arXiv subjects

Stephen Bonner

Publications and source records attributed to Stephen Bonner.

At least 19 recordsLinked to original sources

arXiv2024

The Role of Graph Topology in the Performance of Biomedical Knowledge Graph Completion Models

Knowledge Graph Completion has been increasingly adopted as a useful method for helping address several tasks in biomedical research, such as drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models have been proposed over the years. However, little is known about the properties that render a dataset, and associated modelling choices, useful for a given task. Moreover, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. In this work, we conduct a comprehensive investigation into the topological properties of publicly available biomedical Knowledge Graphs and establish links to the accuracy observed in real-world tasks. By releasing all model predictions and a new suite of analysis tools we invite the community to build upon our work and continue improving the understanding of these crucial applications.

cs.LG↗

arXiv2021

Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs

Adoption of recently developed methods from machine learning has given rise to creation of drug-discovery knowledge graphs (KG) that utilize the interconnected nature of the domain. Graph-based modelling of the data, combined with KG embedding (KGE) methods, are promising as they provide a more intuitive representation and are suitable for inference tasks such as predicting missing links. One common application is to produce ranked lists of genes for a given disease, where the rank is based on the perceived likelihood of association between the gene and the disease. It is thus critical that these predictions are not only pertinent but also biologically meaningful. However, KGs can be biased either directly due to the underlying data sources that are integrated or due to modeling choices in the construction of the graph, one consequence of which is that certain entities can get topologically overrepresented. We demonstrate the effect of these inherent structural imbalances, resulting in densely-connected entities being highly ranked no matter the context. We provide support for this observation across different datasets, models as well as predictive tasks. Further, we present various graph perturbation experiments which yield more support to the observation that KGE models can be more influenced by the frequency of entities rather than any biological information encoded within the relations. Our results highlight the importance of data modeling choices, and emphasizes the need for practitioners to be mindful of these issues when interpreting model outputs and during KG composition.

cs.LG↗

arXiv2021

A Unified View of Relational Deep Learning for Drug Pair Scoring

In recent years, numerous machine learning models which attempt to solve polypharmacy side effect identification, drug-drug interaction prediction and combination therapy design tasks have been proposed. Here, we present a unified theoretical view of relational machine learning models which can address these tasks. We provide fundamental definitions, compare existing model architectures and discuss performance metrics, datasets and evaluation protocols. In addition, we emphasize possible high impact applications and important future research directions in this domain.

cs.LG↗

arXiv2021

A Knowledge Graph-Enhanced Tensor Factorisation Model for Discovering Drug Targets

The drug discovery and development process is a long and expensive one, costing over 1 billion USD on average per drug and taking 10-15 years. To reduce the high levels of attrition throughout the process, there has been a growing interest in applying machine learning methodologies to various stages of drug discovery and development in the recent decade, especially at the earliest stage identification of druggable disease genes. In this paper, we have developed a new tensor factorisation model to predict potential drug targets (genes or proteins) for treating diseases. We created a three dimensional data tensor consisting of 1,048 gene targets, 860 diseases and 230,011 evidence attributes and clinical outcomes connecting them, using data extracted from the Open Targets and PharmaProjects databases. We enriched the data with gene target representations learned from a drug discovery oriented knowledge graph and applied our proposed method to predict the clinical outcomes for unseen gene target and disease pairs. We designed three evaluation strategies to measure the prediction performance and benchmarked several commonly used machine learning classifiers together with Bayesian matrix and tensor factorisation methods. The result shows that incorporating knowledge graph embeddings significantly improves the prediction accuracy and that training tensor factorisation alongside a dense neural network outperforms all other baselines. In summary, our framework combines two actively studied machine learning approaches to disease target identification, namely tensor factorisation and knowledge graph representation learning, which could be a promising avenue for further exploration in data driven drug discovery.

q-bio.QM↗

arXiv2021

Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery

Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug discovery domain, KGs can be employed as part of a process which can result in lab-based experiments being performed, or impact on other decisions, incurring significant time and financial costs and most importantly, ultimately influencing patient healthcare. For KGE models to have impact in this domain, a better understanding of not only of performance, but also the various factors which determine it, is required. In this study we investigate, over the course of many thousands of experiments, the predictive performance of five KGE models on two public drug discovery-oriented KGs. Our goal is not to focus on the best overall model or configuration, instead we take a deeper look at how performance can be affected by changes in the training setup, choice of hyperparameters, model parameter initialisation seed and different splits of the datasets. Our results highlight that these factors have significant impact on performance and can even affect the ranking of models. Indeed these factors should be reported along with model architectures to ensure complete reproducibility and fair comparisons of future work, and we argue this is critical for the acceptance of use, and impact of KGEs in a biomedical setting.

