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The surge of pelagic \emph{Sargassum} in the Intra-America Seas, particularly the Caribbean Sea, since the early 2010s has raised significant ecological concerns. This study emphasizes the need for a mechanistic understanding of \emph{Sargassum} dynamics to elucidate the ecological impacts and uncertainties associated with blooms. By introducing a novel transport model, physical components such as ocean currents and winds are integrated with biological aspects affecting the \emph{Sargassum} life cycle, including reproduction, grounded in an enhanced Maxey--Riley theory for floating particles. Nonlinear elastic forces among the particles are included to simulate interactions within and among \emph{Sargassum} rafts. This promotes aggregation, consistent with observations, within oceanic eddies, which facilitate their transport. This cannot be achieved by the so-called leeway approach to transport, which forms the basis of current \emph{Sargassum} modeling. Using satellite-derived data, the model is validated, outperforming the leeway model. Publicly accessible codes are provided to support further research and ecosystem management efforts. This comprehensive approach is expected to improve predictive capabilities and management strategies regarding \emph{Sargassum} dynamics in affected regions, thus contributing to a deeper understanding of marine ecosystem dynamics and resilience., Comment: To appear in PNAS Nexus

How does the human visual cortex encode sensory information? To address this question, we explore the covariance structure of neural representations. We perform a cross-decomposition analysis of fMRI responses to natural images in multiple individuals from the Natural Scenes Dataset and find that neural representations systematically exhibit a power-law covariance spectrum over four orders of magnitude in ranks. This scale-free structure is found in multiple regions along the visual hierarchy, pointing to the existence of a generic encoding strategy in visual cortex. We also show that, up to a rotation, a large ensemble of principal axes of these population codes are shared across subjects, showing the existence of a universal high-dimensional representation. This suggests a high level of convergence in how the human brain learns to represent natural scenes despite individual differences in neuroanatomy and experience. We further demonstrate that a spectral approach is critical for characterizing population codes in their full extent, and in doing so, we reveal a vast space of uncharted dimensions that have been out of reach for conventional variance-weighted methods. A global view of neural representations thus requires embracing their high-dimensional nature and understanding them statistically rather than through visual or semantic interpretation of individual dimensions., Comment: 22 pages, 4 main figures, 7 supplementary figures

Knowledge Graph Completion has been increasingly adopted as a useful method for several tasks in biomedical research, like drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models has been proposed over the years. However, little is known about the properties that render a dataset useful for a given task and, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. 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 applications. 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.

Do neural network models of vision learn brain-aligned representations because they share architectural constraints and task objectives with biological vision or because they learn universal features of natural image processing? We characterized the universality of hundreds of thousands of representational dimensions from visual neural networks with varied construction. We found that networks with varied architectures and task objectives learn to represent natural images using a shared set of latent dimensions, despite appearing highly distinct at a surface level. Next, by comparing these networks with human brain representations measured with fMRI, we found that the most brain-aligned representations in neural networks are those that are universal and independent of a network's specific characteristics. Remarkably, each network can be reduced to fewer than ten of its most universal dimensions with little impact on its representational similarity to the human brain. These results suggest that the underlying similarities between artificial and biological vision are primarily governed by a core set of universal image representations that are convergently learned by diverse systems.

Maintaining a robust communication network plays an important role in the success of a multi-robot team jointly performing an optimization task. A key characteristic of a robust cooperative multi-robot system is the ability to repair the communication topology in the case of robot failure. In this paper, we focus on the Fast k-connectivity Restoration (FCR) problem, which aims to repair a network to make it k-connected with minimum robot movement. We develop a Quadratically Constrained Program (QCP) formulation of the FCR problem, which provides a way to optimally solve the problem, but cannot handle large instances due to high computational overhead. We therefore present a scalable algorithm, called EA-SCR, for the FCR problem using graph theoretic concepts. By conducting empirical studies, we demonstrate that the EA-SCR algorithm performs within 10 percent of the optimal while being orders of magnitude faster. We also show that EA-SCR outperforms existing solutions by 30 percent in terms of the FCR distance metric., Comment: 17 pages, 6 figures, 3 algorithms. arXiv admin note: text overlap with arXiv:2011.00685

