Bayesian correlated clustering to integrate multiple datasets

Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct – but often complementary – information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured via parameters that describe the agreement among the datasets. Results: Using a set of 6 artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real S. cerevisiae datasets. In the 2-dataset case, we show that MDI’s performance is comparable to the present state of the art. We then move beyond the capabilities of current approaches and integrate gene expression, ChIP-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques – as well as to non-integrative approaches – demonstrate that MDI is very competitive, while also providing information that would be difficult or impossible to extract using other methods

A resource aware distributed LSI algorithm for scalable information retrieval

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Latent Semantic Indexing (LSI) is one of the popular techniques in the information retrieval fields. Different from the traditional information retrieval techniques, LSI is not based on the keyword matching simply. It uses statistics and algebraic computations. Based on Singular Value Decomposition (SVD), the higher dimensional matrix is converted to a lower dimensional approximate matrix, of which the noises could be filtered. And also the issues of synonymy and polysemy in the traditional techniques can be overcome based on the investigations of the terms related with the documents. However, it is notable that LSI suffers a scalability issue due to the computing complexity of SVD. This thesis presents a resource aware distributed LSI algorithm MR-LSI which can solve the scalability issue using Hadoop framework based on the distributed computing model MapReduce. It also solves the overhead issue caused by the involved clustering algorithm. The evaluations indicate that MR-LSI can gain significant enhancement compared to the other strategies on processing large scale of documents. One remarkable advantage of Hadoop is that it supports heterogeneous computing environments so that the issue of unbalanced load among nodes is highlighted. Therefore, a load balancing algorithm based on genetic algorithm for balancing load in static environment is proposed. The results show that it can improve the performance of a cluster according to heterogeneity levels. Considering dynamic Hadoop environments, a dynamic load balancing strategy with varying window size has been proposed. The algorithm works depending on data selecting decision and modeling Hadoop parameters and working mechanisms. Employing improved genetic algorithm for achieving optimized scheduler, the algorithm enhances the performance of a cluster with certain heterogeneity levels

Representation learning in finance

Finance studies often employ heterogeneous datasets from different sources with different structures and frequencies. Some data are noisy, sparse, and unbalanced with missing values; some are unstructured, containing text or networks. Traditional techniques often struggle to combine and effectively extract information from these datasets. This work explores representation learning as a proven machine learning technique in learning informative embedding from complex, noisy, and dynamic financial data. This dissertation proposes novel factorization algorithms and network modeling techniques to learn the local and global representation of data in two specific financial applications: analysts’ earnings forecasts and asset pricing. Financial analysts’ earnings forecast is one of the most critical inputs for security valuation and investment decisions. However, it is challenging to fully utilize this type of data due to the missing values. This work proposes one matrix-based algorithm, “Coupled Matrix Factorization,” and one tensor-based algorithm, “Nonlinear Tensor Coupling and Completion Framework,” to impute missing values in analysts’ earnings forecasts and then use the imputed data to predict firms’ future earnings. Experimental analysis shows that missing value imputation and representation learning by coupled matrix/tensor factorization from the observed entries improve the accuracy of firm earnings prediction. The results confirm that representing financial time-series in their natural third-order tensor form improves the latent representation of the data. It learns high-quality embedding by overcoming information loss of flattening data in spatial or temporal dimensions. Traditional asset pricing models focus on linear relationships among asset pricing factors and often ignore nonlinear interaction among firms and factors. This dissertation formulates novel methods to identify nonlinear asset pricing factors and develops asset pricing models that capture global and local properties of data. First, this work proposes an artificial neural network “auto enco der” based model to capture the latent asset pricing factors from the global representation of an equity index. It also shows that autoencoder effectively identifies communal and non-communal assets in an index to facilitate portfolio optimization. Second, the global representation is augmented by propagating information from local communities, where the network determines the strength of this information propagation. Based on the Laplacian spectrum of the equity market network, a network factor “Z-score” is proposed to facilitate pertinent information propagation and capture dynamic changes in network structures. Finally, a “Dynamic Graph Learning Framework for Asset Pricing” is proposed to combine both global and local representations of data into one end-to-end asset pricing model. Using graph attention mechanism and information diffusion function, the proposed model learns new connections for implicit networks and refines connections of explicit networks. Experimental analysis shows that the proposed model incorporates information from negative and positive connections, captures the network evolution of the equity market over time, and outperforms other state-of-the-art asset pricing and predictive machine learning models in stock return prediction. In a broader context, this is a pioneering work in FinTech, particularly in understanding complex financial market structures and developing explainable artificial intelligence models for finance applications. This work effectively demonstrates the application of machine learning to model financial networks, capture nonlinear interactions on data, and provide investors with powerful data-driven techniques for informed decision-making