q-bio.BM↗

arXiv2021

A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective

Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use Knowledge Graphs (KG) have promise in many tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritisation. In a drug discovery KG, crucial elements including genes, diseases and drugs are represented as entities, whilst relationships between them indicate an interaction. However, to construct high-quality KGs, suitable data is required. In this review, we detail publicly available sources suitable for use in constructing drug discovery focused KGs. We aim to help guide machine learning and KG practitioners who are interested in applying new techniques to the drug discovery field, but who may be unfamiliar with the relevant data sources. The datasets are selected via strict criteria, categorised according to the primary type of information contained within and are considered based upon what information could be extracted to build a KG. We then present a comparative analysis of existing public drug discovery KGs and a evaluation of selected motivating case studies from the literature. Additionally, we raise numerous and unique challenges and issues associated with the domain and its datasets, whilst also highlighting key future research directions. We hope this review will motivate KGs use in solving key and emerging questions in the drug discovery domain.

cs.AI↗

arXiv2020

Not Half Bad: Exploring Half-Precision in Graph Convolutional Neural Networks

With the growing significance of graphs as an effective representation of data in numerous applications, efficient graph analysis using modern machine learning is receiving a growing level of attention. Deep learning approaches often operate over the entire adjacency matrix -- as the input and intermediate network layers are all designed in proportion to the size of the adjacency matrix -- leading to intensive computation and large memory requirements as the graph size increases. It is therefore desirable to identify efficient measures to reduce both run-time and memory requirements allowing for the analysis of the largest graphs possible. The use of reduced precision operations within the forward and backward passes of a deep neural network along with novel specialised hardware in modern GPUs can offer promising avenues towards efficiency. In this paper, we provide an in-depth exploration of the use of reduced-precision operations, easily integrable into the highly popular PyTorch framework, and an analysis of the effects of Tensor Cores on graph convolutional neural networks. We perform an extensive experimental evaluation of three GPU architectures and two widely-used graph analysis tasks (vertex classification and link prediction) using well-known benchmark and synthetically generated datasets. Thus allowing us to make important observations on the effects of reduced-precision operations and Tensor Cores on computational and memory usage of graph convolutional neural networks -- often neglected in the literature.

cs.LG↗

arXiv2020

Neuronal graphs: a graph theory primer for microscopic, functional networks of neurons recorded by Calcium imaging

Connected networks are a fundamental structure of neurobiology. Understanding these networks will help us elucidate the neural mechanisms of computation. Mathematically speaking these networks are `graphs' - structures containing objects that are connected. In neuroscience, the objects could be regions of the brain, e.g. fMRI data, or be individual neurons, e.g. calcium imaging with fluorescence microscopy. The formal study of graphs, graph theory, can provide neuroscientists with a large bank of algorithms for exploring networks. Graph theory has already been applied in a variety of ways to fMRI data but, more recently, has begun to be applied at the scales of neurons, e.g. from functional calcium imaging. In this primer we explain the basics of graph theory and relate them to features of microscopic functional networks of neurons from calcium imaging - neuronal graphs. We explore recent examples of graph theory applied to calcium imaging and we highlight some areas where researchers new to the field could go awry.

q-bio.NC↗

arXiv2020

Rank over Class: The Untapped Potential of Ranking in Natural Language Processing

Text classification has long been a staple within Natural Language Processing (NLP) with applications spanning across diverse areas such as sentiment analysis, recommender systems and spam detection. With such a powerful solution, it is often tempting to use it as the go-to tool for all NLP problems since when you are holding a hammer, everything looks like a nail. However, we argue here that many tasks which are currently addressed using classification are in fact being shoehorned into a classification mould and that if we instead address them as a ranking problem, we not only improve the model, but we achieve better performance. We propose a novel end-to-end ranking approach consisting of a Transformer network responsible for producing representations for a pair of text sequences, which are in turn passed into a context aggregating network outputting ranking scores used to determine an ordering to the sequences based on some notion of relevance. We perform numerous experiments on publicly-available datasets and investigate the applications of ranking in problems often solved using classification. In an experiment on a heavily-skewed sentiment analysis dataset, converting ranking results to classification labels yields an approximately 22% improvement over state-of-the-art text classification, demonstrating the efficacy of text ranking over text classification in certain scenarios.

cs.CL↗

arXiv2020

BLOB : A Probabilistic Model for Recommendation that Combines Organic and Bandit Signals

