arXiv subjects

Pietro Liò

Publications and source records attributed to Pietro Liò.

At least 199 records · Page 11Linked to original sources

arXiv2022

Heavy-tailed denoising score matching

Score-based model research in the last few years has produced state of the art generative models by employing Gaussian denoising score-matching (DSM). However, the Gaussian noise assumption has several high-dimensional limitations, motivating a more concrete route toward even higher dimension PDF estimation in future. We outline this limitation, before extending the theory to a broader family of noising distributions -- namely, the generalised normal distribution. To theoretically ground this, we relax a key assumption in (denoising) score matching theory, demonstrating that distributions which are differentiable almost everywhere permit the same objective simplification as Gaussians. For noise vector norm distributions, we demonstrate favourable concentration of measure in the high-dimensional spaces prevalent in deep learning. In the process, we uncover a skewed noise vector norm distribution and develop an iterative noise scaling algorithm to consistently initialise the multiple levels of noise in annealed Langevin dynamics (LD). On the practical side, our use of heavy-tailed DSM leads to improved score estimation, controllable sampling convergence, and more balanced unconditional generative performance for imbalanced datasets.

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arXiv2022

Adaptive Gaussian Processes on Graphs via Spectral Graph Wavelets

Graph-based models require aggregating information in the graph from neighbourhoods of different sizes. In particular, when the data exhibit varying levels of smoothness on the graph, a multi-scale approach is required to capture the relevant information. In this work, we propose a Gaussian process model using spectral graph wavelets, which can naturally aggregate neighbourhood information at different scales. Through maximum likelihood optimisation of the model hyperparameters, the wavelets automatically adapt to the different frequencies in the data, and as a result our model goes beyond capturing low frequency information. We achieve scalability to larger graphs by using a spectrum-adaptive polynomial approximation of the filter function, which is designed to yield a low approximation error in dense areas of the graph spectrum. Synthetic and real-world experiments demonstrate the ability of our model to infer scales accurately and produce competitive performances against state-of-the-art models in graph-based learning tasks.

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arXiv2022

Modular multi-source prediction of drug side-effects with DruGNN

Drug Side-Effects (DSEs) have a high impact on public health, care system costs, and drug discovery processes. Predicting the probability of side-effects, before their occurrence, is fundamental to reduce this impact, in particular on drug discovery. Candidate molecules could be screened before undergoing clinical trials, reducing the costs in time, money, and health of the participants. Drug side-effects are triggered by complex biological processes involving many different entities, from drug structures to protein-protein interactions. To predict their occurrence, it is necessary to integrate data from heterogeneous sources. In this work, such heterogeneous data is integrated into a graph dataset, expressively representing the relational information between different entities, such as drug molecules and genes. The relational nature of the dataset represents an important novelty for drug side-effect predictors. Graph Neural Networks (GNNs) are exploited to predict DSEs on our dataset with very promising results. GNNs are deep learning models that can process graph-structured data, with minimal information loss, and have been applied on a wide variety of biological tasks. Our experimental results confirm the advantage of using relationships between data entities, suggesting interesting future developments in this scope. The experimentation also shows the importance of specific subsets of data in determining associations between drugs and side-effects.

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arXiv2022

Weisfeiler and Lehman Go Cellular: CW Networks

Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the computational graph and the input graph structure. The recently proposed Message Passing Simplicial Networks naturally decouple these elements by performing message passing on the clique complex of the graph. Nevertheless, these models can be severely constrained by the rigid combinatorial structure of Simplicial Complexes (SCs). In this work, we extend recent theoretical results on SCs to regular Cell Complexes, topological objects that flexibly subsume SCs and graphs. We show that this generalisation provides a powerful set of graph "lifting" transformations, each leading to a unique hierarchical message passing procedure. The resulting methods, which we collectively call CW Networks (CWNs), are strictly more powerful than the WL test and not less powerful than the 3-WL test. In particular, we demonstrate the effectiveness of one such scheme, based on rings, when applied to molecular graph problems. The proposed architecture benefits from provably larger expressivity than commonly used GNNs, principled modelling of higher-order signals and from compressing the distances between nodes. We demonstrate that our model achieves state-of-the-art results on a variety of molecular datasets.

