Screening potential lncRNA biomarkers for breast cancer and colorectal cancer combining random walk and logistic matrix factorization

Breast cancer and colorectal cancer are two of the most common malignant tumors worldwide. They cause the leading causes of cancer mortality. Many researches have demonstrated that long noncoding RNAs (lncRNAs) have close linkages with the occurrence and development of the two cancers. Therefore, it is essential to design an effective way to identify potential lncRNA biomarkers for them. In this study, we developed a computational method (LDA-RWLMF) by integrating random walk with restart and Logistic Matrix Factorization to investigate the roles of lncRNA biomarkers in the prognosis and diagnosis of the two cancers. We first fuse disease semantic and Gaussian association profile similarities and lncRNA functional and Gaussian association profile similarities. Second, we design a negative selection algorithm to extract negative LncRNA-Disease Associations (LDA) based on random walk. Third, we develop a logistic matrix factorization model to predict possible LDAs. We compare our proposed LDA-RWLMF method with four classical LDA prediction methods, that is, LNCSIM1, LNCSIM2, ILNCSIM, and IDSSIM. The results from 5-fold cross validation on the MNDR dataset show that LDA-RWLMF computes the best AUC value of 0.9312, outperforming the above four LDA prediction methods. Finally, we rank all lncRNA biomarkers for the two cancers after determining the performance of LDA-RWLMF, respectively. We find that 48 and 50 lncRNAs have the highest association scores with breast cancer and colorectal cancer among all lncRNAs known to associate with them on the MNDR dataset, respectively. We predict that lncRNAs HULC and HAR1A could be separately potential biomarkers for breast cancer and colorectal cancer and need to biomedical experimental validation

One-class SVM and supervised machine learning models for uncovering associations of non-coding RNA with diseases

The study of MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs) and gene interactions may be expected to provide new technologies to serve as valuable biomarkers for personalized treatments of diseases and to aid in the prognosis of certain conditions. These molecules act at the genome level by regulating or suppressing their protein expression functions. The primary challenge in the study of these non-coding molecules involves the necessity of finding labeled data indicating positive and negative interactions when predicting interactions using machine-learning or deep-learning techniques. However, usually we end up with a scenario of unbalanced data or unstable scenarios for using these models. An additional problem involves the extraction of features derived from the binding of these non-coding RNAs and genes. This binding process usually occurs fully or partially in animal genetics, which leads to considerable complexity in studying the process. Therefore, the main objective of the present work is to demonstrate that it is possible to use features extracted for miRNAs sequences in the development of diseases such as breast cancer, breast neoplasms, or if there is any influence with immune genes related to the SARS-COV-2. We performed experiments focusing on the erb-b2 receptor tyrosine kinase 2 (ERBB2) gene involved in breast cancer. For this purpose, we gathered miRNA-mRNA information from the binding between these two genetic molecules. In this part of our research, we applied a One-Class SVM and an Isolation Forest to discriminate between weak interactions, outliers given by the one-class model, and strong interactions that could occur between miRNA and mRNA (messenger RNA). Additionally, this study aimed to differentiate between breast cancer cases and breast neoplasm conditions. In this section we used the information encoded in lncRNAs. The additional feature used in this part was the frequency of k-mers, i.e., small portions of nucleotides, along with the data from the energy released in miRNA folding. The models used to discriminate between these diseases were One-Class SVM, SVM, and Random Forest. In the final part of the present work, we described a subset of probable miRNA binding with SARS-COV-2 RNA, focusing on those miRNAs with a relationship with genes involved in the immunological system of the human body. The models used as classifiers were One-Class SVM, SVM, and Random Forest. The results obtained in the present study are comparable to those found in the current literature and demonstrate the feasibility of using one-class models combined with features from the coupling of non-coding genes or mRNAs and their relationships with forms of breast cancer and viral infections. This work is expected to establish a basis for future avenues of research to apply one-class machine-learning models with feature extraction based on genomic sequences to the study of the relationship between non-coding RNAs and various diseases.School of ComputingPh. D. (Computing

