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Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two typical types of non-coding RNAs that interact and play important regulatory roles in many animal organisms. Exploring the unknown interactions between lncRNAs and miRNAs contributes to a better understanding of their functional involvement. Currently, studying the interactions between lncRNAs and miRNAs heavily relies on laborious biological experiments. Therefore, it is necessary to design a computational method for predicting lncRNA-miRNA interactions. In this work, we propose a method called MPGK-LMI, which utilizes a graph attention network (GAT) to predict lncRNA-miRNA interactions in animals. First, we construct a meta-path similarity matrix based on known lncRNA-miRNA interaction information. Then, we use GAT to aggregate the constructed meta-path similarity matrix and the computed Gaussian kernel similarity matrix to update the feature matrix with neighbourhood information. Finally, a scoring module is used for prediction. By comparing with three state-of-the-art algorithms, MPGK-LMI achieves the best results in terms of performance, with AUC value of 0.9077, AUPR of 0.9327, ACC of 0.9080, F1-score of 0.9143 and precision of 0.8739. These results validate the effectiveness and reliability of MPGK-LMI. Additionally, we conduct detailed case studies to demonstrate the effectiveness and feasibility of our approach in practical applications. Through these empirical results, we gain deeper insights into the functional roles and mechanisms of lncRNA-miRNA interactions, providing significant breakthroughs and advancements in this field of research. In summary, our method not only outperforms others in terms of performance but also establishes its practicality and reliability in biological research through real-case analysis, offering strong support and guidance for future studies and applications., (© 2024 The Author(s). Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.)

Using wet experimental methods to discover new thermophilic proteins or improve protein thermostability is time-consuming and expensive. Machine learning methods have shown powerful performance in the study of protein thermostability in recent years. However, how to make full use of multiview sequence information to predict thermostability effectively is still a challenge. In this study, we proposed a deep learning-based classifier named DeepPPThermo that fuses features of classical sequence features and deep learning representation features for classifying thermophilic and mesophilic proteins. In this model, deep neural network (DNN) and bi-long short-term memory (Bi-LSTM) are used to mine hidden features. Furthermore, local attention and global attention mechanisms give different importance to multiview features. The fused features are fed to a fully connected network classifier to distinguish thermophilic and mesophilic proteins. Our model is comprehensively compared with advanced machine learning algorithms and deep learning algorithms, proving that our model performs better. We further compare the effects of removing different features on the classification results, demonstrating the importance of each feature and the robustness of the model. Our DeepPPThermo model can be further used to explore protein diversity, identify new thermophilic proteins, and guide directed mutations of mesophilic proteins.

Human-virus protein-protein interactions (PPIs) play critical roles in viral infection. For example, the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds primarily to human angiotensin-converting enzyme 2 (ACE2) protein to infect human cells. Thus, identifying and blocking these PPIs contribute to controlling and preventing viruses. However, wet-lab experiment-based identification of human-virus PPIs is usually expensive, labor-intensive, and time-consuming, which presents the need for computational methods. Many machine-learning methods have been proposed recently and achieved good results in predicting human-virus PPIs. However, most methods are based on protein sequence features and apply manually extracted features, such as statistical characteristics, phylogenetic profiles, and physicochemical properties. In this work, we present an embedding-based neural framework with convolutional neural network (CNN) and bi-directional long short-term memory unit (Bi-LSTM) architecture, named Emvirus, to predict human-virus PPIs (including human-SARS-CoV-2 PPIs). In addition, we conduct cross-viral experiments to explore the generalization ability of Emvirus. Compared to other feature extraction methods, Emvirus achieves better prediction accuracy., (© 2023 Chinese Medical Association Publishing House. Published by Elsevier BV.)