Dimension reduction techniques are among the most essential analytical tools in the analysis of high-dimensional data. Generalized principal component analysis (PCA) is an extension to standard PCA that has been widely used to identify low-dimensional features in high-dimensional discrete data, such as binary, multi-category and count data. For microbiome count data in particular, the multinomial PCA is a natural counterpart of the standard PCA. However, this technique fails to account for the excessive number of zero values, which is frequently observed in microbiome count data. To allow for sparsity, zero-inflated multivariate distributions can be used. We propose a zero-inflated probabilistic PCA model for latent factor analysis. The proposed model is a fully Bayesian factor analysis technique that is appropriate for microbiome count data analysis. In addition, we use the mean-field-type variational family to approximate the marginal likelihood and develop a classification variational approximation algorithm to fit the model. We demonstrate the efficiency of our procedure for predictions based on the latent factors and the model parameters through simulation experiments, showcasing its superiority over competing methods. This efficiency is further illustrated with two real microbiome count datasets. The method is implemented in R., Comment: 2 figures, 3 tables

A recent Maxey--Riley theory for \sarg raft motion, which models a raft as a network of elastically interacting finite-size, buoyant particles, predicts the carrying flow velocity to be given by the weighted sum of the water and air velocities $(1-\alpha)\mathbf{v} + \alpha \mathbf w$. The theory provides a closed formula for parameter $\alpha$, referred to as \emph{windage}, depending on water-to-particle-density ratio or buoyancy ($\delta$). From a series of laboratory experiments in an air--water stream flume facility under controlled conditions, we estimate $\alpha$ ranging from 0.02 to 0.96\pct. On average, our windage estimates can be up to 9 times smaller than considered in conventional \emph{Sargassum} raft transport modeling, wherein it is customary to add a fraction of $\mathbf w$ to $\mathbf{v}$ chosen in an ad-hoc piecemeal manner. Using the formula provided by the Maxey--Riley theory, we estimate $\delta$ ranging from 1.00 to 1.49. This is consistent with direct $\delta$ measurements, ranging from 0.9 to 1.25, which provide support for our $\alpha$ estimation.

Let $\{U(n)\}_{n \geq 0}$ be a sequence of independent random variables such that $U(n)$ is distributed uniformly on $\{0, 1, 2 \dots n\}$. The Ulam-Kac adder is the history-dependent random sequence defined by $X_{n + 1} = X_{n} + X_{U(n)}$ with the initial condition $X_0 = 1$. We show that for each $m \geq 1$, it holds that $\log E[X_n^m]/\sqrt{n}$ approaches a constant $c_m$ as $n \to \infty$. Loose bounds are provided for the constants $c_m$., Comment: Fixed typos, updated references/end matter. Removed citation of a conjecture which has actually been decided (in the negative.)

Transition Path Theory (TPT) provides a rigorous statistical characterization of the ensemble of trajectories connecting directly, i.e., without detours, two disconnected (sets of) states in a Markov chain, a stochastic process that undergoes transitions from one state to another with probability depending on the state attained in the previous step. Markov chains can be constructed using trajectory data via counting of transitions between cells covering the domain spanned by trajectories. With sparse trajectory data, the use of regular cells is observed to result in unstable estimates of the total duration of transition paths. Using Voronoi cells resulting from k-means clustering of the trajectory data, we obtain stable estimates of this TPT statistic, which is generalized to frame the remaining duration of transition paths, a new TPT statistic suitable for investigating connectivity., Comment: Submitted to Chaos. Comments welcomed!

Background: Deep learning (DL) can extract predictive and prognostic biomarkers from routine pathology slides in colorectal cancer. For example, a DL test for the diagnosis of microsatellite instability (MSI) in CRC has been approved in 2022. Current approaches rely on convolutional neural networks (CNNs). Transformer networks are outperforming CNNs and are replacing them in many applications, but have not been used for biomarker prediction in cancer at a large scale. In addition, most DL approaches have been trained on small patient cohorts, which limits their clinical utility. Methods: In this study, we developed a new fully transformer-based pipeline for end-to-end biomarker prediction from pathology slides. We combine a pre-trained transformer encoder and a transformer network for patch aggregation, capable of yielding single and multi-target prediction at patient level. We train our pipeline on over 9,000 patients from 10 colorectal cancer cohorts. Results: A fully transformer-based approach massively improves the performance, generalizability, data efficiency, and interpretability as compared with current state-of-the-art algorithms. After training on a large multicenter cohort, we achieve a sensitivity of 0.97 with a negative predictive value of 0.99 for MSI prediction on surgical resection specimens. We demonstrate for the first time that resection specimen-only training reaches clinical-grade performance on endoscopic biopsy tissue, solving a long-standing diagnostic problem. Interpretation: A fully transformer-based end-to-end pipeline trained on thousands of pathology slides yields clinical-grade performance for biomarker prediction on surgical resections and biopsies. Our new methods are freely available under an open source license., Comment: Updated Figure 2 and Table A.5