Large-scale Data Analysis and Deep Learning Using Distributed Cyberinfrastructures and High Performance Computing

Data in many research fields continues to grow in both size and complexity. For instance, recent technological advances have caused an increased throughput in data in various biological-related endeavors, such as DNA sequencing, molecular simulations, and medical imaging. In addition, the variance in the types of data (textual, signal, image, etc.) adds an additional complexity in analyzing the data. As such, there is a need for uniquely developed applications that cater towards the type of data. Several considerations must be made when attempting to create a tool for a particular dataset. First, we must consider the type of algorithm required for analyzing the data. Next, since the size and complexity of the data imposes high computation and memory requirements, it is important to select a proper hardware environment on which to build the application. By carefully both developing the algorithm and selecting the hardware, we can provide an effective environment in which to analyze huge amounts of highly complex data in a large-scale manner. In this dissertation, I go into detail regarding my applications using big data and deep learning techniques to analyze complex and large data. I investigate how big data frameworks, such as Hadoop, can be applied to problems such as large-scale molecular dynamics simulations. Following this, many popular deep learning frameworks are evaluated and compared to find those that suit certain hardware setups and deep learning models. Then, we explore an application of deep learning to a biomedical problem, namely ADHD diagnosis from fMRI data. Lastly, I demonstrate a framework for real-time and fine-grained vehicle detection and classification. With each of these works in this dissertation, a unique large-scale analysis algorithm or deep learning model is implemented that caters towards the problem and leverages specialized computing resources

Enabling Multi-LiDAR Sensing in GNSS-Denied Environments: SLAM Dataset, Benchmark, and UAV Tracking with LiDAR-as-a-camera

The rise of Light Detection and Ranging (LiDAR) sensors has profoundly impacted industries ranging from automotive to urban planning. As these sensors become increasingly affordable and compact, their applications are diversifying, driving precision, and innovation. This thesis delves into LiDAR's advancements in autonomous robotic systems, with a focus on its role in simultaneous localization and mapping (SLAM) methodologies and LiDAR as a camera-based tracking for Unmanned Aerial Vehicles (UAV). Our contributions span two primary domains: the Multi-Modal LiDAR SLAM Benchmark, and the LiDAR-as-a-camera UAV Tracking. In the former, we have expanded our previous multi-modal LiDAR dataset by adding more data sequences from various scenarios. In contrast to the previous dataset, we employ different ground truth-generating approaches. We propose a new multi-modal multi-lidar SLAM-assisted and ICP-based sensor fusion method for generating ground truth maps. Additionally, we also supplement our data with new open road sequences with GNSS-RTK. This enriched dataset, supported by high-resolution LiDAR, provides detailed insights through an evaluation of ten configurations, pairing diverse LiDAR sensors with state-of-the-art SLAM algorithms. In the latter contribution, we leverage a custom YOLOv5 model trained on panoramic low-resolution images from LiDAR reflectivity (LiDAR-as-a-camera) to detect UAVs, demonstrating the superiority of this approach over point cloud or image-only methods. Additionally, we evaluated the real-time performance of our approach on the Nvidia Jetson Nano, a popular mobile computing platform. Overall, our research underscores the transformative potential of integrating advanced LiDAR sensors with autonomous robotics. By bridging the gaps between different technological approaches, we pave the way for more versatile and efficient applications in the future

