arXiv subjects

Anthony C. C. Coolen

Publications and source records attributed to Anthony C. C. Coolen.

8 recordsLinked to original sources

arXiv2025

Dynamical Properties of Dense Associative Memory

Dense associative memory, a fundamental instance of modern Hopfield networks, can store a large number of memory patterns as equilibrium states of recurrent networks. While the stationary-state storage capacity has been investigated, its dynamical properties have not yet been discussed. In this paper, we analyze the dynamics using an exact approach based on generating functional analysis. We show results on convergence properties of memory retrieval, such as the convergence time and the size of the attraction basins. Our analysis enables a quantitative evaluation of the convergence time and the storage capacity of dense associative memory, which is useful for model design. Unlike the traditional Hopfield model, the retrieval of a pattern does not act as additional noise to itself, suggesting that the structure of modern networks makes recall more robust. Furthermore, the methodology addressed here can be applied to other energy-based models, and thus has the potential to contribute to the design of future architectures.

cond-mat.dis-nn↗

arXiv2021

Retarded kernels for longitudinal survival analysis and dynamic prediction

Predicting patient survival probabilities based on observed covariates is an important assessment in clinical practice. These patient-specific covariates are often measured over multiple follow-up appointments. It is then of interest to predict survival based on the history of these longitudinal measurements, and to update predictions as more observations become available. The standard approaches to these so-called `dynamic prediction' assessments are joint models and landmark analysis. Joint models involve high-dimensional parametrisations, and their computational complexity often prohibits including multiple longitudinal covariates. Landmark analysis is simpler, but discards a proportion of the available data at each `landmark time'. In this work we propose a `retarded kernel' approach to dynamic prediction that sits somewhere in between the two standard methods in terms of complexity. By conditioning hazard rates directly on the covariate measurements over the observation time frame, we define a model that takes into account the full history of covariate measurements but is more practical and parsimonious than joint modelling. Time-dependent association kernels describe the impact of covariate changes at earlier times on the patient's hazard rate at later times. Under the constraints that our model (i) reduces to the standard Cox model for time-independent covariates, and (ii) contains the instantaneous Cox model as a special case, we derive two natural kernel parameterisations. Upon application to three clinical data sets, we find that the predictive accuracy of the retarded kernel approach is comparable to that of the two existing standard methods.

stat.ME↗

arXiv2019

Roles of repertoire diversity in robustness of humoral immune response

The adaptive immune system relies on diversity of its repertoire of receptors to protect the organism from a great variety of pathogens. Since the initial repertoire is the result of random gene rearrangement, binding of receptors is not limited to pathogen-associated antigens but also includes self antigens. There is a fine balance between having a diverse repertoire, protecting from many different pathogens, and yet reducing its self-reactivity as far as possible to avoid damage to self. In the ageing immune system this balance is altered, manifesting in reduced specificity of response to pathogens or vaccination on a background of higher self-reactivity. To answer the question whether age-related changes of repertoire in the diversity and self/non-self affinity balance of antibodies could explain the reduced efficacy of the humoral response in older people, we construct a minimal mathematical model of the humoral immune response. The principle of least damage allows us, for a given repertoire of antibodies, to resolve a tension between the necessity to neutralise target antigens as quickly as possible and the requirement to limit the damage to self antigens leading to an optimal dynamics of immune response. The model predicts slowing down of immune response for repertoires with reduced diversity and increased self-reactivity.

q-bio.CB↗

arXiv2016

Covariate dimension reduction for survival data via the Gaussian process latent variable model

