Transcription Factor Binding Site Prediction Using CnNet Approach.

Controlling the gene expression is the most important development in a living organism, which makes it easier to find different kinds of diseases and their causes. It's very difficult to know what factors control the gene expression. Transcription Factor (TF) is a protein that plays an important role in gene expression. Discovering the transcription factor has immense biological significance, however, it is challenging to develop novel techniques and evaluation for regulatory developments in biological structures. In this research, we mainly focus on 'sequence specificities' that can be ascertained from experimental data with 'deep learning' techniques, which offer a scalable, flexible and unified computational approach for predicting transcription factor binding. Specifically, Multiple Expression motifs for Motif Elicitation (MEME) technique with Convolution Neural Network (CNN) named as CnNet, has been used for discovering the 'sequence specificities' of DNA gene sequences dataset. This process involves two steps: a) discovering the motifs that are capable of identifying useful TF binding site by using MEME technique, and b) computing a score indicating the likelihood of a given sequence being a useful binding site by using CNN technique. The proposed CnNet approach predicts the TF binding score with much better accuracy compared to existing approaches. The source code and datasets used in this work are available at https://github.com/masoodbai/CnNet-Approach-for-TFBS.git.

A microbiological identification and recovery actions of critical symptoms of anammox image bacteria.

Currently, the risks posed by bacteria are becoming increasingly important. It now appears that the cell wall of Anammox image bacteria is very different from what has been generally considered for many years. Not every textbook contains the peptidoglycan on the cell wall of Anammox image bacteria - the sugar-protein chain that strengthens the cells of most bacteria. Most researchers in this Anammox image bacteria diseased identification wanted to find out what gave the Anammox image cell its stability. It used powerful cryo-electron microscopes to examine the bacterial cell wall and find the exact structure of the peptidoglycan. A new algorithm is proposed to discover that Anammox image bacteria contain peptidoglycan, which completes a theory in microbiology. The identification of different diseases is listed, and the proposed model compares the exact results while comparing the parameters like accuracy, precision, recall, and F1-Score. Keywords: Anammox image bacteria, cell wall, cell stability, cryo-electron, microscope images, accuracy, precision, recall, F1-score.

Extraction of knowledge graph of Covid-19 through mining of unstructured biomedical corpora.

The number of biomedical articles published is increasing rapidly over the years. Currently there are about 30 million articles in PubMed and over 25 million mentions in Medline. Among these fundamentals, Biomedical Named Entity Recognition (BioNER) and Biomedical Relation Extraction (BioRE) are the most essential in analysing the literature. In the biomedical domain, Knowledge Graph is used to visualize the relationships between various entities such as proteins, chemicals and diseases. Scientific publications have increased dramatically as a result of the search for treatments and potential cures for the new Coronavirus, but efficiently analysing, integrating, and utilising related sources of information remains a difficulty. In order to effectively combat the disease during pandemics like COVID-19, literature must be used quickly and effectively. In this paper, we introduced a fully automated framework consists of BERT-BiLSTM, Knowledge graph, and Representation Learning model to extract the top diseases, chemicals, and proteins related to COVID-19 from the literature. The proposed framework uses Named Entity Recognition models for disease recognition, chemical recognition, and protein recognition. Then the system uses the Chemical - Disease Relation Extraction and Chemical - Protein Relation Extraction models. And the system extracts the entities and relations from the CORD-19 dataset using the models. The system then creates a Knowledge Graph for the extracted relations and entities. The system performs Representation Learning on this KG to get the embeddings of all entities and get the top related diseases, chemicals, and proteins with respect to COVID-19.

Emotion Correlation Mining Through Deep Learning Models on Natural Language Text.

Emotion analysis has been attracting researchers' attention. Most previous works in the artificial-intelligence field focus on recognizing emotion rather than mining the reason why emotions are not or wrongly recognized. The correlation among emotions contributes to the failure of emotion recognition. In this article, we try to fill the gap between emotion recognition and emotion correlation mining through natural language text from Web news. The correlation among emotions, expressed as the confusion and evolution of emotion, is primarily caused by human emotion cognitive bias. To mine emotion correlation from emotion recognition through text, three kinds of features and two deep neural-network models are presented. The emotion confusion law is extracted through an orthogonal basis. The emotion evolution law is evaluated from three perspectives: one-step shift, limited-step shifts, and shortest path transfer. The method is validated using three datasets: 1) the titles; 2) the bodies; and 3) the comments of news articles, covering both objective and subjective texts in varying lengths (long and short). The experimental results show that in subjective comments, emotions are easily mistaken as anger. Comments tend to arouse emotion circulations of love-anger and sadness-anger. In objective news, it is easy to recognize text emotion as love and cause fear-joy circulation. These findings could provide insights for applications regarding affective interaction, such as network public sentiment, social media communication, and human-computer interaction.

Character level and word level embedding with bidirectional LSTM - Dynamic recurrent neural network for biomedical named entity recognition from literature.

Named Entity Recognition is the process of identifying different entities in a given context. Biomedical Named Entity Recognition (BNER) is the task of extracting chemical names from biomedical texts to support biomedical and translational research. The aim of the system is to extract useful chemical names from biomedical literature text without a lot of handcrafted engineering features. This approach introduces a novel neural network architecture with the composition of bidirectional long short-term memory (BLSTM), dynamic recurrent neural network (RNN) and conditional random field (CRF) that uses character level and word level embedding as the only features to identify the chemical entities. Using this approach we have achieved the F1 score of 89.98 on BioCreAtIvE II GM corpus and 90.84 on NCBI corpus by outperforming the existing systems. Our system is based on the deep neural architecture that uses both character and word level embedding which captures the morphological and orthographic information eliminating the need for handcrafted engineering features. The proposed system outperforms the existing systems without a lot of handcrafted engineering features. The embedding concept along with the bidirectional LSTM network proved to be an effective method to identify most of the chemical entities.

Categorization of Images Using Autoencoder Hashing and Training of Intra Bin Classifiers for Image Classification and Annotation.

Automatic annotation of images is considered to be an important research problem in image retrieval. Traditional methods are computationally complex and fail to annotate correctly when the number of image classes is large and related. This paper proposes a novel approach, an autoencoder hashing, to categorize images of large-scale image classes. The intra bin classifiers are trained to classify the query image, and the tag weight and tag frequency are computed to achieve a more effective annotation of the query image. The proposed approach has been compared with other existing approaches in the literature using performance measures, such as precision, accuracy, mean average precision (MAP), and F1 score. The experimental results indicate that our proposed approach outperforms the existing approaches.

Collection and preparation of sensor network data to support modeling and analysis of outpatient clinics.

Simulation studies of outpatient clinics often involve significant data collection challenges. We describe an approach for data collection using sensor networks which facilitates the collection of a large volume of very detailed patient flow data through healthcare clinics. Such data requires extensive preprocessing before it is ready for analysis. We present a general data preparation framework for sensor network generated data with particular emphasis on the creation and analysis of patient path strings. Several examples of the analysis of sensor network data are also presented. Our approach has been used in two large outpatient clinics in the United States.