An Evaluation of Non-Contact Photoplethysmography-Based Methods for Remote Respiratory Rate Estimation.

The respiration rate (RR) is one of the physiological signals deserving monitoring for assessing human health and emotional states. However, traditional devices, such as the respiration belt to be worn around the chest, are not always a feasible solution (e.g., telemedicine, device discomfort). Recently, novel approaches have been proposed aiming at estimating RR in a less invasive yet reliable way, requiring the acquisition and processing of contact or remote Photoplethysmography (contact reference and remote-PPG, respectively). The aim of this paper is to address the lack of systematic evaluation of proposed methods on publicly available datasets, which currently impedes a fair comparison among them. In particular, we evaluate two prominent families of PPG processing methods estimating Respiratory Induced Variations (RIVs): the first encompasses methods based on the direct extraction of morphological features concerning the RR; and the second group includes methods modeling respiratory artifacts adopting, in the most promising cases, single-channel blind source separation. Extensive experiments have been carried out on the public BP4D+ dataset, showing that the morphological estimation of RIVs is more reliable than those produced by a single-channel blind source separation method (both in contact and remote testing phases), as well as in comparison with a representative state-of-the-art Deep Learning-based approach for remote respiratory information estimation.

UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction.

BACKGROUND: One of the main issues in the automated protein function prediction (AFP) problem is the integration of multiple networked data sources. The UNIPred algorithm was thereby proposed to efficiently integrate -in a function-specific fashion- the protein networks by taking into account the imbalance that characterizes protein annotations, and to subsequently predict novel hypotheses about unannotated proteins. UNIPred is publicly available as R code, which might result of limited usage for non-expert users. Moreover, its application requires efforts in the acquisition and preparation of the networks to be integrated. Finally, the UNIPred source code does not handle the visualization of the resulting consensus network, whereas suitable views of the network topology are necessary to explore and interpret existing protein relationships. RESULTS: We address the aforementioned issues by proposing UNIPred-Web, a user-friendly Web tool for the application of the UNIPred algorithm to a variety of biomolecular networks, already supplied by the system, and for the visualization and exploration of protein networks. We support different organisms and different types of networks -e.g., co-expression, shared domains and physical interaction networks. Users are supported in the different phases of the process, ranging from the selection of the networks and the protein function to be predicted, to the navigation of the integrated network. The system also supports the upload of user-defined protein networks. The vertex-centric and the highly interactive approach of UNIPred-Web allow a narrow exploration of specific proteins, and an interactive analysis of large sub-networks with only a few mouse clicks. CONCLUSIONS: UNIPred-Web offers a practical and intuitive (visual) guidance to biologists interested in gaining insights into protein biomolecular functions. UNIPred-Web provides facilities for the integration of networks, and supplies a framework for the imbalance-aware protein network integration of nine organisms, the prediction of thousands of GO protein functions, and a easy-to-use graphical interface for the visual analysis, navigation and interpretation of the integrated networks and of the functional predictions.

Robust Single-Sample Face Recognition by Sparsity-Driven Sub-Dictionary Learning Using Deep Features.

Face recognition using a single reference image per subject is challenging, above all when referring to a large gallery of subjects. Furthermore, the problem hardness seriously increases when the images are acquired in unconstrained conditions. In this paper we address the challenging Single Sample Per Person (SSPP) problem considering large datasets of images acquired in the wild, thus possibly featuring illumination, pose, face expression, partial occlusions, and low-resolution hurdles. The proposed technique alternates a sparse dictionary learning technique based on the method of optimal direction and the iterative ℓ 0 -norm minimization algorithm called k-LiMapS. It works on robust deep-learned features, provided that the image variability is extended by standard augmentation techniques. Experiments show the effectiveness of our method against the hardness introduced above: first, we report extensive experiments on the unconstrained LFW dataset when referring to large galleries up to 1680 subjects; second, we present experiments on very low-resolution test images up to 8 × 8 pixels; third, tests on the AR dataset are analyzed against specific disguises such as partial occlusions, facial expressions, and illumination problems. In all the three scenarios our method outperforms the state-of-the-art approaches adopting similar configurations.

A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks.