A common task for recommender systems is to build a pro le of the interests of a user from items in their browsing history and later to recommend items to the user from the same catalog. The users' behavior consists of two parts: the sequence of items that they viewed without intervention (the organic part) and the sequences of items recommended to them and their outcome (the bandit part). In this paper, we propose Bayesian Latent Organic Bandit model (BLOB), a probabilistic approach to combine the 'or-ganic' and 'bandit' signals in order to improve the estimation of recommendation quality. The bandit signal is valuable as it gives direct feedback of recommendation performance, but the signal quality is very uneven, as it is highly concentrated on the recommendations deemed optimal by the past version of the recom-mender system. In contrast, the organic signal is typically strong and covers most items, but is not always relevant to the recommendation task. In order to leverage the organic signal to e ciently learn the bandit signal in a Bayesian model we identify three fundamental types of distances, namely action-history, action-action and history-history distances. We implement a scalable approximation of the full model using variational auto-encoders and the local re-paramerization trick. We show using extensive simulation studies that our method out-performs or matches the value of both state-of-the-art organic-based recommendation algorithms, and of bandit-based methods (both value and policy-based) both in organic and bandit-rich environments.

stat.ML↗

arXiv2020

Camera Bias in a Fine Grained Classification Task

We show that correlations between the camera used to acquire an image and the class label of that image can be exploited by convolutional neural networks (CNN), resulting in a model that "cheats" at an image classification task by recognizing which camera took the image and inferring the class label from the camera. We show that models trained on a dataset with camera / label correlations do not generalize well to images in which those correlations are absent, nor to images from unencountered cameras. Furthermore, we investigate which visual features they are exploiting for camera recognition. Our experiments present evidence against the importance of global color statistics, lens deformation and chromatic aberration, and in favor of high frequency features, which may be introduced by image processing algorithms built into the cameras.

cs.CV↗

arXiv2020

Leveraging Synthetic Subject Invariant EEG Signals for Zero Calibration BCI

Recently, substantial progress has been made in the area of Brain-Computer Interface (BCI) using modern machine learning techniques to decode and interpret brain signals. While Electroencephalography (EEG) has provided a non-invasive method of interfacing with a human brain, the acquired data is often heavily subject and session dependent. This makes seamless incorporation of such data into real-world applications intractable as the subject and session data variance can lead to long and tedious calibration requirements and cross-subject generalisation issues. Focusing on a Steady State Visual Evoked Potential (SSVEP) classification systems, we propose a novel means of generating highly-realistic synthetic EEG data invariant to any subject, session or other environmental conditions. Our approach, entitled the Subject Invariant SSVEP Generative Adversarial Network (SIS-GAN), produces synthetic EEG data from multiple SSVEP classes using a single network. Additionally, by taking advantage of a fixed-weight pre-trained subject classification network, we ensure that our generative model remains agnostic to subject-specific features and thus produces subject-invariant data that can be applied to new previously unseen subjects. Our extensive experimental evaluation demonstrates the efficacy of our synthetic data, leading to superior performance, with improvements of up to 16 percentage points in zero-calibration classification tasks when trained using our subject-invariant synthetic EEG signals.

eess.SP↗

arXiv2019

Volenti non fit injuria: Ransomware and its Victims

With the recent growth in the number of malicious activities on the internet, cybersecurity research has seen a boost in the past few years. However, as certain variants of malware can provide highly lucrative opportunities for bad actors, significant resources are dedicated to innovations and improvements by vast criminal organisations. Among these forms of malware, ransomware has experienced a significant recent rise as it offers the perpetrators great financial incentive. Ransomware variants operate by removing system access from the user by either locking the system or encrypting some or all of the data, and subsequently demanding payment or ransom in exchange for returning system access or providing a decryption key to the victim. Due to the ubiquity of sensitive data in many aspects of modern life, many victims of such attacks, be they an individual home user or operators of a business, are forced to pay the ransom to regain access to their data, which in many cases does not happen as renormalisation of system operations is never guaranteed. As the problem of ransomware does not seem to be subsiding, it is very important to investigate the underlying forces driving and facilitating such attacks in order to create preventative measures. As such, in this paper, we discuss and provide further insight into variants of ransomware and their victims in order to understand how and why they have been targeted and what can be done to prevent or mitigate the effects of such attacks.