The analysis of high dimensional survival data is challenging, primarily due to the problem of overfitting which occurs when spurious relationships are inferred from data that subsequently fail to exist in test data. Here we propose a novel method of extracting a low dimensional representation of covariates in survival data by combining the popular Gaussian Process Latent Variable Model (GPLVM) with a Weibull Proportional Hazards Model (WPHM). The combined model offers a flexible non-linear probabilistic method of detecting and extracting any intrinsic low dimensional structure from high dimensional data. By reducing the covariate dimension we aim to diminish the risk of overfitting and increase the robustness and accuracy with which we infer relationships between covariates and survival outcomes. In addition, we can simultaneously combine information from multiple data sources by expressing multiple datasets in terms of the same low dimensional space. We present results from several simulation studies that illustrate a reduction in overfitting and an increase in predictive performance, as well as successful detection of intrinsic dimensionality. We provide evidence that it is advantageous to combine dimensionality reduction with survival outcomes rather than performing unsupervised dimensionality reduction on its own. Finally, we use our model to analyse experimental gene expression data and detect and extract a low dimensional representation that allows us to distinguish high and low risk groups with superior accuracy compared to doing regression on the original high dimensional data.

math.ST↗

arXiv2015

Protein interaction networks and biology: towards the connection

Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at understanding the connection between true protein interactions and the protein interaction datasets that have been obtained using the most popular experimental techniques, i.e. mass spectronomy (MS) and yeast two-hybrid (Y2H). We show that the most natural adjacency matrix of protein interaction networks has a separable form, and this induces precise relations between moments of the degree distribution and the number of short loops. These relations provide powerful tools to test the reliability of datasets and hint at the underlying biological mechanism with which proteins and complexes recruit each other.

cond-mat.dis-nn↗

arXiv2014

Gaussian process regression for survival data with competing risks

We apply Gaussian process (GP) regression, which provides a powerful non-parametric probabilistic method of relating inputs to outputs, to survival data consisting of time-to-event and covariate measurements. In this context, the covariates are regarded as the `inputs' and the event times are the `outputs'. This allows for highly flexible inference of non-linear relationships between covariates and event times. Many existing methods, such as the ubiquitous Cox proportional hazards model, focus primarily on the hazard rate which is typically assumed to take some parametric or semi-parametric form. Our proposed model belongs to the class of accelerated failure time models where we focus on directly characterising the relationship between covariates and event times without any explicit assumptions on what form the hazard rates take. It is straightforward to include various types and combinations of censored and truncated observations. We apply our approach to both simulated and experimental data. We then apply multiple output GP regression, which can handle multiple potentially correlated outputs for each input, to competing risks survival data where multiple event types can occur. By tuning one of the model parameters we can control the extent to which the multiple outputs (the time-to-event for each risk) are dependent thus allowing the specification of correlated risks. Simulation studies suggest that in some cases assuming dependence can lead to more accurate predictions.

math.ST↗

arXiv2013

Dimensionality Detection and Integration of Multiple Data Sources via the GP-LVM

The Gaussian Process Latent Variable Model (GP-LVM) is a non-linear probabilistic method of embedding a high dimensional dataset in terms low dimensional `latent' variables. In this paper we illustrate that maximum a posteriori (MAP) estimation of the latent variables and hyperparameters can be used for model selection and hence we can determine the optimal number or latent variables and the most appropriate model. This is an alternative to the variational approaches developed recently and may be useful when we want to use a non-Gaussian prior or kernel functions that don't have automatic relevance determination (ARD) parameters. Using a second order expansion of the latent variable posterior we can marginalise the latent variables and obtain an estimate for the hyperparameter posterior. Secondly, we use the GP-LVM to integrate multiple data sources by simultaneously embedding them in terms of common latent variables. We present results from synthetic data to illustrate the successful detection and retrieval of low dimensional structure from high dimensional data. We demonstrate that the integration of multiple data sources leads to more robust performance. Finally, we show that when the data are used for binary classification tasks we can attain a significant gain in prediction accuracy when the low dimensional representation is used.

stat.ML↗

arXiv2009

Entropies of complex networks with hierarchically constrained topologies

The entropy of a hierarchical network topology in an ensemble of sparse random networks with "hidden variables" associated to its nodes, is the log-likelihood that a given network topology is present in the chosen ensemble.We obtain a general formula for this entropy,which has a clear simple interpretation in some simple limiting cases. The results provide new keys with which to solve the general problem of "fitting" a given network with an appropriate ensemble of random networks.

cond-mat.dis-nn↗