Trending topics are the most discussed topics at the moment on social media platforms, particularly on Twitter and Facebook. While the access to trending topics are free and available to everyone, marketing specialists and specific software are more expensive, therefore there are companies that do not have the budget to support those costs. The main goal of this work is to search for associations between trending topics and companies on social media platforms and HotRivers prototype was developed to fill this gap. This approach was applied to Twitter and used text mining techniques to process tweets, train personalized models of companies and deliver a list of the matched trending topics of the target company. So, in this work were tested different pre-processing text techniques and a method to select tweets called Centroid Strategy used on trending topics to avoid unwanted tweets. Also, were tested three models, an embedding vectors approach with Doc2Vec model, a probabilistic model with Latent Dirichlet Allocation, and a classification task approach with a Convolutional Neural Network used on the final architecture. The approach was validated with real cases like Adidas, Nike and Portsmouth Hospitals University. In the results stand out that trending topic Nike has an association with the company Nike and #WorldPatientSafetyDay has an association with Portsmouth Hospitals University. This prototype, HotRivers, can be a new marketing tool that points the direction to the next campaign., Competing Interests: Conflict of InterestsThe authors declare that they have no conflict of interest., (© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2022, Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Currently, as an effect of the COVID-19 pandemic, bioinformatics, genomics, and biological computations are gaining increased attention. Genomes of viruses can be represented by character strings based on their nucleobases. Document similarity metrics can be applied to these strings to measure their similarities. Clustering algorithms can be applied to the results of their document similarities to cluster them. P systems or membrane systems are computation models inspired by the flow of information in the membrane cells. These can be used for various purposes, one of them being data clustering. This paper studies a novel and versatile clustering method for genomes and the utilization of such membrane clustering models using document similarity metrics, which is not yet a well-studied use of membrane clustering models.

The special nature, volume and broadness of biomedical literature pose barriers for automated classification methods. On the other hand, manually indexing is time-consuming, costly and error prone. We argue that current word embedding algorithms can be efficiently used to support the task of biomedical text classification even in a multilabel setting, with many distinct labels. The ontology representation of Medical Subject Headings provides machine-readable labels and specifies the dimensionality of the problem space. Both deep- and shallow network approaches are implemented. Predictions are determined by the similarity between extracted features from contextualized representations of abstracts and headings. The addition of a separate classifier for transfer learning is also proposed and evaluated. Large datasets of biomedical citations are harvested for their metadata and used for training and testing. These automated approaches are still far from entirely substituting human experts, yet they can be useful as a mechanism for validation and recommendation. Dataset balancing, distributed processing and training parallelization in GPUs, all play an important part regarding the effectiveness and performance of proposed methods., Competing Interests: Conflict of interestThe authors have no conflicts of interest to declare that are relevant to the content of this article., (© The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2021.)

With the exponential increase in information, it has become imperative to design mechanisms that allow users to access what matters to them as quickly as possible. The recommendation system (RS) with information technology development is the solution, it is an intelligent system. Various types of data can be collected on items of interest to users and presented as recommendations. RS also play a very important role in e-commerce. The purpose of recommending a product is to designate the most appropriate designation for a specific product. The major challenge when recommending products is insufficient information about the products and the categories to which they belong. In this paper, we transform the product data using two methods of document representation: bag-of-words (BOW) and the neural network-based document combination known as vector-based (Doc2Vec). We propose three-criteria recommendation systems (product, package and health) for each document representation method to foster online grocery shopping, which depends on product characteristics such as composition, packaging, nutrition table, allergen, and so forth. For our evaluation, we conducted a user and expert survey. Finally, we compared the performance of these three criteria for each document representation method, discovering that the neural network-based (Doc2Vec) performs better and completely alters the results.

Natural language inference (NLI) is an essential subtask in many natural language processing applications. It is a directional relationship from premise to hypothesis. A pair of texts is defined as entailed if a text infers its meaning from the other text. The NLI is also known as textual entailment recognition, and it recognizes entailed and contradictory sentences in various NLP systems like Question Answering, Summarization and Information retrieval systems. This paper describes the NLI problem attempted for a low resource Indian language Malayalam, the regional language of Kerala. More than 30 million people speak this language. The paper is about the Malayalam NLI dataset, named MaNLI dataset, and its application of NLI in Malayalam language using different models, namely Doc2Vec (paragraph vector), fastText, BERT (Bidirectional Encoder Representation from Transformers), and LASER (Language Agnostic Sentence Representation). Our work attempts NLI in two ways, as binary classification and as multiclass classification. For both the classifications, LASER outperformed the other techniques. For multiclass classification, NLI using LASER based sentence embedding technique outperformed the other techniques by a significant margin of 12% accuracy. There was also an accuracy improvement of 9% for LASER based NLI system for binary classification over the other techniques., Competing Interests: The authors declare that they have no competing interests., (© 2021 Renjit and Idicula.)

