arXiv subjects

Pietro Liò

Publications and source records attributed to Pietro Liò.

At least 235 records · Page 13Linked to original sources

arXiv2020

A Multiscale Graph Convolutional Network Using Hierarchical Clustering

The information contained in hierarchical topology, intrinsic to many networks, is currently underutilised. A novel architecture is explored which exploits this information through a multiscale decomposition. A dendrogram is produced by a Girvan-Newman hierarchical clustering algorithm. It is segmented and fed through graph convolutional layers, allowing the architecture to learn multiple scale latent space representations of the network, from fine to coarse grained. The architecture is tested on a benchmark citation network, demonstrating competitive performance. Given the abundance of hierarchical networks, possible applications include quantum molecular property prediction, protein interface prediction and multiscale computational substrates for partial differential equations.

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arXiv2020

tvGP-VAE: Tensor-variate Gaussian Process Prior Variational Autoencoder

Variational autoencoders (VAEs) are a powerful class of deep generative latent variable model for unsupervised representation learning on high-dimensional data. To ensure computational tractability, VAEs are often implemented with a univariate standard Gaussian prior and a mean-field Gaussian variational posterior distribution. This results in a vector-valued latent variables that are agnostic to the original data structure which might be highly correlated across and within multiple dimensions. We propose a tensor-variate extension to the VAE framework, the tensor-variate Gaussian process prior variational autoencoder (tvGP-VAE), which replaces the standard univariate Gaussian prior and posterior distributions with tensor-variate Gaussian processes. The tvGP-VAE is able to explicitly model correlation structures via the use of kernel functions over the dimensions of tensor-valued latent variables. Using spatiotemporally correlated image time series as an example, we show that the choice of which correlation structures to explicitly represent in the latent space has a significant impact on model performance in terms of reconstruction.

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arXiv2020

MARLeME: A Multi-Agent Reinforcement Learning Model Extraction Library

Multi-Agent Reinforcement Learning (MARL) encompasses a powerful class of methodologies that have been applied in a wide range of fields. An effective way to further empower these methodologies is to develop libraries and tools that could expand their interpretability and explainability. In this work, we introduce MARLeME: a MARL model extraction library, designed to improve explainability of MARL systems by approximating them with symbolic models. Symbolic models offer a high degree of interpretability, well-defined properties, and verifiable behaviour. Consequently, they can be used to inspect and better understand the underlying MARL system and corresponding MARL agents, as well as to replace all/some of the agents that are particularly safety and security critical.

cs.LG↗

arXiv2020

Adaptive Prediction Timing for Electronic Health Records

In realistic scenarios, multivariate timeseries evolve over case-by-case time-scales. This is particularly clear in medicine, where the rate of clinical events varies by ward, patient, and application. Increasingly complex models have been shown to effectively predict patient outcomes, but have failed to adapt granularity to these inherent temporal resolutions. As such, we introduce a novel, more realistic, approach to generating patient outcome predictions at an adaptive rate based on uncertainty accumulation in Bayesian recurrent models. We use a Recurrent Neural Network (RNN) and a Bayesian embedding layer with a new aggregation method to demonstrate adaptive prediction timing. Our model predicts more frequently when events are dense or the model is certain of event latent representations, and less frequently when readings are sparse or the model is uncertain. At 48 hours after patient admission, our model achieves equal performance compared to its static-windowed counterparts, while generating patient- and event-specific prediction timings that lead to improved predictive performance over the crucial first 12 hours of the patient stay.

cs.LG↗

arXiv2020

Towards a predictive spatio-temporal representation of brain data

The characterisation of the brain as a "connectome", in which the connections are represented by correlational values across timeseries and as summary measures derived from graph theory analyses, has been very popular in the last years. However, although this representation has advanced our understanding of the brain function, it may represent an oversimplified model. This is because the typical fMRI datasets are constituted by complex and highly heterogeneous timeseries that vary across space (i.e., location of brain regions). We compare various modelling techniques from deep learning and geometric deep learning to pave the way for future research in effectively leveraging the rich spatial and temporal domains of typical fMRI datasets, as well as of other similar datasets. As a proof-of-concept, we compare our approaches in the homogeneous and publicly available Human Connectome Project (HCP) dataset on a supervised binary classification task. We hope that our methodological advances relative to previous "connectomic" measures can ultimately be clinically and computationally relevant by leading to a more nuanced understanding of the brain dynamics in health and disease. Such understanding of the brain can fundamentally reduce the constant specialised clinical expertise in order to accurately understand brain variability.

