Computer Science

Drug discovery and development is an extremely complex process, with high attrition contributing to the costs of delivering new medicines to patients. Recently, various machine learning approaches have been proposed and investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Among these techniques, it is especially those using Knowledge Graphs that are proving to have considerable promise across a range of tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritisation. In such a knowledge graph-based representation of drug discovery domains, crucial elements including genes, diseases and drugs are represented as entities or vertices, whilst relationships or edges between them indicate some level of interaction. For example, an edge between a disease and drug entity might represent a successful clinical trial, or an edge between two drug entities could indicate a potentially harmful interaction. In order to construct high-quality and ultimately informative knowledge graphs however, suitable data and information is of course required. In this review, we detail publicly available primary data sources containing information suitable for use in constructing various drug discovery focused knowledge graphs. We aim to help guide machine learning and knowledge graph practitioners who are interested in applying new techniques to the drug discovery field, but who may be unfamiliar with the relevant data sources. Overall we hope this review will help motivate more machine learning researchers to explore combining knowledge graphs and machine learning to help solve key and emerging questions in the drug discovery domain.

Machine learning (ML) is ubiquitous in modern life. Since it is being deployed in technologies that affect our privacy and safety, it is often crucial to understand the reasoning behind its decisions, warranting the need for explainable AI. Rule-based models, such as decision trees, decision lists, and decision sets, are conventionally deemed to be the most interpretable. Recent work uses propositional satisfiability (SAT) solving (and its optimization variants) to generate minimum-size decision sets. Motivated by limited practical scalability of these earlier methods, this paper proposes a novel approach to learn minimum-size decision sets by enumerating individual rules of the target decision set independently of each other, and then solving a set cover problem to select a subset of rules. The approach makes use of modern maximum satisfiability and integer linear programming technologies. Experiments on a wide range of publicly available datasets demonstrate the advantage of the new approach over the state of the art in SAT-based decision set learning.

Computer modeling of human decision making is of large importance for, e.g., sustainable transport, urban development, and online recommendation systems. In this paper we present a model for predicting the behavior of an individual during a binary game under different amounts of risk, gain, and time pressure. The model is based on Quantum Decision Theory (QDT), which has been shown to enable modeling of the irrational and subjective aspects of the decision making, not accounted for by the classical Cumulative Prospect Theory (CPT). Experiments on two different datasets show that our QDT-based approach outperforms both a CPT-based approach and data driven approaches such as feed-forward neural networks and random forests.

Evolutionary Algorithms are naturally inspired approximation optimisation algorithms that usually interfere with science problems when common mathematical methods are unable to provide a good solution or finding the exact solution requires an unreasonable amount of time using traditional exhaustive search algorithms. The success of these population-based frameworks is mainly due to their flexibility and ease of adaptation to the most different and complex optimisation problems. This paper presents a metaheuristic algorithm called Stochastic Fractal Search, inspired by the natural phenomenon of growth based on a mathematical concept called the fractal, which is shown to be able to explore the search space more efficiently. This paper also focuses on the algorithm steps and some example applications of engineering design optimisation problems commonly used in the literature being applied to the proposed algorithm.

We present xclingo, a tool for generating explanations from ASP programs annotated with text and labels. These annotations allow tracing the application of rules or the atoms derived by them. The input of xclingo is a markup language written as ASP comment lines, so the programs annotated in this way can still be accepted by a standard ASP solver. xclingo translates the annotations into additional predicates and rules and uses the ASP solver clingo to obtain the extension of those auxiliary predicates. This information is used afterwards to construct derivation trees containing textual explanations. The language allows selecting which atoms to explain and, in its turn, which atoms or rules to include in those explanations. We illustrate the basic features through a diagnosis problem from the literature.

