arXiv subjects

Pietro Liò

Publications and source records attributed to Pietro Liò.

250 records · Page 14Linked to original sources

arXiv2018

Deep Graph Infomax

We present Deep Graph Infomax (DGI), a general approach for learning node representations within graph-structured data in an unsupervised manner. DGI relies on maximizing mutual information between patch representations and corresponding high-level summaries of graphs---both derived using established graph convolutional network architectures. The learnt patch representations summarize subgraphs centered around nodes of interest, and can thus be reused for downstream node-wise learning tasks. In contrast to most prior approaches to unsupervised learning with GCNs, DGI does not rely on random walk objectives, and is readily applicable to both transductive and inductive learning setups. We demonstrate competitive performance on a variety of node classification benchmarks, which at times even exceeds the performance of supervised learning.

stat.ML↗

arXiv2018

GenHap: A Novel Computational Method Based on Genetic Algorithms for Haplotype Assembly

The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. Indeed, the knowledge of complete haplotypes is generally more informative than analyzing single SNPs and plays a fundamental role in many medical applications. To reconstruct the two haplotypes, we addressed the weighted Minimum Error Correction (wMEC) problem, which is a successful approach for haplotype assembly. This NP-hard problem consists in computing the two haplotypes that partition the sequencing reads into two disjoint sub-sets, with the least number of corrections to the SNP values. To this aim, we propose here GenHap, a novel computational method for haplotype assembly based on Genetic Algorithms, yielding optimal solutions by means of a global search process. In order to evaluate the effectiveness of our approach, we run GenHap on two synthetic (yet realistic) datasets, based on the Roche/454 and PacBio RS II sequencing technologies. We compared the performance of GenHap against HapCol, an efficient state-of-the-art algorithm for haplotype phasing. Our results show that GenHap always obtains high accuracy solutions (in terms of haplotype error rate), and is up to 4x faster than HapCol in the case of Roche/454 instances and up to 20x faster when compared on the PacBio RS II dataset. Finally, we assessed the performance of GenHap on two different real datasets. Future-generation sequencing technologies, producing longer reads with higher coverage, can highly benefit from GenHap, thanks to its capability of efficiently solving large instances of the haplotype assembly problem.

q-bio.GN↗

arXiv2018

Modelling trait dependent speciation with Approximate Bayesian Computation

Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is hampered by the lack of robust software to estimate the numerous parameters of the speciation process. In this work we present an R package, pcmabc, based on Approximate Bayesian Computations, that implements three novel phylogenetic algorithms for trait-dependent speciation modelling. Our phylogenetic comparative methodology takes into account both the simulated traits and phylogeny, attempting to estimate the parameters of the processes generating the phenotype and the trait. The user is not restricted to a predefined set of models and can specify a variety of evolutionary and branching models. We illustrate the software with a simulation-reestimation study focused around the branching Ornstein-Uhlenbeck process, where the branching rate depends non-linearly on the value of the driving Ornstein-Uhlenbeck process. Included in this work is a tutorial on how to use the software.

q-bio.PE↗

arXiv2018

Structure-Based Networks for Drug Validation

Classifying chemicals according to putative modes of action (MOAs) is of paramount importance in the context of risk assessment. However, current methods are only able to handle a very small proportion of the existing chemicals. We address this issue by proposing an integrative deep learning architecture that learns a joint representation from molecular structures of drugs and their effects on human cells. Our choice of architecture is motivated by the significant influence of a drug's chemical structure on its MOA. We improve on the strong ability of a unimodal architecture (F1 score of 0.803) to classify drugs by their toxic MOAs (Verhaar scheme) through adding another learning stream that processes transcriptional responses of human cells affected by drugs. Our integrative model achieves an even higher classification performance on the LINCS L1000 dataset - the error is reduced by 4.6%. We believe that our method can be used to extend the current Verhaar scheme and constitute a basis for fast drug validation and risk assessment.

q-bio.QM↗

arXiv2018

Towards Sparse Hierarchical Graph Classifiers

Recent advances in representation learning on graphs, mainly leveraging graph convolutional networks, have brought a substantial improvement on many graph-based benchmark tasks. While novel approaches to learning node embeddings are highly suitable for node classification and link prediction, their application to graph classification (predicting a single label for the entire graph) remains mostly rudimentary, typically using a single global pooling step to aggregate node features or a hand-designed, fixed heuristic for hierarchical coarsening of the graph structure. An important step towards ameliorating this is differentiable graph coarsening---the ability to reduce the size of the graph in an adaptive, data-dependent manner within a graph neural network pipeline, analogous to image downsampling within CNNs. However, the previous prominent approach to pooling has quadratic memory requirements during training and is therefore not scalable to large graphs. Here we combine several recent advances in graph neural network design to demonstrate that competitive hierarchical graph classification results are possible without sacrificing sparsity. Our results are verified on several established graph classification benchmarks, and highlight an important direction for future research in graph-based neural networks.

