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"Big data Graphic methods."
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A multimodal graph neural network framework for cancer molecular subtype classification
Background
The recent development of high-throughput sequencing has created a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating multi-omics data has been proven to be effective for building more precise classification models. Most current multi-omics integrative models use either an early fusion in the form of concatenation or late fusion with a separate feature extractor for each omic, which are mainly based on deep neural networks. Due to the nature of biological systems, graphs are a better structural representation of bio-medical data. Although few graph neural network (GNN) based multi-omics integrative methods have been proposed, they suffer from three common disadvantages. One is most of them use only one type of connection, either inter-omics or intra-omic connection; second, they only consider one kind of GNN layer, either graph convolution network (GCN) or graph attention network (GAT); and third, most of these methods have not been tested on a more complex classification task, such as cancer molecular subtypes.
Results
In this study, we propose a novel end-to-end multi-omics GNN framework for accurate and robust cancer subtype classification. The proposed model utilizes multi-omics data in the form of heterogeneous multi-layer graphs, which combine both inter-omics and intra-omic connections from established biological knowledge. The proposed model incorporates learned graph features and global genome features for accurate classification. We tested the proposed model on the Cancer Genome Atlas (TCGA) Pan-cancer dataset and TCGA breast invasive carcinoma (BRCA) dataset for molecular subtype and cancer subtype classification, respectively. The proposed model shows superior performance compared to four current state-of-the-art baseline models in terms of accuracy, F1 score, precision, and recall. The comparative analysis of GAT-based models and GCN-based models reveals that GAT-based models are preferred for smaller graphs with less information and GCN-based models are preferred for larger graphs with extra information.
Journal Article
Application of machine learning in ocean data
In recent years, machine learning has become a hot research method in various fields and has been applied to every aspect of our life, providing an intelligent solution to problems that could not be solved or difficult to be solved before. Machine learning is driven by data. It learns from a part of the input data and builds a model. The model is used to predict and analyze another part of the data to get the results people want. With the continuous advancement of ocean observation technology, the amount of ocean data and data dimensions are rising sharply. The use of traditional data analysis methods to analyze massive amounts of data has revealed many shortcomings. The development of machine learning has solved these shortcomings. Nowadays, the use of machine learning technology to analyze and apply ocean data becomes the focus of scientific research. This method has important practical and long-term significance for protecting the ocean environment, predicting ocean elements, exploring the unknown, and responding to extreme weather. This paper focuses on the analysis of the state of the art and specific practices of machine learning in ocean data, review the application examples of machine learning in various fields such as ocean sound source identification and positioning, ocean element prediction, ocean biodiversity monitoring, and deep-sea resource monitoring. We also point out some constraints that still exist in the research and put forward the future development direction and application prospects.
Journal Article
Metrics for graph comparison: A practitioner’s guide
Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience, cyber security, social network analysis, and bioinformatics, among others. Discovery and comparison of structures such as modular communities, rich clubs, hubs, and trees yield insight into the generative mechanisms and functional properties of the graph. Often, two graphs are compared via a pairwise distance measure, with a small distance indicating structural similarity and vice versa. Common choices include spectral distances and distances based on node affinities. However, there has of yet been no comparative study of the efficacy of these distance measures in discerning between common graph topologies at different structural scales. In this work, we compare commonly used graph metrics and distance measures, and demonstrate their ability to discern between common topological features found in both random graph models and real world networks. We put forward a multi-scale picture of graph structure wherein we study the effect of global and local structures on changes in distance measures. We make recommendations on the applicability of different distance measures to the analysis of empirical graph data based on this multi-scale view. Finally, we introduce the Python library NetComp that implements the graph distances used in this work.
Journal Article
Time-Shifted Maps for Industrial Data Analysis: Monitoring Production Processes and Predicting Undesirable Situations
The rapid advancement of computing power, combined with the ability to collect vast amounts of data, has unlocked new possibilities for industrial applications. While traditional time–domain industrial signals generally do not allow for direct stability assessment or the detection of abnormal situations, alternative representations can reveal hidden patterns. This paper introduces time-shifted maps (TSMs) as a novel method for analyzing industrial data—an approach that is not yet widely adopted in the field. Unlike contemporary machine learning techniques, TSM relies on a simple and interpretable algorithm designed to process data from standard industrial automation systems. By creating clear, visual representations, TSM facilitates the monitoring and control of production process. Specifically, TSMs are constructed from time series data collected by an acceleration sensor mounted on a robot base. To evaluate the effectiveness of TSM, its results are compared with those obtained using classical signal processing methods, such as the fast Fourier transform (FFT) and wavelet transform. Additionally, TSMs are classified using computed correlation dimensions and entropy measures. To further validate the method, we numerically simulate three distinct anomalous scenarios and present their corresponding TSM-based graphical representations.
