restricted Boltzmann machine

The global dissemination of SARS-CoV-2 resulted in the emergence of several variants, including Alpha, Alpha + E484K, Beta, and Omicron. Our research integrated the study of eukaryotic translation factors and fundamental components in general protein synthesis with the analysis of SARS-CoV-2 variants and vaccination status. Utilizing statistical methods, we successfully differentiated between variants in infected individuals and, to a lesser extent, between vaccinated and non-vaccinated infected individuals, relying on the expression profiles of translation factors...

Artificial intelligence has surged forward with the advent of generative models, which rely heavily on stochastic computing architectures enhanced by true random number generators with adjustable sampling probabilities. In this study, we develop spin-orbit torque magnetic tunnel junctions (SOT-MTJs), investigating their sigmoid-style switching probability as a function of the driving voltage. This feature proves to be ideally suited for stochastic computing algorithms such as the restricted Boltzmann machines (RBM) prevalent in pretraining processes...

Unsupervised learning based on restricted Boltzmann machine or autoencoders has become an important research domain in the area of neural networks. In this paper mathematical expressions to adaptive learning step calculation for RBM with ReLU transfer function are proposed. As a result, we can automatically estimate the step size that minimizes the loss function of the neural network and correspondingly update the learning step in every iteration. We give a theoretical justification for the proposed adaptive learning rate approach, which is based on the steepest descent method...

Many studies suggest that probabilistic spiking in biological neural systems is beneficial as it aids learning and provides Bayesian inference-like dynamics. If appropriately utilised, noise and stochasticity in nanoscale devices can benefit neuromorphic systems. In this paper, we build stochastic spiking neurons, a stochastic leaky integrate and fire(LIF) neuron and a probabilistic sigmoid neuron, utilising a Mott memristor's inherent stochastic switching dynamics. We demonstrate that the developed LIF neuron is capable of biological neural dynamics...

INTRODUCTION: Intravenous (IV) medications are a fundamental cause of fluid overload (FO) in the intensive care unit (ICU); however, the association between IV medication use (including volume), administration timing, and FO occurrence remains unclear. METHODS: This retrospective cohort study included consecutive adults admitted to an ICU ≥72 hours with available fluid balance data. FO was defined as a positive fluid balance ≥7% of admission body weight within 72 hours of ICU admission...

The crucial aspect of the medical sector is healthcare in today's modern society. To analyze a massive quantity of medical information, a medical system is necessary to gain additional perspectives and facilitate prediction and diagnosis. This device should be intelligent enough to analyze a patient's state of health through social activities, individual health information, and behavior analysis. The Health Recommendation System (HRS) has become an essential mechanism for medical care. In this sense, efficient healthcare networks are critical for medical decision-making processes...

The restricted Boltzmann machine (RBM) is a generative neural network that can learn in an unsupervised way. This machine has been proven to help understand complex systems, using its ability to generate samples of the system with the same observed distribution. In this work, an Ising system is simulated, creating configurations via Monte Carlo sampling and then using them to train RBMs at different temperatures. Then, 1. the ability of the machine to reconstruct system configurations and 2. its ability to be used as a detector of configurations at specific temperatures are evaluated...

We present here an approach to protein design that combines (i) scarce functional information such as experimental data (ii) evolutionary information learned from a natural sequence variants and (iii) physics-grounded modeling. Using a Restricted Boltzmann Machine (RBM), we learn a sequence model of a protein family. We use semi-supervision to leverage available functional information during the RBM training. We then propose a strategy to explore the protein representation space that can be informed by external models such as an empirical force-field method (FoldX)...

Applications of generative models for genomic data have gained significant momentum in the past few years, with scopes ranging from data characterization to generation of genomic segments and functional sequences. In our previous study, we demonstrated that generative adversarial networks (GANs) and restricted Boltzmann machines (RBMs) can be used to create novel high-quality artificial genomes (AGs) which can preserve the complex characteristics of real genomes such as population structure, linkage disequilibrium and selection signals...

Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that Streptococcus agalactiae MprF synthesizes lysyl-phosphatidylglycerol (Lys-PG) from anionic PG, and a novel cationic lipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), from neutral glycolipid Glc-DAG. This unexpected result prompted us to investigate whether Lys-Glc-DAG occurs in other MprF-containing bacteria, and whether other novel MprF products exist...