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arXiv2021

AI-based Reconstruction for Fast MRI -- A Systematic Review and Meta-analysis

Compressed sensing (CS) has been playing a key role in accelerating the magnetic resonance imaging (MRI) acquisition process. With the resurgence of artificial intelligence, deep neural networks and CS algorithms are being integrated to redefine the state of the art of fast MRI. The past several years have witnessed substantial growth in the complexity, diversity, and performance of deep learning-based CS techniques that are dedicated to fast MRI. In this meta-analysis, we systematically review the deep learning-based CS techniques for fast MRI, describe key model designs, highlight breakthroughs, and discuss promising directions. We have also introduced a comprehensive analysis framework and a classification system to assess the pivotal role of deep learning in CS-based acceleration for MRI.

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arXiv2021

Spectral Transform Forms Scalable Transformer

Many real-world relational systems, such as social networks and biological systems, contain dynamic interactions. When learning dynamic graph representation, it is essential to employ sequential temporal information and geometric structure. Mainstream work achieves topological embedding via message passing networks (e.g., GCN, GAT). The temporal evolution, on the other hand, is conventionally expressed via memory units (e.g., LSTM or GRU) that possess convenient information filtration in a gate mechanism. Though, such a design prevents large-scale input sequence due to the over-complicated encoding. This work learns from the philosophy of self-attention and proposes an efficient spectral-based neural unit that employs informative long-range temporal interaction. The developed spectral window unit (SWINIT) model predicts scalable dynamic graphs with assured efficiency. The architecture is assembled with a few simple effective computational blocks that constitute randomized SVD, MLP, and graph Framelet convolution. The SVD plus MLP module encodes the long-short-term feature evolution of the dynamic graph events. A fast framelet graph transform in the framelet convolution embeds the structural dynamics. Both strategies enhance the model's ability on scalable analysis. In particular, the iterative SVD approximation shrinks the computational complexity of attention to O(Nd\log(d)) for the dynamic graph with N edges and d edge features, and the multiscale transform of framelet convolution allows sufficient scalability in the network training. Our SWINIT achieves state-of-the-art performance on a variety of online continuous-time dynamic graph learning tasks, while compared to baseline methods, the number of its learnable parameters reduces by up to seven times.

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arXiv2021

Structure-aware generation of drug-like molecules

Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design), avoiding exhaustive virtual screening of chemical space. Most generative de-novo models fail to incorporate detailed ligand-protein interactions and 3D pocket structures. We propose a novel supervised model that generates molecular graphs jointly with 3D pose in a discretised molecular space. Molecules are built atom-by-atom inside pockets, guided by structural information from crystallographic data. We evaluate our model using a docking benchmark and find that guided generation improves predicted binding affinities by 8% and drug-likeness scores by 10% over the baseline. Furthermore, our model proposes molecules with binding scores exceeding some known ligands, which could be useful in future wet-lab studies.

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arXiv2021

Neural Distance Embeddings for Biological Sequences

The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that models evolution and the hierarchical relationship that characterises real-world datasets. We present Neural Distance Embeddings (NeuroSEED), a general framework to embed sequences in geometric vector spaces, and illustrate the effectiveness of the hyperbolic space that captures the hierarchical structure and provides an average 22% reduction in embedding RMSE against the best competing geometry. The capacity of the framework and the significance of these improvements are then demonstrated devising supervised and unsupervised NeuroSEED approaches to multiple core tasks in bioinformatics. Benchmarked with common baselines, the proposed approaches display significant accuracy and/or runtime improvements on real-world datasets. As an example for hierarchical clustering, the proposed pretrained and from-scratch methods match the quality of competing baselines with 30x and 15x runtime reduction, respectively.

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arXiv2021

An investigation of pre-upsampling generative modelling and Generative Adversarial Networks in audio super resolution

There have been several successful deep learning models that perform audio super-resolution. Many of these approaches involve using preprocessed feature extraction which requires a lot of domain-specific signal processing knowledge to implement. Convolutional Neural Networks (CNNs) improved upon this framework by automatically learning filters. An example of a convolutional approach is AudioUNet, which takes inspiration from novel methods of upsampling images. Our paper compares the pre-upsampling AudioUNet to a new generative model that upsamples the signal before using deep learning to transform it into a more believable signal. Based on the EDSR network for image super-resolution, the newly proposed model outperforms UNet with a 20% increase in log spectral distance and a mean opinion score of 4.06 compared to 3.82 for the two times upsampling case. AudioEDSR also has 87% fewer parameters than AudioUNet. How incorporating AudioUNet into a Wasserstein GAN (with gradient penalty) (WGAN-GP) structure can affect training is also explored. Finally the effects artifacting has on the current state of the art is analysed and solutions to this problem are proposed. The methods used in this paper have broad applications to telephony, audio recognition and audio generation tasks.

