arXiv subjects

Pietro Lió

Publications and source records attributed to Pietro Lió.

16 recordsLinked to original sources

arXiv2023

A Feature Reuse Framework with Texture-adaptive Aggregation for Reference-based Super-Resolution

Reference-based super-resolution (RefSR) has gained considerable success in the field of super-resolution with the addition of high-resolution reference images to reconstruct low-resolution (LR) inputs with more high-frequency details, thereby overcoming some limitations of single image super-resolution (SISR). Previous research in the field of RefSR has mostly focused on two crucial aspects. The first is accurate correspondence matching between the LR and the reference (Ref) image. The second is the effective transfer and aggregation of similar texture information from the Ref images. Nonetheless, an important detail of perceptual loss and adversarial loss has been underestimated, which has a certain adverse effect on texture transfer and reconstruction. In this study, we propose a feature reuse framework that guides the step-by-step texture reconstruction process through different stages, reducing the negative impacts of perceptual and adversarial loss. The feature reuse framework can be used for any RefSR model, and several RefSR approaches have improved their performance after being retrained using our framework. Additionally, we introduce a single image feature embedding module and a texture-adaptive aggregation module. The single image feature embedding module assists in reconstructing the features of the LR inputs itself and effectively lowers the possibility of including irrelevant textures. The texture-adaptive aggregation module dynamically perceives and aggregates texture information between the LR inputs and the Ref images using dynamic filters. This enhances the utilization of the reference texture while reducing reference misuse. The source code is available at https://github.com/Yi-Yang355/FRFSR.

cs.CV↗

arXiv2023

Global Concept-Based Interpretability for Graph Neural Networks via Neuron Analysis

Graph neural networks (GNNs) are highly effective on a variety of graph-related tasks; however, they lack interpretability and transparency. Current explainability approaches are typically local and treat GNNs as black-boxes. They do not look inside the model, inhibiting human trust in the model and explanations. Motivated by the ability of neurons to detect high-level semantic concepts in vision models, we perform a novel analysis on the behaviour of individual GNN neurons to answer questions about GNN interpretability, and propose new metrics for evaluating the interpretability of GNN neurons. We propose a novel approach for producing global explanations for GNNs using neuron-level concepts to enable practitioners to have a high-level view of the model. Specifically, (i) to the best of our knowledge, this is the first work which shows that GNN neurons act as concept detectors and have strong alignment with concepts formulated as logical compositions of node degree and neighbourhood properties; (ii) we quantitatively assess the importance of detected concepts, and identify a trade-off between training duration and neuron-level interpretability; (iii) we demonstrate that our global explainability approach has advantages over the current state-of-the-art -- we can disentangle the explanation into individual interpretable concepts backed by logical descriptions, which reduces potential for bias and improves user-friendliness.

cs.LG↗

arXiv2022

Entropy-based Logic Explanations of Neural Networks

Explainable artificial intelligence has rapidly emerged since lawmakers have started requiring interpretable models for safety-critical domains. Concept-based neural networks have arisen as explainable-by-design methods as they leverage human-understandable symbols (i.e. concepts) to predict class memberships. However, most of these approaches focus on the identification of the most relevant concepts but do not provide concise, formal explanations of how such concepts are leveraged by the classifier to make predictions. In this paper, we propose a novel end-to-end differentiable approach enabling the extraction of logic explanations from neural networks using the formalism of First-Order Logic. The method relies on an entropy-based criterion which automatically identifies the most relevant concepts. We consider four different case studies to demonstrate that: (i) this entropy-based criterion enables the distillation of concise logic explanations in safety-critical domains from clinical data to computer vision; (ii) the proposed approach outperforms state-of-the-art white-box models in terms of classification accuracy and matches black box performances.

cs.AI↗

arXiv2022

Approximate Latent Force Model Inference

Physically-inspired latent force models offer an interpretable alternative to purely data driven tools for inference in dynamical systems. They carry the structure of differential equations and the flexibility of Gaussian processes, yielding interpretable parameters and dynamics-imposed latent functions. However, the existing inference techniques associated with these models rely on the exact computation of posterior kernel terms which are seldom available in analytical form. Most applications relevant to practitioners, such as Hill equations or diffusion equations, are hence intractable. In this paper, we overcome these computational problems by proposing a variational solution to a general class of non-linear and parabolic partial differential equation latent force models. Further, we show that a neural operator approach can scale our model to thousands of instances, enabling fast, distributed computation. We demonstrate the efficacy and flexibility of our framework by achieving competitive performance on several tasks where the kernels are of varying degrees of tractability.

