream. The most widely adopted metric to address this problem is Dynamic Time Warping (DTW), but its computational complexity is a well-known issue. In this paper, we present an approach aimed at learning a kernel approximating DTW for efficiently analyzing streaming data collected from wearable sensors, while reducing the burden of DTW computation. Contrary to kernel, DTW allows for comparing two time-series with different length. To enable the use of kernel for comparing two time-series with different length, a feature embedding is required in order to obtain a fixed length vector representation. Each vector component is the DTW between the given time-series and a set of "basis" series, randomly chosen. The approach has been validated on two benchmark datasets and on a real-life application for supporting self-rehabilitation in elderly subjects has been addressed. A comparison with traditional DTW implementations and other state-of-the-art algorithms is provided: results show a slight decrease in accuracy, which is counterbalanced by a significant reduction in computational costs.

A p-Median approach for predicting drug response in tumour cells.

BACKGROUND: The complexity of biological data related to the genetic origins of tumour cells, originates significant challenges to glean valuable knowledge that can be used to predict therapeutic responses. In order to discover a link between gene expression profiles and drug responses, a computational framework based on Consensus p-Median clustering is proposed. The main goal is to simultaneously predict (in silico) anticancer responses by extracting common patterns among tumour cell lines, selecting genes that could potentially explain the therapy outcome and finally learning a probabilistic model able to predict the therapeutic responses. RESULTS: The experimental investigation performed on the NCI60 dataset highlights three main findings: (1) Consensus p-Median is able to create groups of cell lines that are highly correlated both in terms of gene expression and drug response; (2) from a biological point of view, the proposed approach enables the selection of genes that are strongly involved in several cancer processes; (3) the final prediction of drug responses, built upon Consensus p-Median and the selected genes, represents a promising step for predicting potential useful drugs. CONCLUSION: The proposed learning framework represents a promising approach predicting drug response in tumour cells.

A new clustering approach for learning transcriptional modules.

In modern biology, we had an explosion of genomic data from multiple sources, like measurements of RNA levels, gene sequences, annotations or interaction data. These heterogeneous data provide important information that should be integrated through suitable learning methods aimed at elucidating regulatory networks. We propose an iterative relational clustering procedure for finding modules of co-regulated genes. This approach integrates information concerning known Transcription Factors (TFs)--gene interactions with gene expression data to find clusters of genes that share a common regulatory program. The results obtained on two well-known gene expression data sets from Saccharomyces cerevisiae are shown.