Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure

Interacting Agents and Continuous Opinions Dynamics

We present a model of opinion dynamics in which agents adjust continuous opinions as a result of random binary encounters whenever their difference in opinion is below a given threshold. High thresholds yield convergence of opinions towards an average opinion, whereas low thresholds result in several opinion clusters. The model is further generalised to network interactions, threshold heterogeneity, adaptive thresholds and binary strings of opinions.Comment: 21 pages, 13 figures. http://www.lps.ens.fr/~weisbuch/contopidyn/contopidyn.htm

Branch-specific plasticity enables self-organization of nonlinear computation in single neurons

It has been conjectured that nonlinear processing in dendritic branches endows individual neurons with the capability to perform complex computational operations that are needed in order to solve for example the binding problem. However, it is not clear how single neurons could acquire such functionality in a self-organized manner, since most theoretical studies of synaptic plasticity and learning concentrate on neuron models without nonlinear dendritic properties. In the meantime, a complex picture of information processing with dendritic spikes and a variety of plasticity mechanisms in single neurons has emerged from experiments. In particular, new experimental data on dendritic branch strength potentiation in rat hippocampus have not yet been incorporated into such models. In this article, we investigate how experimentally observed plasticity mechanisms, such as depolarization-dependent STDP and branch-strength potentiation could be integrated to self-organize nonlinear neural computations with dendritic spikes. We provide a mathematical proof that in a simplified setup these plasticity mechanisms induce a competition between dendritic branches, a novel concept in the analysis of single neuron adaptivity. We show via computer simulations that such dendritic competition enables a single neuron to become member of several neuronal ensembles, and to acquire nonlinear computational capabilities, such as for example the capability to bind multiple input features. Hence our results suggest that nonlinear neural computation may self-organize in single neurons through the interaction of local synaptic and dendritic plasticity mechanisms