cs.LG↗

arXiv2021

Logic Explained Networks

The large and still increasing popularity of deep learning clashes with a major limit of neural network architectures, that consists in their lack of capability in providing human-understandable motivations of their decisions. In situations in which the machine is expected to support the decision of human experts, providing a comprehensible explanation is a feature of crucial importance. The language used to communicate the explanations must be formal enough to be implementable in a machine and friendly enough to be understandable by a wide audience. In this paper, we propose a general approach to Explainable Artificial Intelligence in the case of neural architectures, showing how a mindful design of the networks leads to a family of interpretable deep learning models called Logic Explained Networks (LENs). LENs only require their inputs to be human-understandable predicates, and they provide explanations in terms of simple First-Order Logic (FOL) formulas involving such predicates. LENs are general enough to cover a large number of scenarios. Amongst them, we consider the case in which LENs are directly used as special classifiers with the capability of being explainable, or when they act as additional networks with the role of creating the conditions for making a black-box classifier explainable by FOL formulas. Despite supervised learning problems are mostly emphasized, we also show that LENs can learn and provide explanations in unsupervised learning settings. Experimental results on several datasets and tasks show that LENs may yield better classifications than established white-box models, such as decision trees and Bayesian rule lists, while providing more compact and meaningful explanations.

cs.LG↗

arXiv2020

Gene Regulatory Network Inference with Latent Force Models

Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug side-effects. We present a model which incorporates translation delays by combining mechanistic equations and Bayesian approaches to fit to experimental data. This enables greater biological interpretability, and the use of Gaussian processes enables non-linear expressivity through kernels as well as naturally accounting for biological variation.

q-bio.MN↗

arXiv2020

Graph representation forecasting of patient's medical conditions: towards a digital twin

Objective: Modern medicine needs to shift from a wait and react, curative discipline to a preventative, interdisciplinary science aiming at providing personalised, systemic and precise treatment plans to patients. The aim of this work is to present how the integration of machine learning approaches with mechanistic computational modelling could yield a reliable infrastructure to run probabilistic simulations where the entire organism is considered as a whole. Methods: We propose a general framework that composes advanced AI approaches and integrates mathematical modelling in order to provide a panoramic view over current and future physiological conditions. The proposed architecture is based on a graph neural network (GNNs) forecasting clinically relevant endpoints (such as blood pressure) and a generative adversarial network (GANs) providing a proof of concept of transcriptomic integrability. Results: We show the results of the investigation of pathological effects of overexpression of ACE2 across different signalling pathways in multiple tissues on cardiovascular functions. We provide a proof of concept of integrating a large set of composable clinical models using molecular data to drive local and global clinical parameters and derive future trajectories representing the evolution of the physiological state of the patient. Significance: We argue that the graph representation of a computational patient has potential to solve important technological challenges in integrating multiscale computational modelling with AI. We believe that this work represents a step forward towards a healthcare digital twin.

stat.ML↗

arXiv2020

The Computational Patient has Diabetes and a COVID

Medicine is moving from a curative discipline to a preventative discipline relying on personalised and precise treatment plans. The complex and multi level pathophysiological patterns of most diseases require a systemic medicine approach and are challenging current medical therapies. On the other hand, computational medicine is a vibrant interdisciplinary field that could help move from an organ-centered approach to a process-oriented approach. The ideal computational patient would require an international interdisciplinary effort, of larger scientific and technological interdisciplinarity than the Human Genome Project. When deployed, such a patient would have a profound impact on how healthcare is delivered to patients. Here we present a computational patient model that integrates, refines and extends recent mechanistic or phenomenological models of cardiovascular, RAS and diabetic processes. Our aim is twofold: analyse the modularity and composability of the model-building blocks of the computational patient and to study the dynamical properties of well-being and disease states in a broader functional context. We present results from a number of experiments among which we characterise the dynamic impact of COVID-19 and type-2 diabetes (T2D) on cardiovascular and inflammation conditions. We tested these experiments under different exercise, meal and drug regimens. We report results showing the striking importance of transient dynamical responses to acute state conditions and we provide guidelines for system design principles for the inter-relationship between modules and components in systemic medicine. Finally this initial computational Patient can be used as a toolbox for further modifications and extensions.