Computational Approaches to Drug Profiling and Drug-Protein Interactions

Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster

Models of everywhere revisited: a technological perspective

The concept ‘models of everywhere’ was first introduced in the mid 2000s as a means of reasoning about the environmental science of a place, changing the nature of the underlying modelling process, from one in which general model structures are used to one in which modelling becomes a learning process about specific places, in particular capturing the idiosyncrasies of that place. At one level, this is a straightforward concept, but at another it is a rich multi-dimensional conceptual framework involving the following key dimensions: models of everywhere, models of everything and models at all times, being constantly re-evaluated against the most current evidence. This is a compelling approach with the potential to deal with epistemic uncertainties and nonlinearities. However, the approach has, as yet, not been fully utilised or explored. This paper examines the concept of models of everywhere in the light of recent advances in technology. The paper argues that, when first proposed, technology was a limiting factor but now, with advances in areas such as Internet of Things, cloud computing and data analytics, many of the barriers have been alleviated. Consequently, it is timely to look again at the concept of models of everywhere in practical conditions as part of a trans-disciplinary effort to tackle the remaining research questions. The paper concludes by identifying the key elements of a research agenda that should underpin such experimentation and deployment

Computation in Complex Networks

Complex networks are one of the most challenging research focuses of disciplines, including physics, mathematics, biology, medicine, engineering, and computer science, among others. The interest in complex networks is increasingly growing, due to their ability to model several daily life systems, such as technology networks, the Internet, and communication, chemical, neural, social, political and financial networks. The Special Issue “Computation in Complex Networks" of Entropy offers a multidisciplinary view on how some complex systems behave, providing a collection of original and high-quality papers within the research fields of: • Community detection • Complex network modelling • Complex network analysis • Node classification • Information spreading and control • Network robustness • Social networks • Network medicin

Investigating the attainment of optimum data quality for EHR Big Data: proposing a new methodological approach

The value derivable from the use of data is continuously increasing since some years. Both commercial and non-commercial organisations have realised the immense benefits that might be derived if all data at their disposal could be analysed and form the basis of decision taking. The technological tools required to produce, capture, store, transmit and analyse huge amounts of data form the background to the development of the phenomenon of Big Data. With Big Data, the aim is to be able to generate value from huge amounts of data, often in non-structured format and produced extremely frequently. However, the potential value derivable depends on general level of governance of data, more precisely on the quality of the data. The field of data quality is well researched for traditional data uses but is still in its infancy for the Big Data context. This dissertation focused on investigating effective methods to enhance data quality for Big Data. The principal deliverable of this research is in the form of a methodological approach which can be used to optimize the level of data quality in the Big Data context. Since data quality is contextual, (that is a non-generalizable field), this research study focuses on applying the methodological approach in one use case, in terms of the Electronic Health Records (EHR). The first main contribution to knowledge of this study systematically investigates which data quality dimensions (DQDs) are most important for EHR Big Data. The two most important dimensions ascertained by the research methods applied in this study are accuracy and completeness. These are two well-known dimensions, and this study confirms that they are also very important for EHR Big Data. The second important contribution to knowledge is an investigation into whether Artificial Intelligence with a special focus upon machine learning could be used in improving the detection of dirty data, focusing on the two data quality dimensions of accuracy and completeness. Regression and clustering algorithms proved to be more adequate for accuracy and completeness related issues respectively, based on the experiments carried out. However, the limits of implementing and using machine learning algorithms for detecting data quality issues for Big Data were also revealed and discussed in this research study. It can safely be deduced from the knowledge derived from this part of the research study that use of machine learning for enhancing data quality issues detection is a promising area but not yet a panacea which automates this entire process. The third important contribution is a proposed guideline to undertake data repairs most efficiently for Big Data; this involved surveying and comparing existing data cleansing algorithms against a prototype developed for data reparation. Weaknesses of existing algorithms are highlighted and are considered as areas of practice which efficient data reparation algorithms must focus upon. Those three important contributions form the nucleus for a new data quality methodological approach which could be used to optimize Big Data quality, as applied in the context of EHR. Some of the activities and techniques discussed through the proposed methodological approach can be transposed to other industries and use cases to a large extent. The proposed data quality methodological approach can be used by practitioners of Big Data Quality who follow a data-driven strategy. As opposed to existing Big Data quality frameworks, the proposed data quality methodological approach has the advantage of being more precise and specific. It gives clear and proven methods to undertake the main identified stages of a Big Data quality lifecycle and therefore can be applied by practitioners in the area. This research study provides some promising results and deliverables. It also paves the way for further research in the area. Technical and technological changes in Big Data is rapidly evolving and future research should be focusing on new representations of Big Data, the real-time streaming aspect, and replicating same research methods used in this current research study but on new technologies to validate current results