Topic modeling, or identifying the set of topics that occur in a collection of articles, is one of the primary objectives of text mining. One of the big challenges in topic modeling is determining the correct number of topics: underestimating the number of topics results in a loss of information, i.e., omission of topics, underfitting, while overestimating leads to noisy and unexplainable topics and overfitting. In this paper, we consider a semantic-assisted non-negative matrix factorization (NMF) topics model, which we call SeNMFk, based on Kullback-Leibler(KL) divergence and integrated with a method for determining the number of latent topics. SeNMFk involves (i) creating a random ensemble of pairs of matrices whose mean is equal to the initial words-by-documents matrix representing the text corpus and the Shifted Positive Pointwise Mutual Information (SPPMI) matrix, which encodes the context information, respectively, and (ii) jointly factorizing each of these pairs with different number of topics to acquire sets of latent topics that are stable to noise. We demonstrate the performance of our method by identifying the number of topics in several benchmark text corpora, when compared to other state-of-the-art techniques. We also show that the number of document classes in the input text corpus may differ from the number of the extracted latent topics, but these classes can be retrieved by clustering the column-vectors of one of the factor matrices. Additionally, we introduce a software called pyDNMFk to estimate the number of topics. We demonstrate that our unsupervised method, SeNMFk, not only determines the correct number of topics, but also extracts topics with a high coherence and accurately classifies the documents of the corpus.

Intelligent detection and processing capabilities can be instrumental in improving the safety, efficiency, and successful completion of rescue missions conducted by firefighters in emergency first response settings. The objective of this research is to create an automated system that is capable of real-time, intelligent object detection and recognition and facilitates the improved situational awareness of firefighters during an emergency response. We have explored state-of-the-art machine/deep learning techniques to achieve this objective. The goal of this work is to enhance the situational awareness of firefighters by effectively exploiting the infrared video that is actively recorded by firefighters on the scene. To accomplish this, we use a trained deep Convolutional Neural Network (CNN) system to classify and identify objects of interest from thermal imagery in real-time. In the midst of those critical circumstances created by a structure fire, this system is able to accurately inform the decision-making process of firefighters with up-to-date scene information by extracting, processing, and analyzing crucial information. Utilizing the new information produced by the framework, firefighters are able to make more informed inferences about the circumstances for their safe navigation through such hazardous and potentially catastrophic environments.

It was previously shown that DNA breathing, thermodynamic stability, as well as transcriptional activity and transcription factor (TF) bindings are functionally correlated. To ascertain the precise relationship between TF binding and DNA breathing, we developed the multi-modal deep learning model EPBDxDNABERT-2, which is based on the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA dynamics model. To train our EPBDxDNABERT-2, we used chromatin immunoprecipitation sequencing (ChIP-Seq) data comprising 690 ChIP-seq experimental results encompassing 161 distinct TFs and 91 human cell types. EPBDxDNABERT-2 significantly improves the prediction of over 660 TF-DNA, with an increase in the area under the receiver operating characteristic (AUROC) metric of up to 9.6% when compared to the baseline model that does not leverage DNA biophysical properties. We expanded our analysis to in vitro high-throughput Systematic Evolution of Ligands by Exponential enrichment (HT-SELEX) dataset of 215 TFs from 27 families, comparing EPBD with established frameworks. The integration of the DNA breathing features with DNABERT-2 foundational model, greatly enhanced TF-binding predictions. Notably, EPBDxDNABERT-2, trained on a large-scale multi-species genomes, with a cross-attention mechanism, improved predictive power shedding light on the mechanisms underlying disease-related non-coding variants discovered in genome-wide association studies.

Identification of the family to which a malware specimen belongs is essential in understanding the behavior of the malware and developing mitigation strategies. Solutions proposed by prior work, however, are often not practicable due to the lack of realistic evaluation factors. These factors include learning under class imbalance, the ability to identify new malware, and the cost of production-quality labeled data. In practice, deployed models face prominent, rare, and new malware families. At the same time, obtaining a large quantity of up-to-date labeled malware for training a model can be expensive. In this article, we address these problems and propose a novel hierarchical semi-supervised algorithm, which we call the HNMFk Classifier , that can be used in the early stages of the malware family labeling process. Our method is based on non-negative matrix factorization with automatic model selection, that is, with an estimation of the number of clusters. With HNMFk Classifier , we exploit the hierarchical structure of the malware data together with a semi-supervised setup, which enables us to classify malware families under conditions of extreme class imbalance. Our solution can perform abstaining predictions, or rejection option, which yields promising results in the identification of novel malware families and helps with maintaining the performance of the model when a low quantity of labeled data is used. We perform bulk classification of nearly 2,900 both rare and prominent malware families, through static analysis, using nearly 388,000 samples from the EMBER-2018 corpus. In our experiments, we surpass both supervised and semi-supervised baseline models with an F1 score of 0.80.