Deep learning in food category recognition

Integrating artificial intelligence with food category recognition has been a field of interest for research for the past few decades. It is potentially one of the next steps in revolutionizing human interaction with food. The modern advent of big data and the development of data-oriented fields like deep learning have provided advancements in food category recognition. With increasing computational power and ever-larger food datasets, the approach’s potential has yet to be realized. This survey provides an overview of methods that can be applied to various food category recognition tasks, including detecting type, ingredients, quality, and quantity. We survey the core components for constructing a machine learning system for food category recognition, including datasets, data augmentation, hand-crafted feature extraction, and machine learning algorithms. We place a particular focus on the field of deep learning, including the utilization of convolutional neural networks, transfer learning, and semi-supervised learning. We provide an overview of relevant studies to promote further developments in food category recognition for research and industrial applicationsMRC (MC_PC_17171)Royal Society (RP202G0230)BHF (AA/18/3/34220)Hope Foundation for Cancer Research (RM60G0680)GCRF (P202PF11)Sino-UK Industrial Fund (RP202G0289)LIAS (P202ED10Data Science Enhancement Fund (P202RE237)Fight for Sight (24NN201);Sino-UK Education Fund (OP202006)BBSRC (RM32G0178B8

Tracking the Temporal-Evolution of Supernova Bubbles in Numerical Simulations

The study of low-dimensional, noisy manifolds embedded in a higher dimensional space has been extremely useful in many applications, from the chemical analysis of multi-phase flows to simulations of galactic mergers. Building a probabilistic model of the manifolds has helped in describing their essential properties and how they vary in space. However, when the manifold is evolving through time, a joint spatio-temporal modelling is needed, in order to fully comprehend its nature. We propose a first-order Markovian process that propagates the spatial probabilistic model of a manifold at fixed time, to its adjacent temporal stages. The proposed methodology is demonstrated using a particle simulation of an interacting dwarf galaxy to describe the evolution of a cavity generated by a Supernov

2022 - The Third Annual Fall Symposium of Student Scholars

The full program book from the Fall 2022 Symposium of Student Scholars, held on November 17, 2022. Includes abstracts from the presentations and posters.https://digitalcommons.kennesaw.edu/sssprograms/1026/thumbnail.jp

XVI Agricultural Science Congress 2023: Transformation of Agri-Food Systems for Achieving Sustainable Development Goals

The XVI Agricultural Science Congress being jointly organized by the National Academy of Agricultural Sciences (NAAS) and the Indian Council of Agricultural Research (ICAR) during 10-13 October 2023, at hotel Le Meridien, Kochi, is a mega event echoing the theme “Transformation of Agri-Food Systems for achieving Sustainable Development Goals”. ICAR-Central Marine Fisheries Research Institute takes great pride in hosting the XVI ASC, which will be the perfect point of convergence of academicians, researchers, students, farmers, fishers, traders, entrepreneurs, and other stakeholders involved in agri-production systems that ensure food and nutritional security for a burgeoning population. With impeding challenges like growing urbanization, increasing unemployment, growing population, increasing food demands, degradation of natural resources through human interference, climate change impacts and natural calamities, the challenges ahead for India to achieve the Sustainable Development Goals (SDGs) set out by the United Nations are many. The XVI ASC will provide an interface for dissemination of useful information across all sectors of stakeholders invested in developing India’s agri-food systems, not only to meet the SDGs, but also to ensure a stable structure on par with agri-food systems around the world. It is an honour to present this Book of Abstracts which is a compilation of a total of 668 abstracts that convey the results of R&D programs being done in India. The abstracts have been categorized under 10 major Themes – 1. Ensuring Food & Nutritional Security: Production, Consumption and Value addition; 2. Climate Action for Sustainable Agri-Food Systems; 3. Frontier Science and emerging Genetic Technologies: Genome, Breeding, Gene Editing; 4. Livestock-based Transformation of Food Systems; 5. Horticulture-based Transformation of Food Systems; 6. Aquaculture & Fisheries-based Transformation of Food Systems; 7. Nature-based Solutions for Sustainable AgriFood Systems; 8. Next Generation Technologies: Digital Agriculture, Precision Farming and AI-based Systems; 9. Policies and Institutions for Transforming Agri-Food Systems; 10. International Partnership for Research, Education and Development. This Book of Abstracts sets the stage for the mega event itself, which will see a flow of knowledge emanating from a zeal to transform and push India’s Agri-Food Systems to perform par excellence and achieve not only the SDGs of the UN but also to rise as a world leader in the sector. I thank and congratulate all the participants who have submitted abstracts for this mega event, and I also applaud the team that has strived hard to publish this Book of Abstracts ahead of the event. I wish all the delegates and participants a very vibrant and memorable time at the XVI ASC