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arXiv2021

Neural ODE Processes

Neural Ordinary Differential Equations (NODEs) use a neural network to model the instantaneous rate of change in the state of a system. However, despite their apparent suitability for dynamics-governed time-series, NODEs present a few disadvantages. First, they are unable to adapt to incoming data points, a fundamental requirement for real-time applications imposed by the natural direction of time. Second, time series are often composed of a sparse set of measurements that could be explained by many possible underlying dynamics. NODEs do not capture this uncertainty. In contrast, Neural Processes (NPs) are a family of models providing uncertainty estimation and fast data adaptation but lack an explicit treatment of the flow of time. To address these problems, we introduce Neural ODE Processes (NDPs), a new class of stochastic processes determined by a distribution over Neural ODEs. By maintaining an adaptive data-dependent distribution over the underlying ODE, we show that our model can successfully capture the dynamics of low-dimensional systems from just a few data points. At the same time, we demonstrate that NDPs scale up to challenging high-dimensional time-series with unknown latent dynamics such as rotating MNIST digits.

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arXiv2021

Neural message passing for joint paratope-epitope prediction

Antibodies are proteins in the immune system which bind to antigens to detect and neutralise them. The binding sites in an antibody-antigen interaction are known as the paratope and epitope, respectively, and the prediction of these regions is key to vaccine and synthetic antibody development. Contrary to prior art, we argue that paratope and epitope predictors require asymmetric treatment, and propose distinct neural message passing architectures that are geared towards the specific aspects of paratope and epitope prediction, respectively. We obtain significant improvements on both tasks, setting the new state-of-the-art and recovering favourable qualitative predictions on antigens of relevance to COVID-19.

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arXiv2021

GCExplainer: Human-in-the-Loop Concept-based Explanations for Graph Neural Networks

While graph neural networks (GNNs) have been shown to perform well on graph-based data from a variety of fields, they suffer from a lack of transparency and accountability, which hinders trust and consequently the deployment of such models in high-stake and safety-critical scenarios. Even though recent research has investigated methods for explaining GNNs, these methods are limited to single-instance explanations, also known as local explanations. Motivated by the aim of providing global explanations, we adapt the well-known Automated Concept-based Explanation approach (Ghorbani et al., 2019) to GNN node and graph classification, and propose GCExplainer. GCExplainer is an unsupervised approach for post-hoc discovery and extraction of global concept-based explanations for GNNs, which puts the human in the loop. We demonstrate the success of our technique on five node classification datasets and two graph classification datasets, showing that we are able to discover and extract high-quality concept representations by putting the human in the loop. We achieve a maximum completeness score of 1 and an average completeness score of 0.753 across the datasets. Finally, we show that the concept-based explanations provide an improved insight into the datasets and GNN models compared to the state-of-the-art explanations produced by GNNExplainer (Ying et al., 2019).

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arXiv2021

High Frequency EEG Artifact Detection with Uncertainty via Early Exit Paradigm

Electroencephalography (EEG) is crucial for the monitoring and diagnosis of brain disorders. However, EEG signals suffer from perturbations caused by non-cerebral artifacts limiting their efficacy. Current artifact detection pipelines are resource-hungry and rely heavily on hand-crafted features. Moreover, these pipelines are deterministic in nature, making them unable to capture predictive uncertainty. We propose E4G, a deep learning framework for high frequency EEG artifact detection. Our framework exploits the early exit paradigm, building an implicit ensemble of models capable of capturing uncertainty. We evaluate our approach on the Temple University Hospital EEG Artifact Corpus (v2.0) achieving state-of-the-art classification results. In addition, E4G provides well-calibrated uncertainty metrics comparable to sampling techniques like Monte Carlo dropout in just a single forward pass. E4G opens the door to uncertainty-aware artifact detection supporting clinicians-in-the-loop frameworks.