cs.CE↗

arXiv2020

Proximal Distilled Evolutionary Reinforcement Learning

Reinforcement Learning (RL) has achieved impressive performance in many complex environments due to the integration with Deep Neural Networks (DNNs). At the same time, Genetic Algorithms (GAs), often seen as a competing approach to RL, had limited success in scaling up to the DNNs required to solve challenging tasks. Contrary to this dichotomic view, in the physical world, evolution and learning are complementary processes that continuously interact. The recently proposed Evolutionary Reinforcement Learning (ERL) framework has demonstrated mutual benefits to performance when combining the two methods. However, ERL has not fully addressed the scalability problem of GAs. In this paper, we show that this problem is rooted in an unfortunate combination of a simple genetic encoding for DNNs and the use of traditional biologically-inspired variation operators. When applied to these encodings, the standard operators are destructive and cause catastrophic forgetting of the traits the networks acquired. We propose a novel algorithm called Proximal Distilled Evolutionary Reinforcement Learning (PDERL) that is characterised by a hierarchical integration between evolution and learning. The main innovation of PDERL is the use of learning-based variation operators that compensate for the simplicity of the genetic representation. Unlike traditional operators, our proposals meet the functional requirements of variation operators when applied on directly-encoded DNNs. We evaluate PDERL in five robot locomotion settings from the OpenAI gym. Our method outperforms ERL, as well as two state-of-the-art RL algorithms, PPO and TD3, in all tested environments.

cs.LG↗

arXiv2019

Perturbation theory approach to study the latent space degeneracy of Variational Autoencoders

The use of Variational Autoencoders in different Machine Learning tasks has drastically increased in the last years. They have been developed as denoising, clustering and generative tools, highlighting a large potential in a wide range of fields. Their embeddings are able to extract relevant information from highly dimensional inputs, but the converged models can differ significantly and lead to degeneracy on the latent space. We leverage the relation between theoretical physics and machine learning to explain this behaviour, and introduce a new approach to correct for degeneration by using perturbation theory. The re-formulation of the embedding as multi-dimensional generative distribution, allows mapping to a new set of functions and their corresponding energy spectrum. We optimise for a perturbed Hamiltonian, with an additional energy potential that is related to the unobserved topology of the data. Our results show the potential of a new theoretical approach that can be used to interpret the latent space and generative nature of unsupervised learning, while the energy landscapes defined by the perturbations can be further used for modelling and dynamical purposes.

cs.LG↗

arXiv2019

Factorised Neural Relational Inference for Multi-Interaction Systems

Many complex natural and cultural phenomena are well modelled by systems of simple interactions between particles. A number of architectures have been developed to articulate this kind of structure, both implicitly and explicitly. We consider an unsupervised explicit model, the NRI model, and make a series of representational adaptations and physically motivated changes. Most notably we factorise the inferred latent interaction graph into a multiplex graph, allowing each layer to encode for a different interaction-type. This fNRI model is smaller in size and significantly outperforms the original in both edge and trajectory prediction, establishing a new state-of-the-art. We also present a simplified variant of our model, which demonstrates the NRI's formulation as a variational auto-encoder is not necessary for good performance, and make an adaptation to the NRI's training routine, significantly improving its ability to model complex physical dynamical systems.

cs.LG↗

arXiv2018

Seeing the wood for the trees: a forest of methods for optimisation and omic-network integration in metabolic modelling

Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees. Driven by this analogy, we here present a "forest" of principal methods used for constraint-based modelling in systems biology. This provides a tree-based view of methods available to prospective modellers, also available in interactive version at http://modellingmetabolism.net, where it will be kept updated with new methods after the publication of the present manuscript. Our updated classification of existing methods and tools highlights the most promising in the different branches, with the aim to develop a vision of how existing methods could hybridise and become more complex. We then provide the first hands-on tutorial for multi-objective optimisation of metabolic models in R. We finally discuss the implementation of multi-view machine-learning approaches in poly-omic integration. Throughout this work, we demonstrate the optimisation of trade-offs between multiple metabolic objectives, with a focus on omic data integration through machine learning. We anticipate that the combination of a survey, a perspective on multi-view machine learning, and a step-by-step R tutorial should be of interest for both the beginner and the advanced user.

q-bio.MN↗

arXiv2017

Learning Rare Word Representations using Semantic Bridging

We propose a methodology that adapts graph embedding techniques (DeepWalk (Perozzi et al., 2014) and node2vec (Grover and Leskovec, 2016)) as well as cross-lingual vector space mapping approaches (Least Squares and Canonical Correlation Analysis) in order to merge the corpus and ontological sources of lexical knowledge. We also perform comparative analysis of the used algorithms in order to identify the best combination for the proposed system. We then apply this to the task of enhancing the coverage of an existing word embedding's vocabulary with rare and unseen words. We show that our technique can provide considerable extra coverage (over 99%), leading to consistent performance gain (around 10% absolute gain is achieved with w2v-gn-500K cf.§3.3) on the Rare Word Similarity dataset.

cs.CL↗

arXiv2017

Comparative Study of Inference Methods for Bayesian Nonnegative Matrix Factorisation

In this paper, we study the trade-offs of different inference approaches for Bayesian matrix factorisation methods, which are commonly used for predicting missing values, and for finding patterns in the data. In particular, we consider Bayesian nonnegative variants of matrix factorisation and tri-factorisation, and compare non-probabilistic inference, Gibbs sampling, variational Bayesian inference, and a maximum-a-posteriori approach. The variational approach is new for the Bayesian nonnegative models. We compare their convergence, and robustness to noise and sparsity of the data, on both synthetic and real-world datasets. Furthermore, we extend the models with the Bayesian automatic relevance determination prior, allowing the models to perform automatic model selection, and demonstrate its efficiency.

stat.ML↗

arXiv2017

Modelling the order of driver mutations and metabolic mutations as structures in cancer dynamics

Recent works have stressed the important role that random mutations have in the development of cancer phenotype. We challenge this current view by means of bioinformatic data analysis and computational modelling approaches. Not all the mutations are equally important for the development of metastasis. The survival of cancer cells from the primary tumour site to the secondary seeding sites depends on the occurrence of very few driver mutations promoting oncogenic cell behaviours and on the order with which these mutations occur. We introduce a model in the framework of Cellular Automata to investigate the effects of metabolic mutations and mutation order on cancer stemness and tumour cell migration in bone metastasised breast cancers. The metabolism of the cancer cell is a key factor in its proliferation rate. Bioinformatics analysis on a cancer mutation database shows that metabolism-modifying alterations constitute an important class of key cancer mutations. Our approach models three types of mutations: drivers, the order of which is relevant for the dynamics, metabolic which support cancer growth and are estimated from existing databases, and non--driver mutations. Our results provide a quantitative basis of how the order of driver mutations and the metabolic mutations in different cancer clones could impact proliferation of therapy-resistant clonal populations and patient survival. Further mathematical modelling of the order of mutations is presented in terms of operators. We believe our work is novel because it quantifies two important factors in cancer spreading models: the order of driver mutations and the effects of metabolic mutations.

q-bio.CB↗

arXiv2017

Bayesian Hybrid Matrix Factorisation for Data Integration

We introduce a novel Bayesian hybrid matrix factorisation model (HMF) for data integration, based on combining multiple matrix factorisation methods, that can be used for in- and out-of-matrix prediction of missing values. The model is very general and can be used to integrate many datasets across different entity types, including repeated experiments, similarity matrices, and very sparse datasets. We apply our method on two biological applications, and extensively compare it to state-of-the-art machine learning and matrix factorisation models. For in-matrix predictions on drug sensitivity datasets we obtain consistently better performances than existing methods. This is especially the case when we increase the sparsity of the datasets. Furthermore, we perform out-of-matrix predictions on methylation and gene expression datasets, and obtain the best results on two of the three datasets, especially when the predictivity of datasets is high.

stat.ML↗