BACKGROUND: Several problems in network biology and medicine can be cast into a framework where entities are represented through partially labeled networks, and the aim is inferring the labels (usually binary) of the unlabeled part. Connections represent functional or genetic similarity between entities, while the labellings often are highly unbalanced, that is one class is largely under-represented: for instance in the automated protein function prediction (AFP) for most Gene Ontology terms only few proteins are annotated, or in the disease-gene prioritization problem only few genes are actually known to be involved in the etiology of a given disease. Imbalance-aware approaches to accurately predict node labels in biological networks are thereby required. Furthermore, such methods must be scalable, since input data can be large-sized as, for instance, in the context of multi-species protein networks. RESULTS: We propose a novel semi-supervised parallel enhancement of COSNET, an imbalance-aware algorithm build on Hopfield neural model recently suggested to solve the AFP problem. By adopting an efficient representation of the graph and assuming a sparse network topology, we empirically show that it can be efficiently applied to networks with millions of nodes. The key strategy to speed up the computations is to partition nodes into independent sets so as to process each set in parallel by exploiting the power of GPU accelerators. This parallel technique ensures the convergence to asymptotically stable attractors, while preserving the asynchronous dynamics of the original model. Detailed experiments on real data and artificial big instances of the problem highlight scalability and efficiency of the proposed method. CONCLUSIONS: By parallelizing COSNET we achieved on average a speed-up of 180x in solving the AFP problem in the S. cerevisiae, Mus musculus and Homo sapiens organisms, while lowering memory requirements. In addition, to show the potential applicability of the method to huge biomolecular networks, we predicted node labels in artificially generated sparse networks involving hundreds of thousands to millions of nodes.

Sum signal dosimetry: A new approach for high dose quality assurance with Gafchromic EBT3.

Gafchromic EBT3 film dosimetry in radiosurgery (RS) and hypofractionated radiotherapy (HRT) is complicated by the limited film accuracy at high fractional doses. The aim of this study is to develop and evaluate sum signal (SS) film dosimetry to increase dose resolution at high fractional doses, thus allowing for use of EBT3 for dose distribution verification of RS/HRT treatments. To characterize EBT3 dose-response, a calibration was performed in the dose range 0.44-26.43 Gy. Red (RC) and green (GC) channel net optical densities were linearly added to produce the SS. Dose resolution and overall accuracy of the dosimetric protocol were estimated and compared for SS,RC, and GC. A homemade Matlab software was developed to compare, in terms of gamma analysis, dose distributions delivered by a Cyberknife on EBT3 films to dose distributions calculated by the treatment planning system. The new SS and conventional single channel (SC) methods were compared, using 3%/1 and 4%/1 mm acceptance criteria, for 20 patient plans. Our analysis shows that the SS dose-response curve is characterized by a steeper trend in comparison with SC, with SS providing a higher dose resolution in the whole dose range investigated. Gamma analysis confirms that the percentage of points satisfying the agreement criteria is significantly higher for SS compared to SC: 95.03% vs. 88.41% (P = 0.014) for 3%/1 mm acceptance criteria and 97.24% vs. 93.58% (P = 0.048) for 4%/1 mm acceptance criteria. This study demonstrates that the SS approach is a new and effective method to improve dosimetric accuracy in the framework of the RS-HRT patient-specific quality assurance protocol.

Real-time face mask position recognition system based on MobileNet model.

COVID-19 is a highly contagious disease that was first identified in 2019, and has since taken more than six million lives world wide till date, while also causing considerable economic, social, cultural and political turmoil. As a way to limit its spread, the World Health Organization and medical experts have advised properly wearing face masks, social distancing and hand sanitization, besides vaccination. However, people wear masks sometimes uncovering their mouths and/or noses consciously or unconsciously, thereby lessening the effectiveness of the protection they provide. A system capable of automatic recognition of face mask position could alert and ensure that an individual is wearing a mask properly before entering a crowded public area and putting themselves and others at risk. We first develop and publicly release a dataset of face mask images, which are collected from 391 individuals of different age groups and gender. Then, we study six different architectures of pre-trained deep learning models, and finally propose a model developed by fine tuning the pre-trained state of the art MobileNet model. We evaluate the performance (accuracy, F1-score, and Cohen's Kappa) of this model on the proposed dataset and MaskedFace-Net, a publicly available synthetic dataset created by image editing. Its performance is also compared to other existing methods. The proposed MobileNet is found as the best model providing an accuracy, F1-score, and Cohen's Kappa of 99.23%, 99.22%, and 99.19%, respectively for face mask position recognition. It outperforms the accuracy of the best existing model by about 2%. Finally, an automatic face mask position recognition system has been developed, which can recognize if an individual is wearing a mask correctly or incorrectly. The proposed model performs very well with no drop in recognition accuracy from real images captured by a camera.

pyVHR: a Python framework for remote photoplethysmography.