Multimodal object recognition is still an emerging field. Thus, publicly available datasets are still rare and of small size. This dataset was developed to help fill this void and presents multimodal data for 63 objects with some visual and haptic ambiguity. The dataset contains visual, kinesthetic and tactile (audio/vibrations) data. To completely solve sensory ambiguity, sensory integration/fusion would be required. This report describes the creation and structure of the dataset. The first section explains the underlying approach used to capture the visual and haptic properties of the objects. The second section describes the technical aspects (experimental setup) needed for the collection of the data. The third section introduces the objects, while the final section describes the structure and content of the dataset.

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., Comment: Briefings in Bioinformatics, 2022

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.

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., Comment: 16 pages, 4 figures, IEEE/ACM Transactions on Computational Biology and Bioinformatics

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.

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.

An overview of the UAM chatbot application.

Contact tracing apps have become one of the main approaches to control and slow down the spread of COVID-19 and ease up lockdown measures. While these apps can be very effective in stopping the transmission chain and saving lives, their adoption remains under the expected critical mass. The public debate about contact tracing apps emphasizes general privacy reservations and is conducted at an expert level, but lacks the user perspective related to actual designs. To address this gap, we explore user preferences for contact tracing apps using market research techniques, and specifically conjoint analysis. Our main contributions are empirical insights into individual and group preferences, as well as insights for prescriptive design. While our results confirm the privacy-preserving design of most European contact tracing apps, they also provide a more nuanced understanding of acceptable features. Based on market simulation and variation analysis, we conclude that adding goal-congruent features will play an important role in fostering mass adoption.

We report a large area photo-diode based homodyne detector for free-space quantum coherent communication. The detector's performance is studied in terms of detection bandwidth and electronic noise for shot-noise limited quantum signal detection. Using large area photo-diodes increases signal collection efficiency from turbulent atmospheric channels, in comparison with typical fibre based free-space homodyne detectors. Under identical atmospheric turbulence and receiver aperture conditions, our homodyne detector based on 1mm diameter photo-diode experiences 0dB loss due to turbulence while a 10um fibre based detector experiences 13.5dB of signal loss over a 700km free-space link, at 90 degree elevation angle., Comment: 6 pages, 6 figures

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.

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., Comment: 28 pages, 11 figures, 1 table, 2 boxes

We study a model for the entanglement of a two-dimensional reflecting Brownian motion in a bounded region divided into two halves by a wall with three or more small windows. We map the Brownian motion into a Markov Chain on the fundamental groupoid of the region. We quantify entanglement of the path with the length of the appropriate element in this groupoid. Our main results are a law of large numbers and a central limit theorem for this quantity. The constants appearing in the limit theorems are expressed in terms of a coupled system of quadratic equations., Comment: 30 pages, 5 figures. AMSart style with Tikz

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., Comment: 2021 IEEE International Conference on Big Data (IEEE BigData 2021)

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., Comment: 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Aug 2020, San Diego, United States

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., Comment: Accepted as a full paper at the 25th International Conference on Pattern Recognition (ICPR2020)

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.

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., Comment: 2019 IEEE International Conference on Big Data 2019

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., Comment: 8 pages 2 figures

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., Comment: IEEE International Conference on Big Data 2019

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., Comment: Submitted to 2019 IEEE International Conference on Big Data

Measuring graph clustering quality remains an open problem. To address it, we introduce quality measures based on comparisons of intra- and inter-cluster densities, an accompanying statistical test of the significance of their differences and a step-by-step routine for clustering quality assessment. Our null hypothesis does not rely on any generative model for the graph, unlike modularity which uses the configuration model as a null model. Our measures are shown to meet the axioms of a good clustering quality function, unlike the very commonly used modularity measure. They also have an intuitive graph-theoretic interpretation, a formal statistical interpretation and can be easily tested for significance. Our work is centered on the idea that well clustered graphs will display a significantly larger intra-cluster density than inter-cluster density. We develop tests to validate the existence of such a cluster structure. We empirically explore the behavior of our measures under a number of stress test scenarios and compare their behavior to the commonly used modularity and conductance measures. Empirical stress test results confirm that our measures compare very favorably to the established ones. In particular, they are shown to be more responsive to graph structure and less sensitive to sample size and breakdowns during numerical implementation and less sensitive to uncertainty in connectivity. These features are especially important in the context of larger data sets or when the data may contain errors in the connectivity patterns.

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.