Artificial Intelligence (AI), and in particular, the explainability thereof, has gained phenomenal attention over the last few years. Whilst we usually do not question the decision-making process of these systems in situations where only the outcome is of interest, we do however pay close attention when these systems are applied in areas where the decisions directly influence the lives of humans. It is especially noisy and uncertain observations close to the decision boundary which results in predictions which cannot necessarily be explained that may foster mistrust among end-users. This drew attention to AI methods for which the outcomes can be explained. Bayesian networks are probabilistic graphical models that can be used as a tool to manage uncertainty. The probabilistic framework of a Bayesian network allows for explainability in the model, reasoning and evidence. The use of these methods is mostly ad hoc and not as well organised as explainability methods in the wider AI research field. As such, we introduce a taxonomy of explainability in Bayesian networks. We extend the existing categorisation of explainability in the model, reasoning or evidence to include explanation of decisions. The explanations obtained from the explainability methods are illustrated by means of a simple medical diagnostic scenario. The taxonomy introduced in this paper has the potential not only to encourage end-users to efficiently communicate outcomes obtained, but also support their understanding of how and, more importantly, why certain predictions were made.

Recently, hetero-functional graph theory (HFGT) has developed as a means to mathematically model the structure of large flexible engineering systems. In that regard, it intellectually resembles a fusion of network science and model-based systems engineering. With respect to the former, it relies on multiple graphs as data structures so as to support matrix-based quantitative analysis. In the meantime, HFGT explicitly embodies the heterogeneity of conceptual and ontological constructs found in model-based systems engineering including system form, system function, and system concept. At their foundation, these disparate conceptual constructs suggest multi-dimensional rather than two-dimensional relationships. This paper provides the first tensor-based treatment of some of the most important parts of hetero-functional graph theory. In particular, it addresses the "system concept", the hetero-functional adjacency matrix, and the hetero-functional incidence tensor. The tensor-based formulation described in this work makes a stronger tie between HFGT and its ontological foundations in MBSE. Finally, the tensor-based formulation facilitates an understanding of the relationships between HFGT and multi-layer networks.

The Clustered Shortest-Path Tree Problem (CluSPT) plays an important role in various types of optimization problems in real-life. Recently, some Multifactorial Evolutionary Algorithm (MFEA) have been introduced to deal with the CluSPT, however these researches still have some shortcomings such as evolution operators only perform on complete graphs, huge resource consumption for finding the solution on large search spaces. To overcome these limitations, this paper describes a MFEA-based approach to solve the CluSPT. The proposed algorithm utilizes Dijkstra's algorithm to construct the spanning trees in clusters while using evolutionary operators for building the spanning tree connecting clusters. This approach takes advantage of both exact and approximate algorithms so it enables the algorithm to function efficiently on complete and sparse graphs alike. Furthermore, evolutionary operators such as individual encoding and decoding methods are also designed with great consideration regarding performance and memory usage. We have included a proof on the repairing method's efficacy in ensuring all solutions are valid. We have conducted tests on various types of Euclidean instances to assess the effectiveness of the proposed algorithm and methods. Experiment results point out the effectiveness of the proposed algorithm existing heuristic algorithms in most of the test cases. The impact of the proposed MFEA was analyzed and a possible influential factor that may be useful for further study was also pointed out.

This is a perspective paper inspired from the study of Turing Test proposed by A.M. Turing (23 June 1912 - 7 June 1954) in 1950. Following one important implication of Turing Test for enabling a machine with a human-like behavior or performance, we define human-like robustness (HLR) for AI machines. The objective of the new definition aims to enforce AI machines with HLR, including to evaluate them in terms of HLR. A specific task is discussed only on object identification, because it is the most common task for every person in daily life. Similar to the perspective, or design, position by Turing, we provide a solution of how to achieve HLR AI machines without constructing them and conducting real experiments. The solution should consists of three important features in the machines. The first feature of HLR machines is to utilize common sense from humans for realizing a causal inference. The second feature is to make a decision from a semantic space for having interpretations to the decision. The third feature is to include a "human-in-the-loop" setting for advancing HLR machines. We show an "identification game" using proposed design of HLR machines. The present paper shows an attempt to learn and explore further from Turing Test towards the design of human-like AI machines.

We define a modular multi-concept extension of the lexicographic closure semantics for defeasible description logics with typicality. The idea is that of distributing the defeasible properties of concepts into different modules, according to their subject, and of defining a notion of preference for each module based on the lexicographic closure semantics. The preferential semantics of the knowledge base can then be defined as a combination of the preferences of the single modules. The range of possibilities, from fine grained to coarse grained modules, provides a spectrum of alternative semantics.