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arXiv2020

Deep Graph Mapper: Seeing Graphs through the Neural Lens

Recent advancements in graph representation learning have led to the emergence of condensed encodings that capture the main properties of a graph. However, even though these abstract representations are powerful for downstream tasks, they are not equally suitable for visualisation purposes. In this work, we merge Mapper, an algorithm from the field of Topological Data Analysis (TDA), with the expressive power of Graph Neural Networks (GNNs) to produce hierarchical, topologically-grounded visualisations of graphs. These visualisations do not only help discern the structure of complex graphs but also provide a means of understanding the models applied to them for solving various tasks. We further demonstrate the suitability of Mapper as a topological framework for graph pooling by mathematically proving an equivalence with Min-Cut and Diff Pool. Building upon this framework, we introduce a novel pooling algorithm based on PageRank, which obtains competitive results with state of the art methods on graph classification benchmarks.

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arXiv2020

Graph Convolutional Gaussian Processes For Link Prediction

Link prediction aims to reveal missing edges in a graph. We address this task with a Gaussian process that is transformed using simplified graph convolutions to better leverage the inductive bias of the domain. To scale the Gaussian process model to large graphs, we introduce a variational inducing point method that places pseudo inputs on a graph-structured domain. We evaluate our model on eight large graphs with up to thousands of nodes and report consistent improvements over existing Gaussian process models as well as competitive performance when compared to state-of-the-art graph neural network approaches.

cs.LG↗

arXiv2020

A machine learning approach to investigate regulatory control circuits in bacterial metabolic pathways

In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than others in term of their multi-omics follows from the analysis of these circuits . This is a consequence of the alternation of the omic values of codon usage and protein abundance along with the circuits. In this work, the E.Coli's Glycolysis and its multi-omic circuit features are shown as an example.

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arXiv2019

Co-Attentive Cross-Modal Deep Learning for Medical Evidence Synthesis and Decision Making

Modern medicine requires generalised approaches to the synthesis and integration of multimodal data, often at different biological scales, that can be applied to a variety of evidence structures, such as complex disease analyses and epidemiological models. However, current methods are either slow and expensive, or ineffective due to the inability to model the complex relationships between data modes which differ in scale and format. We address these issues by proposing a cross-modal deep learning architecture and co-attention mechanism to accurately model the relationships between the different data modes, while further reducing patient diagnosis time. Differentiating Parkinson's Disease (PD) patients from healthy patients forms the basis of the evaluation. The model outperforms the previous state-of-the-art unimodal analysis by 2.35%, while also being 53% more parameter efficient than the industry standard cross-modal model. Furthermore, the evaluation of the attention coefficients allows for qualitative insights to be obtained. Through the coupling with bioinformatics, a novel link between the interferon-gamma-mediated pathway, DNA methylation and PD was identified. We believe that our approach is general and could optimise the process of medical evidence synthesis and decision making in an actionable way.

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arXiv2019

Dynamic survival prediction in intensive care units from heterogeneous time series without the need for variable selection or pre-processing