cs.CR↗

arXiv2019

Reconsidering Analytical Variational Bounds for Output Layers of Deep Networks

The combination of the re-parameterization trick with the use of variational auto-encoders has caused a sensation in Bayesian deep learning, allowing the training of realistic generative models of images and has considerably increased our ability to use scalable latent variable models. The re-parameterization trick is necessary for models in which no analytical variational bound is available and allows noisy gradients to be computed for arbitrary models. However, for certain standard output layers of a neural network, analytical bounds are available and the variational auto-encoder may be used both without the re-parameterization trick or the need for any Monte Carlo approximation. In this work, we show that using Jaakola and Jordan bound, we can produce a binary classification layer that allows a Bayesian output layer to be trained, using the standard stochastic gradient descent algorithm. We further demonstrate that a latent variable model utilizing the Bouchard bound for multi-class classification allows for fast training of a fully probabilistic latent factor model, even when the number of classes is very large.

stat.ML↗

arXiv2019

Temporal Neighbourhood Aggregation: Predicting Future Links in Temporal Graphs via Recurrent Variational Graph Convolutions

Graphs have become a crucial way to represent large, complex and often temporal datasets across a wide range of scientific disciplines. However, when graphs are used as input to machine learning models, this rich temporal information is frequently disregarded during the learning process, resulting in suboptimal performance on certain temporal infernce tasks. To combat this, we introduce Temporal Neighbourhood Aggregation (TNA), a novel vertex representation model architecture designed to capture both topological and temporal information to directly predict future graph states. Our model exploits hierarchical recurrence at different depths within the graph to enable exploration of changes in temporal neighbourhoods, whilst requiring no additional features or labels to be present. The final vertex representations are created using variational sampling and are optimised to directly predict the next graph in the sequence. Our claims are reinforced by extensive experimental evaluation on both real and synthetic benchmark datasets, where our approach demonstrates superior performance compared to competing methods, out-performing them at predicting new temporal edges by as much as 23% on real-world datasets, whilst also requiring fewer overall model parameters.

cs.SI↗

arXiv2019

A Kings Ransom for Encryption: Ransomware Classification using Augmented One-Shot Learning and Bayesian Approximation

Newly emerging variants of ransomware pose an ever-growing threat to computer systems governing every aspect of modern life through the handling and analysis of big data. While various recent security-based approaches have focused on detecting and classifying ransomware at the network or system level, easy-to-use post-infection ransomware classification for the lay user has not been attempted before. In this paper, we investigate the possibility of classifying the ransomware a system is infected with simply based on a screenshot of the splash screen or the ransom note captured using a consumer camera commonly found in any modern mobile device. To train and evaluate our system, we create a sample dataset of the splash screens of 50 well-known ransomware variants. In our dataset, only a single training image is available per ransomware. Instead of creating a large training dataset of ransomware screenshots, we simulate screenshot capture conditions via carefully designed data augmentation techniques, enabling simple and efficient one-shot learning. Moreover, using model uncertainty obtained via Bayesian approximation, we ensure special input cases such as unrelated non-ransomware images and previously-unseen ransomware variants are correctly identified for special handling and not mis-classified. Extensive experimental evaluation demonstrates the efficacy of our work, with accuracy levels of up to 93.6% for ransomware classification.

cs.CV↗

arXiv2019

Latent Variable Session-Based Recommendation

Session based recommendation provides an attractive alternative to the traditional feature engineering approach to recommendation. Feature engineering approaches require hand tuned features of the users history to be created to produce a context vector. In contrast a session based approach is able to dynamically model the users state as they act. We present a probabilistic framework for session based recommendation. A latent variable for the user state is updated as the user views more items and we learn more about their interests. The latent variable model is conceptually simple and elegant; yet requires sophisticated computational technique to approximate the integral over the latent variable. We provide computational solutions using both the re-parameterization trick and also using the Bouchard bound for the softmax function, we further explore employing a variational auto-encoder and a variational Expectation-Maximization algorithm for tightening the variational bound. The model performs well against a number of baselines. The intuitive nature of the model allows an elegant formulation combining correlations between items and their popularity and that sheds light on other popular recommendation methods. An attractive feature of the latent variable approach is that, as the user continues to act, the posterior on the user's state tightens reflecting the recommender system's increased knowledge about that user.

cs.IR↗

arXiv2019

Causal Embeddings for Recommendation: An Extended Abstract

Recommendations are commonly used to modify user's natural behavior, for example, increasing product sales or the time spent on a website. This results in a gap between the ultimate business objective and the classical setup where recommendations are optimized to be coherent with past user behavior. To bridge this gap, we propose a new learning setup for recommendation that optimizes for the Incremental Treatment Effect (ITE) of the policy. We show this is equivalent to learning to predict recommendation outcomes under a fully random recommendation policy and propose a new domain adaptation algorithm that learns from logged data containing outcomes from a biased recommendation policy and predicts recommendation outcomes according to random exposure. We compare our method against state-of-the-art factorization methods, in addition to new approaches of causal recommendation and show significant improvements.

cs.IR↗