stat.ML↗

arXiv2018

Introducing Curvature to the Label Space

One-hot encoding is a labelling system that embeds classes as standard basis vectors in a label space. Despite seeing near-universal use in supervised categorical classification tasks, the scheme is problematic in its geometric implication that, as all classes are equally distant, all classes are equally different. This is inconsistent with most, if not all, real-world tasks due to the prevalence of ancestral and convergent relationships generating a varying degree of morphological similarity across classes. We address this issue by introducing curvature to the label-space using a metric tensor as a self-regulating method that better represents these relationships as a bolt-on, learning-algorithm agnostic solution. We propose both general constraints and specific statistical parameterizations of the metric and identify a direction for future research using autoencoder-based parameterizations.

cs.LG↗

arXiv2018

Applications of molecular communications to medicine: a survey

In recent years, progresses in nanotechnology have established the foundations for implementing nanomachines capable of carrying out simple but significant tasks. Under this stimulus, researchers have been proposing various solutions for realizing nanoscale communications, considering both electromagnetic and biological communications. Their aim is to extend the capabilities of nanodevices, so as to enable the execution of more complex tasks by means of mutual coordination, achievable through communications. However, although most of these proposals show how devices can communicate at the nanoscales, they leave in the background specific applications of these new technologies. Thus, this paper shows an overview of the actual and potential applications that can rely on a specific class of such communications techniques, commonly referred to as molecular communications. In particular, we focus on health-related applications. This decision is due to the rapidly increasing interests of research communities and companies to minimally invasive, biocompatible, and targeted health-care solutions. Molecular communication techniques have actually the potentials of becoming the main technology for implementing advanced medical solution. Hence, in this paper we provide a taxonomy of potential applications, illustrate them in some details, along with the existing open challenges for them to be actually deployed, and draw future perspectives.

cs.ET↗

arXiv2018

Automatic Inference of Cross-modal Connection Topologies for X-CNNs

This paper introduces a way to learn cross-modal convolutional neural network (X-CNN) architectures from a base convolutional network (CNN) and the training data to reduce the design cost and enable applying cross-modal networks in sparse data environments. Two approaches for building X-CNNs are presented. The base approach learns the topology in a data-driven manner, by using measurements performed on the base CNN and supplied data. The iterative approach performs further optimisation of the topology through a combined learning procedure, simultaneously learning the topology and training the network. The approaches were evaluated agains examples of hand-designed X-CNNs and their base variants, showing superior performance and, in some cases, gaining an additional 9% of accuracy. From further considerations, we conclude that the presented methodology takes less time than any manual approach would, whilst also significantly reducing the design complexity. The application of the methods is fully automated and implemented in Xsertion library.

cs.LG↗

arXiv2018

Graph Attention Networks

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

stat.ML↗

arXiv2017

Cross-modal Recurrent Models for Weight Objective Prediction from Multimodal Time-series Data

We analyse multimodal time-series data corresponding to weight, sleep and steps measurements. We focus on predicting whether a user will successfully achieve his/her weight objective. For this, we design several deep long short-term memory (LSTM) architectures, including a novel cross-modal LSTM (X-LSTM), and demonstrate their superiority over baseline approaches. The X-LSTM improves parameter efficiency by processing each modality separately and allowing for information flow between them by way of recurrent cross-connections. We present a general hyperparameter optimisation technique for X-LSTMs, which allows us to significantly improve on the LSTM and a prior state-of-the-art cross-modal approach, using a comparable number of parameters. Finally, we visualise the model's predictions, revealing implications about latent variables in this task.

stat.ML↗

arXiv2017

Quantifying the Effects of Enforcing Disentanglement on Variational Autoencoders

The notion of disentangled autoencoders was proposed as an extension to the variational autoencoder by introducing a disentanglement parameter $β$, controlling the learning pressure put on the possible underlying latent representations. For certain values of $β$ this kind of autoencoders is capable of encoding independent input generative factors in separate elements of the code, leading to a more interpretable and predictable model behaviour. In this paper we quantify the effects of the parameter $β$ on the model performance and disentanglement. After training multiple models with the same value of $β$, we establish the existence of consistent variance in one of the disentanglement measures, proposed in literature. The negative consequences of the disentanglement to the autoencoder's discriminative ability are also asserted while varying the amount of examples available during training.