We present a machine learning pipeline and model that uses the entire uncurated EHR for prediction of in-hospital mortality at arbitrary time intervals, using all available chart, lab and output events, without the need for pre-processing or feature engineering. Data for more than 45,000 American ICU patients from the MIMIC-III database were used to develop an ICU mortality prediction model. All chart, lab and output events were treated by the model in the same manner inspired by Natural Language Processing (NLP). Patient events were discretized by percentile and mapped to learnt embeddings before being passed to a Recurrent Neural Network (RNN) to provide early prediction of in-patient mortality risk. We compared mortality predictions with the Simplified Acute Physiology Score II (SAPS II) and the Oxford Acute Severity of Illness Score (OASIS). Data were split into an independent test set (10%) and a ten-fold cross-validation was carried out during training to avoid overfitting. 13,233 distinct variables with heterogeneous data types were included without manual selection or pre-processing. Recordings in the first few hours of a patient's stay were found to be strongly predictive of mortality, outperforming models using SAPS II and OASIS scores within just 2 hours and achieving a state of the art Area Under the Receiver Operating Characteristic (AUROC) value of 0.80 (95% CI 0.79-0.80) at 12 hours vs 0.70 and 0.66 for SAPS II and OASIS at 24 hours respectively. Our model achieves a very strong performance of AUROC 0.86 (95% CI 0.85-0.86) for in-patient mortality prediction after 48 hours on the MIMIC-III dataset. Predictive performance increases over the first 48 hours of the ICU stay, but suffers from diminishing returns, providing rationale for time-limited trials of critical care and suggesting that the timing of decision making can be optimised and individualised.

cs.LG↗

arXiv2019

Impact of novel aggregation methods for flexible, time-sensitive EHR prediction without variable selection or cleaning

Dynamic assessment of patient status (e.g. by an automated, continuously updated assessment of outcome) in the Intensive Care Unit (ICU) is of paramount importance for early alerting, decision support and resource allocation. Extraction and cleaning of expert-selected clinical variables discards information and protracts collaborative efforts to introduce machine learning in medicine. We present improved aggregation methods for a flexible deep learning architecture which learns a joint representation of patient chart, lab and output events. Our models outperform recent deep learning models for patient mortality classification using ICU timeseries, by embedding and aggregating all events with no pre-processing or variable selection. Our model achieves a strong performance of AUROC 0.87 at 48 hours on the MIMIC-III dataset while using 13,233 unique un-preprocessed variables in an interpretable manner via hourly softmax aggregation. This demonstrates how our method can be easily combined with existing electronic health record systems for automated, dynamic patient risk analysis.

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arXiv2019

VideoNavQA: Bridging the Gap between Visual and Embodied Question Answering

Embodied Question Answering (EQA) is a recently proposed task, where an agent is placed in a rich 3D environment and must act based solely on its egocentric input to answer a given question. The desired outcome is that the agent learns to combine capabilities such as scene understanding, navigation and language understanding in order to perform complex reasoning in the visual world. However, initial advancements combining standard vision and language methods with imitation and reinforcement learning algorithms have shown EQA might be too complex and challenging for these techniques. In order to investigate the feasibility of EQA-type tasks, we build the VideoNavQA dataset that contains pairs of questions and videos generated in the House3D environment. The goal of this dataset is to assess question-answering performance from nearly-ideal navigation paths, while considering a much more complete variety of questions than current instantiations of the EQA task. We investigate several models, adapted from popular VQA methods, on this new benchmark. This establishes an initial understanding of how well VQA-style methods can perform within this novel EQA paradigm.

cs.CV↗

arXiv2019

ncRNA Classification with Graph Convolutional Networks

Non-coding RNA (ncRNA) are RNA sequences which don't code for a gene but instead carry important biological functions. The task of ncRNA classification consists in classifying a given ncRNA sequence into its family. While it has been shown that the graph structure of an ncRNA sequence folding is of great importance for the prediction of its family, current methods make use of machine learning classifiers on hand-crafted graph features. We improve on the state-of-the-art for this task with a graph convolutional network model which achieves an accuracy of 85.73% and an F1-score of 85.61% over 13 classes. Moreover, our model learns in an end-to-end fashion from the raw RNA graphs and removes the need for expensive feature extraction. To the best of our knowledge, this also represents the first successful application of graph convolutional networks to RNA folding data.

q-bio.GN↗

arXiv2019

On Graph Classification Networks, Datasets and Baselines

Graph classification receives a great deal of attention from the non-Euclidean machine learning community. Recent advances in graph coarsening have enabled the training of deeper networks and produced new state-of-the-art results in many benchmark tasks. We examine how these architectures train and find that performance is highly-sensitive to initialisation and depends strongly on jumping-knowledge structures. We then show that, despite the great complexity of these models, competitive performance is achieved by the simplest of models -- structure-blind MLP, single-layer GCN and fixed-weight GCN -- and propose these be included as baselines in future.