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arXiv2021

Algorithmic Concept-based Explainable Reasoning

Recent research on graph neural network (GNN) models successfully applied GNNs to classical graph algorithms and combinatorial optimisation problems. This has numerous benefits, such as allowing applications of algorithms when preconditions are not satisfied, or reusing learned models when sufficient training data is not available or can't be generated. Unfortunately, a key hindrance of these approaches is their lack of explainability, since GNNs are black-box models that cannot be interpreted directly. In this work, we address this limitation by applying existing work on concept-based explanations to GNN models. We introduce concept-bottleneck GNNs, which rely on a modification to the GNN readout mechanism. Using three case studies we demonstrate that: (i) our proposed model is capable of accurately learning concepts and extracting propositional formulas based on the learned concepts for each target class; (ii) our concept-based GNN models achieve comparative performance with state-of-the-art models; (iii) we can derive global graph concepts, without explicitly providing any supervision on graph-level concepts.

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arXiv2021

Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks

The pairwise interaction paradigm of graph machine learning has predominantly governed the modelling of relational systems. However, graphs alone cannot capture the multi-level interactions present in many complex systems and the expressive power of such schemes was proven to be limited. To overcome these limitations, we propose Message Passing Simplicial Networks (MPSNs), a class of models that perform message passing on simplicial complexes (SCs). To theoretically analyse the expressivity of our model we introduce a Simplicial Weisfeiler-Lehman (SWL) colouring procedure for distinguishing non-isomorphic SCs. We relate the power of SWL to the problem of distinguishing non-isomorphic graphs and show that SWL and MPSNs are strictly more powerful than the WL test and not less powerful than the 3-WL test. We deepen the analysis by comparing our model with traditional graph neural networks (GNNs) with ReLU activations in terms of the number of linear regions of the functions they can represent. We empirically support our theoretical claims by showing that MPSNs can distinguish challenging strongly regular graphs for which GNNs fail and, when equipped with orientation equivariant layers, they can improve classification accuracy in oriented SCs compared to a GNN baseline.

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arXiv2021

An Effective Loss Function for Generating 3D Models from Single 2D Image without Rendering

Differentiable rendering is a very successful technique that applies to a Single-View 3D Reconstruction. Current renderers use losses based on pixels between a rendered image of some 3D reconstructed object and ground-truth images from given matched viewpoints to optimise parameters of the 3D shape. These models require a rendering step, along with visibility handling and evaluation of the shading model. The main goal of this paper is to demonstrate that we can avoid these steps and still get reconstruction results as other state-of-the-art models that are equal or even better than existing category-specific reconstruction methods. First, we use the same CNN architecture for the prediction of a point cloud shape and pose prediction like the one used by Insafutdinov & Dosovitskiy. Secondly, we propose the novel effective loss function that evaluates how well the projections of reconstructed 3D point clouds cover the ground truth object's silhouette. Then we use Poisson Surface Reconstruction to transform the reconstructed point cloud into a 3D mesh. Finally, we perform a GAN-based texture mapping on a particular 3D mesh and produce a textured 3D mesh from a single 2D image. We evaluate our method on different datasets (including ShapeNet, CUB-200-2011, and Pascal3D+) and achieve state-of-the-art results, outperforming all the other supervised and unsupervised methods and 3D representations, all in terms of performance, accuracy, and training time.

cs.CV↗

arXiv2021

Meta-learning using privileged information for dynamics

Neural ODE Processes approach the problem of meta-learning for dynamics using a latent variable model, which permits a flexible aggregation of contextual information. This flexibility is inherited from the Neural Process framework and allows the model to aggregate sets of context observations of arbitrary size into a fixed-length representation. In the physical sciences, we often have access to structured knowledge in addition to raw observations of a system, such as the value of a conserved quantity or a description of an understood component. Taking advantage of the aggregation flexibility, we extend the Neural ODE Process model to use additional information within the Learning Using Privileged Information setting, and we validate our extension with experiments showing improved accuracy and calibration on simulated dynamics tasks.

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arXiv2021

Is Disentanglement all you need? Comparing Concept-based & Disentanglement Approaches

Concept-based explanations have emerged as a popular way of extracting human-interpretable representations from deep discriminative models. At the same time, the disentanglement learning literature has focused on extracting similar representations in an unsupervised or weakly-supervised way, using deep generative models. Despite the overlapping goals and potential synergies, to our knowledge, there has not yet been a systematic comparison of the limitations and trade-offs between concept-based explanations and disentanglement approaches. In this paper, we give an overview of these fields, comparing and contrasting their properties and behaviours on a diverse set of tasks, and highlighting their potential strengths and limitations. In particular, we demonstrate that state-of-the-art approaches from both classes can be data inefficient, sensitive to the specific nature of the classification/regression task, or sensitive to the employed concept representation.

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