Remote photoplethysmography (rPPG) aspires to automatically estimate heart rate (HR) variability from videos in realistic environments. A number of effective methods relying on data-driven, model-based and statistical approaches have emerged in the past two decades. They exhibit increasing ability to estimate the blood volume pulse (BVP) signal upon which BPMs (Beats per Minute) can be estimated. Furthermore, learning-based rPPG methods have been recently proposed. The present pyVHR framework represents a multi-stage pipeline covering the whole process for extracting and analyzing HR fluctuations. It is designed for both theoretical studies and practical applications in contexts where wearable sensors are inconvenient to use. Namely, pyVHR supports either the development, assessment and statistical analysis of novel rPPG methods, either traditional or learning-based, or simply the sound comparison of well-established methods on multiple datasets. It is built up on accelerated Python libraries for video and signal processing as well as equipped with parallel/accelerated ad-hoc procedures paving the way to online processing on a GPU. The whole accelerated process can be safely run in real-time for 30 fps HD videos with an average speedup of around 5. This paper is shaped in the form of a gentle tutorial presentation of the framework.

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction.

Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel network-based approach named Patient-Net (P-Net) in which biomolecular profiles of patients are modeled in a graph-structured space that represents gene expression relationships between patients. Then a kernel-based semi-supervised transductive algorithm is applied to the graph to explore the overall topology of the graph and to predict the phenotype/clinical outcome of patients. Experimental tests involving several publicly available datasets of patients afflicted with pancreatic, breast, colon and colorectal cancer show that our proposed method is competitive with state-of-the-art supervised and semi-supervised predictive systems. Importantly, P-Net also provides interpretable models that can be easily visualized to gain clues about the relationships between patients, and to formulate hypotheses about their stratification.

parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants.

BACKGROUND: Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data. RESULTS: To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version. CONCLUSIONS: parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF.

Adaptiveness in monotone pseudo-Boolean optimization and stochastic neural computation.

Hopfield neural network (HNN) is a nonlinear computational model successfully applied in finding near-optimal solutions of several difficult combinatorial problems. In many cases, the network energy function is obtained through a learning procedure so that its minima are states falling into a proper subspace (feasible region) of the search space. However, because of the network nonlinearity, a number of undesirable local energy minima emerge from the learning procedure, significantly effecting the network performance. In the neural model analyzed here, we combine both a penalty and a stochastic process in order to enhance the performance of a binary HNN. The penalty strategy allows us to gradually lead the search towards states representing feasible solutions, so avoiding oscillatory behaviors or asymptotically instable convergence. Presence of stochastic dynamics potentially prevents the network to fall into shallow local minima of the energy function, i.e., quite far from global optimum. Hence, for a given fixed network topology, the desired final distribution on the states can be reached by carefully modulating such process. The model uses pseudo-Boolean functions both to express problem constraints and cost function; a combination of these two functions is then interpreted as energy of the neural network. A wide variety of NP-hard problems fall in the class of problems that can be solved by the model at hand, particularly those having a monotonic quadratic pseudo-Boolean function as constraint function. That is, functions easily derived by closed algebraic expressions representing the constraint structure and easy (polynomial time) to maximize. We show the asymptotic convergence properties of this model characterizing its state space distribution at thermal equilibrium in terms of Markov chain and give evidence of its ability to find high quality solutions on benchmarks and randomly generated instances of two specific problems taken from the computational graph theory.

FPGA implementation of a stochastic neural network for monotonic pseudo-Boolean optimization.

In this paper a FPGA implementation of a novel neural stochastic model for solving constrained NP-hard problems is proposed and developed. The model exploits pseudo-Boolean functions both to express the constraints and to define the cost function, interpreted as energy of a neural network. A wide variety of NP-hard problems falls in the class of problems that can be solved by this model, particularly those having a quadratic pseudo-Boolean penalty function. The proposed hardware implementation provides high computation speed by exploiting parallelism, as the neuron update and the constraint violation check can be performed in parallel over the whole network. The neural system has been tested on random and benchmark graphs, showing good performance with respect to the same heuristic for the same problems. Furthermore, the computational speed of the FPGA implementation has been measured and compared to software implementation. The developed architecture featured dramatically faster computation, with respect to the software implementation, even adopting a low-cost FPGA chip.

Orthogonal Procrustes Analysis for Dictionary Learning in Sparse Linear Representation.

In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error. Finding the best fitting dictionary remains a very difficult task, leaving the question still open. A well-established heuristic method for tackling this problem is an iterative alternating scheme, adopted for instance in the well-known K-SVD algorithm. Essentially, it consists in repeating two stages; the former promotes sparse coding of the training set and the latter adapts the dictionary to reduce the error. In this paper we present R-SVD, a new method that, while maintaining the alternating scheme, adopts the Orthogonal Procrustes analysis to update the dictionary atoms suitably arranged into groups. Comparative experiments on synthetic data prove the effectiveness of R-SVD with respect to well known dictionary learning algorithms such as K-SVD, ILS-DLA and the online method OSDL. Moreover, experiments on natural data such as ECG compression, EEG sparse representation, and image modeling confirm R-SVD's robustness and wide applicability.