Recently, neuromorphic computing has been proposed to overcome the drawbacks of the current von Neumann computing architecture. Especially, spiking neural network (SNN) has received significant attention due to its ability to mimic the spike-driven behavior of biological neurons and synapses, potentially leading to low-power consumption and other advantages. In this work, we designed the indium-gallium-zinc oxide (IGZO) channel charge-trap flash (CTF) synaptic device based on a HfO2 /Al2 O3 /Si3 N4 /Al2 O3 layer...

OBJECTIVES: We evaluated autoencoders as a feature engineering and pretraining technique to improve major depressive disorder (MDD) prognostic risk prediction. Autoencoders can represent temporal feature relationships not identified by aggregate features. The predictive performance of autoencoders of multiple sequential structures was evaluated as feature engineering and pretraining strategies on an array of prediction tasks and compared to a restricted Boltzmann machine (RBM) and random forests as a benchmark...

Amidst the ongoing higher education reforms in China, the escalated investments in colleges and universities underscore the need for an effective assessment of their performance to ensure sustainable development. However, traditional evaluation methods have proven time-consuming and labor-intensive. In response, a novel approach called CS-RBM (Crow Search Restricted Boltzmann Machine) prediction algorithm has been proposed for the educational management of these institutions. By integrating the CS algorithm and an enhanced RBM algorithm, this method facilitates the scoring of project performance indicators, bolstered by insights from user evaluation form reports...

One of the goals of precision psychiatry is to characterize mental disorders in an individualized manner, taking into account the underlying dynamic processes. Recent advances in mobile technologies have enabled the collection of Ecological Momentary Assessments (EMAs) that capture multiple responses in real-time at high frequency. However, EMA data is often multi-dimensional, correlated, and hierarchical. Mixed-effects models are commonly used but may require restrictive assumptions about the fixed and random effects and the correlation structure...

Unsupervised clustering of intensive care unit (ICU) medications may identify unique medication clusters (i.e., pharmacophenotypes) in critically ill adults. We performed an unsupervised analysis with Restricted Boltzmann Machine of 991 medications profiles of patients managed in the ICU to explore pharmacophenotypes that correlated with ICU complications (e.g., mechanical ventilation) and patient-centered outcomes (e.g., length of stay, mortality). Six unique pharmacophenotypes were observed, with unique medication profiles and clinically relevant differences in ICU complications and patient-centered outcomes...

Antigen immunogenicity and the specificity of binding of T-cell receptors to antigens are key properties underlying effective immune responses. Here we propose diffRBM, an approach based on transfer learning and Restricted Boltzmann Machines, to build sequence-based predictive models of these properties. DiffRBM is designed to learn the distinctive patterns in amino-acid composition that, on the one hand, underlie the antigen's probability of triggering a response, and on the other hand the T-cell receptor's ability to bind to a given antigen...

BACKGROUND: A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. METHODS: This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA)...

Data sets in the real world are often complex and to some degree hierarchical, with groups and subgroups of data sharing common characteristics at different levels of abstraction. Understanding and uncovering the hidden structure of these data sets is an important task that has many practical applications. To address this challenge, we present a general method for building relational data trees by exploiting the learning dynamics of the restricted Boltzmann machine. Our method is based on the mean-field approach, derived from the Plefka expansion, and developed in the context of disordered systems...

Explainable and interpretable unsupervised machine learning helps one to understand the underlying structure of data. We introduce an ensemble analysis of machine learning models to consolidate their interpretation. Its application shows that restricted Boltzmann machines compress consistently into a few bits the information stored in a sequence of five amino acids at the start or end of α-helices or β-sheets. The weights learned by the machines reveal unexpected properties of the amino acids and the secondary structure of proteins: (i) His and Thr have a negligible contribution to the amphiphilic pattern of α-helices; (ii) there is a class of α-helices particularly rich in Ala at their end; (iii) Pro occupies most often slots otherwise occupied by polar or charged amino acids, and its presence at the start of helices is relevant; (iv) Glu and especially Asp on one side and Val, Leu, Iso, and Phe on the other display the strongest tendency to mark amphiphilic patterns, i...

The development of the new liberal arts field places emphasis on the integration of disciplines such as humanities, engineering, medicine, and agriculture. It specifically highlights the incorporation of new technologies into the education and training of liberal arts majors like economics, law, literature, history, and philosophy. However, when dealing with complex talent data, shallow machine learning algorithms may not provide sufficiently accurate evaluations of the relationship between input and output...