Journal Article
Cybersecurity, Data Privacy and Blockchain: A Review
In this paper, we identify and review key challenges to bridge the knowledge-gap between SME’s, companies, organisations, businesses, government institutions and the general public in adopting, promoting and utilising Blockchain technology. The challenges indicated are Cybersecurity and Data privacy in this instance. Additional challenges are set out supported by literature, in researching data security management systems and legal frameworks to ascertaining the types and varieties of valid encryption, data acquisition, policy and outcomes under ISO 27001 and the General Data Protection Regulations. Blockchain, a revolutionary method of storage and immutability, provides a robust storage strategy, and when coupled with a Smart Contract, gives users the ability to form partnerships, share information and consent via a legally-based system of carrying out business transactions in a secure digital domain. Globally, ethical and legal challenges significantly differ; consent and trust in the public and private sectors in deploying such defensive data management strategies, is directly related to the accountability and transparency systems in place to deliver certainty and justice. Therefore, investment and research in these areas is crucial to establishing a dialogue between nations to include health, finance and market strategies that should encompass all levels of society. A framework is proposed with elements to include Big Data, Machine Learning and Visualisation methods and techniques. Through the literature we identify a system necessary in carrying out experiments to detect, capture, process and store data. This includes isolating packet data to inform levels of Cybersecurity and privacy-related activities, and ensuring transparency demonstrated in a secure, smart and effective manner.
Journal Article
Supercharge your data wrangling with a graphics card
Graphics processing units aren’t just of interest to gamers and cryptocurrency miners. Increasingly, they’re being used to turbocharge academic research, too.
Graphics processing units aren’t just of interest to gamers and cryptocurrency miners. Increasingly, they’re being used to turbocharge academic research, too.
Journal Article
Forecasting Models for Coronavirus Disease (COVID-19): A Survey of the State-of-the-Art
COVID-19 is a pandemic that has affected over 170 countries around the world. The number of infected and deceased patients has been increasing at an alarming rate in almost all the affected nations. Forecasting techniques can be inculcated thereby assisting in designing better strategies and in taking productive decisions. These techniques assess the situations of the past thereby enabling better predictions about the situation to occur in the future. These predictions might help to prepare against possible threats and consequences. Forecasting techniques play a very important role in yielding accurate predictions. This study categorizes forecasting techniques into two types, namely, stochastic theory mathematical models and data science/machine learning techniques. Data collected from various platforms also play a vital role in forecasting. In this study, two categories of datasets have been discussed, i.e., big data accessed from World Health Organization/National databases and data from a social media communication. Forecasting of a pandemic can be done based on various parameters such as the impact of environmental factors, incubation period, the impact of quarantine, age, gender and many more. These techniques and parameters used for forecasting are extensively studied in this work. However, forecasting techniques come with their own set of challenges (technical and generic). This study discusses these challenges and also provides a set of recommendations for the people who are currently fighting the global COVID-19 pandemic.
Journal Article
Multimodal Machine Learning in Image-Based and Clinical Biomedicine: Survey and Prospects
Machine learning (ML) applications in medical artificial intelligence (AI) systems have shifted from traditional and statistical methods to increasing application of deep learning models. This survey navigates the current landscape of multimodal ML, focusing on its profound impact on medical image analysis and clinical decision support systems. Emphasizing challenges and innovations in addressing multimodal representation, fusion, translation, alignment, and co-learning, the paper explores the transformative potential of multimodal models for clinical predictions. It also highlights the need for principled assessments and practical implementation of such models, bringing attention to the dynamics between decision support systems and healthcare providers and personnel. Despite advancements, challenges such as data biases and the scarcity of “big data” in many biomedical domains persist. We conclude with a discussion on principled innovation and collaborative efforts to further the mission of seamless integration of multimodal ML models into biomedical practice.
Journal Article