stat.ML↗

arXiv2016

X-CNN: Cross-modal Convolutional Neural Networks for Sparse Datasets

In this paper we propose cross-modal convolutional neural networks (X-CNNs), a novel biologically inspired type of CNN architectures, treating gradient descent-specialised CNNs as individual units of processing in a larger-scale network topology, while allowing for unconstrained information flow and/or weight sharing between analogous hidden layers of the network---thus generalising the already well-established concept of neural network ensembles (where information typically may flow only between the output layers of the individual networks). The constituent networks are individually designed to learn the output function on their own subset of the input data, after which cross-connections between them are introduced after each pooling operation to periodically allow for information exchange between them. This injection of knowledge into a model (by prior partition of the input data through domain knowledge or unsupervised methods) is expected to yield greatest returns in sparse data environments, which are typically less suitable for training CNNs. For evaluation purposes, we have compared a standard four-layer CNN as well as a sophisticated FitNet4 architecture against their cross-modal variants on the CIFAR-10 and CIFAR-100 datasets with differing percentages of the training data being removed, and find that at lower levels of data availability, the X-CNNs significantly outperform their baselines (typically providing a 2--6% benefit, depending on the dataset size and whether data augmentation is used), while still maintaining an edge on all of the full dataset tests.

stat.ML↗

arXiv2014

Estimation and Modelling of PCBs Bioaccumulation in the Adriatic Sea Ecosystem

Persistent Organic Pollutants represent a global ecological concern due to their ability to accumulate in organisms and to spread species-by-species via feeding connections. In this work we focus on the estimation and simulation of the bioaccumulation dynamics of persistent pollutants in the marine ecosystem, and we apply the approach for reconstructing a model of PCBs bioaccumulation in the Adriatic sea, estimated after an extensive review of trophic and PCBs concentration data on Adriatic species. Our estimations evidence the occurrence of PCBs biomagnification in the Adriatic food web, together with a strong dependence of bioaccumulation on trophic dynamics and external factors like fishing activity.

q-bio.PE↗

arXiv2012

Disease processes as hybrid dynamical systems

We investigate the use of hybrid techniques in complex processes of infectious diseases. Since predictive disease models in biomedicine require a multiscale approach for understanding the molecule-cell-tissue-organ-body interactions, heterogeneous methodologies are often employed for describing the different biological scales. Hybrid models provide effective means for complex disease modelling where the action and dosage of a drug or a therapy could be meaningfully investigated: the infection dynamics can be classically described in a continuous fashion, while the scheduling of multiple treatment discretely. We define an algebraic language for specifying general disease processes and multiple treatments, from which a semantics in terms of hybrid dynamical system can be derived. Then, the application of control-theoretic tools is proposed in order to compute the optimal scheduling of multiple therapies. The potentialities of our approach are shown in the case study of the SIR epidemic model and we discuss its applicability on osteomyelitis, a bacterial infection affecting the bone remodelling system in a specific and multiscale manner. We report that formal languages are helpful in giving a general homogeneous formulation for the different scales involved in a multiscale disease process; and that the combination of hybrid modelling and control theory provides solid grounds for computational medicine.

cs.LO↗

arXiv2011

Multiple verification in computational modeling of bone pathologies

We introduce a model checking approach to diagnose the emerging of bone pathologies. The implementation of a new model of bone remodeling in PRISM has led to an interesting characterization of osteoporosis as a defective bone remodeling dynamics with respect to other bone pathologies. Our approach allows to derive three types of model checking-based diagnostic estimators. The first diagnostic measure focuses on the level of bone mineral density, which is currently used in medical practice. In addition, we have introduced a novel diagnostic estimator which uses the full patient clinical record, here simulated using the modeling framework. This estimator detects rapid (months) negative changes in bone mineral density. Independently of the actual bone mineral density, when the decrease occurs rapidly it is important to alarm the patient and monitor him/her more closely to detect insurgence of other bone co-morbidities. A third estimator takes into account the variance of the bone density, which could address the investigation of metabolic syndromes, diabetes and cancer. Our implementation could make use of different logical combinations of these statistical estimators and could incorporate other biomarkers for other systemic co-morbidities (for example diabetes and thalassemia). We are delighted to report that the combination of stochastic modeling with formal methods motivate new diagnostic framework for complex pathologies. In particular our approach takes into consideration important properties of biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could be further expanded, inching towards the complexity of human diseases. Finally, we briefly introduce self-adaptiveness in formal methods which is a key property in the regulative mechanisms of biological systems and well known in other mathematical and engineering areas.

cs.LO↗

arXiv2010

StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.

cs.CE↗