Analyze performance of unsupervised embedding algorithms in sentiment analysis of knowledge-rich data sets. We apply state-of-the-art embedding algorithms Word2Vec and Doc2Vec as the learning techniques. The algorithms build word and document embeddings in an unsupervised manner. To assess the algorithms' performance, we define sentiment metrics and use a semantic lexicon SentiWordNet (SWN) to establish the benchmark measures. Our empirical results are obtained on the Obesity data set from i2b2 clinical discharge summaries and the Reuters Science dataset. We use the Welch's test to analyze the obtained sentiment evaluation. On the Obesity data, the Welch's test found significant difference between the SWN evaluation of the most positive and most negative texts. On the same data, the Word2Vec results support the SWN results, whereas the Doc2Vec results partially correspond to the Word2Vec and the SWN results. On the Reuters data, the Welch's test did not find significant difference between the SWN evaluation of the most positive and most negative texts. On the same data, Word2Vec and Doc2Vec results only in part correspond to the SWN results. In unsupervised sentiment analysis of medical and scientific texts, the Word2Vec sentiment analysis has been more consistent with the SentiWordNet sentiment assessment than the Doc2Vec sentiment analysis. The Welch's test of the SentiWordNet results has been a strong indicator of future correspondence between Word2Vec and SentiWordNet results., Competing Interests: Conflict of interestOn behalf of all authors, the corresponding author states that there is no conflict of interest., (© The Author(s), under exclusive licence to Springer Nature Singapore Pte Ltd 2021.)

Pornographic and gambling websites become increasingly stubborn via disguising, misleading, blocking, and bypassing, which hinder the construction of a safe and healthy network environment. However, most traditional approaches conduct the detection process through a single aspect of these sites, which would fail to handle the more intricate and challenging situations. To alleviate this problem, this study proposed an automatic detection system for porn and gambling websites based on visual and textual content using a decision mechanism (PG-VTDM). This system can be applied to the intelligent wireless router at home or school to realize the identification, blocking, and warning of ill-suited websites. First, Doc2Vec was employed to learn the textual features that can be used to represent the textual content in the hypertext markup language (HTML) source code of the websites. In addition, the traditional bag-of-visual-words (BoVW) was improved by introducing local spatial relationships of feature points for better representing the visual features of the website screenshot. Then, based on these two types of features, a text classifier and an image classifier were both trained. In the decision mechanism, a data fusion algorithm based on logistic regression (LR) was designed to obtain the final prediction result by measuring the contribution of the two classification results to the final category prediction. The efficiency of this proposed approach was substantiated via comparison experiments using gambling and porn website datasets crawled from the Internet. The proposed approach outperformed the approach based on a single feature and some state-of-the-art approaches, with accuracy, precision, and F-measure all over 99%.

The identification of human-virus protein-protein interactions (PPIs) is an essential and challenging research topic, potentially providing a mechanistic understanding of viral infection. Given that the experimental determination of human-virus PPIs is time-consuming and labor-intensive, computational methods are playing an important role in providing testable hypotheses, complementing the determination of large-scale interactome between species. In this work, we applied an unsupervised sequence embedding technique (doc2vec) to represent protein sequences as rich feature vectors of low dimensionality. Training a Random Forest (RF) classifier through a training dataset that covers known PPIs between human and all viruses, we obtained excellent predictive accuracy outperforming various combinations of machine learning algorithms and commonly-used sequence encoding schemes. Rigorous comparison with three existing human-virus PPI prediction methods, our proposed computational framework further provided very competitive and promising performance, suggesting that the doc2vec encoding scheme effectively captures context information of protein sequences, pertaining to corresponding protein-protein interactions. Our approach is freely accessible through our web server as part of our host-pathogen PPI prediction platform (http://zzdlab.com/InterSPPI/). Taken together, we hope the current work not only contributes a useful predictor to accelerate the exploration of human-virus PPIs, but also provides some meaningful insights into human-virus relationships., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2019 The Authors.)

We detect ongoing innovation in empirical data about human technological innovations. Ongoing technological innovation is a form of open-ended evolution, but it occurs in a nonbiological, cultural population that consists of actual technological innovations that exist in the real world. The change over time of this population of innovations seems to be quite open-ended. We take patented inventions as a proxy for technological innovations and mine public patent records for evidence of the ongoing emergence of technological innovations, and we compare two ways to detect it. One way detects the first instances of predefined patent pigeonholes, specifically the technology classes listed in the United States Patent Classification (USPC). The second way embeds patents in a high-dimensional semantic space and detects the emergence of new patent clusters. After analyzing hundreds of years of patent records, both methods detect the emergence of new kinds of technologies, but clusters are much better at detecting innovations that are unanticipated and undetected by USPC pigeonholes. Our clustering methods generalize to detect unanticipated innovations in other evolving populations that generate ongoing streams of digital data.