Graph embedding and geometric deep learning relevance to network biology and structural chemistry

Graphs are used as a model of complex relationships among data in biological science since the advent of systems biology in the early 2000. In particular, graph data analysis and graph data mining play an important role in biology interaction networks, where recent techniques of artificial intelligence, usually employed in other type of networks (e.g., social, citations, and trademark networks) aim to implement various data mining tasks including classification, clustering, recommendation, anomaly detection, and link prediction. The commitment and efforts of artificial intelligence research in network biology are motivated by the fact that machine learning techniques are often prohibitively computational demanding, low parallelizable, and ultimately inapplicable, since biological network of realistic size is a large system, which is characterised by a high density of interactions and often with a non-linear dynamics and a non-Euclidean latent geometry. Currently, graph embedding emerges as the new learning paradigm that shifts the tasks of building complex models for classification, clustering, and link prediction to learning an informative representation of the graph data in a vector space so that many graph mining and learning tasks can be more easily performed by employing efficient non-iterative traditional models (e.g., a linear support vector machine for the classification task). The great potential of graph embedding is the main reason of the flourishing of studies in this area and, in particular, the artificial intelligence learning techniques. In this mini review, we give a comprehensive summary of the main graph embedding algorithms in light of the recent burgeoning interest in geometric deep learning

Bayesian Models Applied to Cyber Security Anomaly Detection Problems

Cyber security is an important concern for all individuals, organisations and governments globally. Cyber attacks have become more sophisticated, frequent and dangerous than ever, and traditional anomaly detection methods have been proved to be less effective when dealing with these new classes of cyber threats. In order to address this, both classical and Bayesian models offer a valid and innovative alternative to the traditional signature-based methods, motivating the increasing interest in statistical research that it has been observed in recent years. In this review we provide a description of some typical cyber security challenges, typical types of data and statistical methods, paying special attention to Bayesian approaches for these problems

Temporally adaptive monitoring procedures with applications in enterprise cyber-security

Due to the perpetual threat of cyber-attacks, enterprises must employ and develop new methods of detection as attack vectors evolve and advance. Enterprise computer networks produce a large volume and variety of data including univariate data streams, time series and network graph streams. Motivated by cyber-security, this thesis develops adaptive monitoring tools for univariate and network graph data streams, however, they are not limited to this domain. In all domains, real data streams present several challenges for monitoring including trend, periodicity and change points. Streams often also have high volume and frequency. To deal with the non-stationarity in the data, the methods applied must be adaptive. Adaptability in the proposed procedures throughout the thesis is introduced using forgetting factors, weighting the data accordingly to recency. Secondly, methods applied must be computationally fast with a small or fixed computation burden and fixed storage requirements for timely processing. Throughout this thesis, sequential or sliding window approaches are employed to achieve this. The first part of the thesis is centred around univariate monitoring procedures. A sequential adaptive parameter estimator is proposed using a Bayesian framework. This procedure is then extended for multiple change point detection, where, unlike existing change point procedures, the proposed method is capable of detecting abrupt changes in the presence of trend. We additionally present a time series model which combines short-term and long-term behaviours of a series for improved anomaly detection. Unlike existing methods which primarily focus on point anomalies detection (extreme outliers), our method is capable of also detecting contextual anomalies, when the data deviates from persistent patterns of the series such as seasonality. Finally, a novel multi-type relational clustering methodology is proposed. As multiple relations exist between the different entities within a network (computers, users and ports), multiple network graphs can be generated. We propose simultaneously clustering over all graphs to produce a single clustering for each entity using Non-Negative Matrix Tri-Factorisation. Through simplifications, the proposed procedure is fast and scalable for large network graphs. Additionally, this methodology is extended for graph streams. This thesis provides an assortment of tools for enterprise network monitoring with a focus on adaptability and scalability making them suitable for intrusion detection and situational awareness.Open Acces

Speaking in unison? Explaining the role of agenda-setter constellations in the ECB policy agenda using a network-based approach

Policy agendas are a well-studied institutional level phenomenon that capture the set of policy issues that an institution pays attention to over time. They are emergent in nature in that individual behaviour shapes institutional level outcomes when policy makers allocate attention to policy issues. To examine the link between individual-level actions and system-level outcomes we introduce the concept of the agenda-setting constellation, defined as a group of policy makers paying attention to a set of policy issues. Taking the European Central Bank as a case study, and using a combination of text-analysis and networks-analysis techniques, we demonstrate how these meso-level structures shape the evolving policy agenda. We then examine the roles of personal experience, institutional constraints, and policy context in driving agenda-setter constellation membership. Our results show the value of studying policy agendas as networked processes and the key role that agenda-setter constellations play in driving policy agenda dynamics

Genuine quantum correlations in quantum many-body systems: a review of recent progress

Quantum information theory has considerably helped in the understanding of quantum many-body systems. The role of quantum correlations and in particular, bipartite entanglement, has become crucial to characterise, classify and simulate quantum many body systems. Furthermore, the scaling of entanglement has inspired modifications to numerical techniques for the simulation of many-body systems leading to the, now established, area of tensor networks. However, the notions and methods brought by quantum information do not end with bipartite entanglement. There are other forms of correlations embedded in the ground, excited and thermal states of quantum many-body systems that also need to be explored and might be utilised as potential resources for quantum technologies. The aim of this work is to review the most recent developments regarding correlations in quantum many-body systems focussing on multipartite entanglement, quantum nonlocality, quantum discord, mutual information but also other non classical measures of correlations based on quantum coherence. Moreover, we also discuss applications of quantum metrology in quantum many-body systems.Comment: Review. Close to published version. Comments are welcome! Please write an email to g.dechiara[(at)]qub.ac.u

Bipartite network models to design combination therapies in acute myeloid leukaemia

Combination therapy is preferred over single-targeted monotherapies for cancer treatment due to its efficiency and safety. However, identifying effective drug combinations costs time and resources. We propose a method for identifying potential drug combinations by bipartite network modelling of patient-related drug response data, specifically the Beat AML dataset. The median of cell viability is used as a drug potency measurement to reconstruct a weighted bipartite network, model drug-biological sample interactions, and find the clusters of nodes inside two projected networks. Then, the clustering results are leveraged to discover effective multi-targeted drug combinations, which are also supported by more evidence using GDSC and ALMANAC databases. The potency and synergy levels of selective drug combinations are corroborated against monotherapy in three cell lines for acute myeloid leukaemia in vitro. In this study, we introduce a nominal data mining approach to improving acute myeloid leukaemia treatment through combinatorial therapy.Peer reviewe