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arXiv2019

Drug-Drug Adverse Effect Prediction with Graph Co-Attention

Complex or co-existing diseases are commonly treated using drug combinations, which can lead to higher risk of adverse side effects. The detection of polypharmacy side effects is usually done in Phase IV clinical trials, but there are still plenty which remain undiscovered when the drugs are put on the market. Such accidents have been affecting an increasing proportion of the population (15% in the US now) and it is thus of high interest to be able to predict the potential side effects as early as possible. Systematic combinatorial screening of possible drug-drug interactions (DDI) is challenging and expensive. However, the recent significant increases in data availability from pharmaceutical research and development efforts offer a novel paradigm for recovering relevant insights for DDI prediction. Accordingly, several recent approaches focus on curating massive DDI datasets (with millions of examples) and training machine learning models on them. Here we propose a neural network architecture able to set state-of-the-art results on this task---using the type of the side-effect and the molecular structure of the drugs alone---by leveraging a co-attentional mechanism. In particular, we show the importance of integrating joint information from the drug pairs early on when learning each drug's representation.

stat.ML↗

arXiv2019

Spatio-Temporal Deep Graph Infomax

Spatio-temporal graphs such as traffic networks or gene regulatory systems present challenges for the existing deep learning methods due to the complexity of structural changes over time. To address these issues, we introduce Spatio-Temporal Deep Graph Infomax (STDGI)---a fully unsupervised node representation learning approach based on mutual information maximization that exploits both the temporal and spatial dynamics of the graph. Our model tackles the challenging task of node-level regression by training embeddings to maximize the mutual information between patches of the graph, at any given time step, and between features of the central nodes of patches, in the future. We demonstrate through experiments and qualitative studies that the learned representations can successfully encode relevant information about the input graph and improve the predictive performance of spatio-temporal auto-regressive forecasting models.

cs.LG↗

arXiv2019

XFlow: Cross-modal Deep Neural Networks for Audiovisual Classification

In recent years, there have been numerous developments towards solving multimodal tasks, aiming to learn a stronger representation than through a single modality. Certain aspects of the data can be particularly useful in this case - for example, correlations in the space or time domain across modalities - but should be wisely exploited in order to benefit from their full predictive potential. We propose two deep learning architectures with multimodal cross-connections that allow for dataflow between several feature extractors (XFlow). Our models derive more interpretable features and achieve better performances than models which do not exchange representations, usefully exploiting correlations between audio and visual data, which have a different dimensionality and are nontrivially exchangeable. Our work improves on existing multimodal deep learning algorithms in two essential ways: (1) it presents a novel method for performing cross-modality (before features are learned from individual modalities) and (2) extends the previously proposed cross-connections which only transfer information between streams that process compatible data. Illustrating some of the representations learned by the connections, we analyse their contribution to the increase in discrimination ability and reveal their compatibility with a lip-reading network intermediate representation. We provide the research community with Digits, a new dataset consisting of three data types extracted from videos of people saying the digits 0-9. Results show that both cross-modal architectures outperform their baselines (by up to 11.5%) when evaluated on the AVletters, CUAVE and Digits datasets, achieving state-of-the-art results.

stat.ML↗

arXiv2019

ChronoMID - Cross-Modal Neural Networks for 3-D Temporal Medical Imaging Data

ChronoMID builds on the success of cross-modal convolutional neural networks (X-CNNs), making the novel application of the technique to medical imaging data. Specifically, this paper presents and compares alternative approaches - timestamps and difference images - to incorporate temporal information for the classification of bone disease in mice, applied to micro-CT scans of mouse tibiae. Whilst much previous work on diseases and disease classification has been based on mathematical models incorporating domain expertise and the explicit encoding of assumptions, the approaches given here utilise the growing availability of computing resources to analyse large datasets and uncover subtle patterns in both space and time. After training on a balanced set of over 75000 images, all models incorporating temporal features outperformed a state-of-the-art CNN baseline on an unseen, balanced validation set comprising over 20000 images. The top-performing model achieved 99.54% accuracy, compared to 73.02% for the CNN baseline.

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