Related papers: A graph model for the evolution of specificity in …
Gene expression dynamics satisfying given input-output relationships were investigated by evolving the networks for an optimal response. We found three types of networks and corresponding dynamics, depending on the sensitivity of gene…
Statistical techniques are needed to analyse data structures with complex dependencies such that clinically useful information can be extracted. Individual-specific networks, which capture dependencies in complex biological systems, are…
The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of…
There is growing recognition that the network structures arising from interactions between different entities in physical, social and biological systems fundamentally alter the evolutionary outcomes. Previous paradigm exploring evolutionary…
Despite vast research in adversarial examples, the root causes of model susceptibility are not well understood. Instead of looking at attack-specific robustness, we propose a notion that evaluates the sensitivity of individual neurons in…
Tuning curves characterizing the response selectivities of biological neurons often exhibit large degrees of irregularity and diversity across neurons. Theoretical network models that feature heterogeneous cell populations or random…
Antibodies are widely used reagents to test for expression of proteins and other antigens. However, they might not always reliably produce results when they do not specifically bind to the target proteins that their providers designed them…
We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph. The relationship between the attractors of this dynamics and the underlying graph theoretic structures like…
Many events in the vertebrate immune system are influenced by some element of chance. The objective of the present work is to describe affinity maturation of B lymphocytes (in which random events are perhaps the most characteristic), and to…
Adversarial attacks optimize against models to defeat defenses. Existing defenses are static, and stay the same once trained, even while attacks change. We argue that models should fight back, and optimize their defenses against attacks at…
The aim of this work is to try to bridge over theoretical immunology and disordered statistical mechanics. Our long term hope is to contribute to the development of a quantitative theoretical immunology from which practical applications may…
Rigidity is an emergent property of materials - it is not a feature of individual components that comprise the structure, but instead arises from interactions between many constituent parts. Recently, it has been recognized that…
The immune system provides a rich metaphor for computer security: anomaly detection that works in nature should work for machines. However, early artificial immune system approaches for computer security had only limited success. Arguably,…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
We analyze the interactions between division, mutation and selection in a simplified evolutionary model, assuming that the population observed can be classified into fitness levels. The construction of our mathematical framework is…
Recent studies show that apparent personality traits can be reflected from human facial behavior dynamics. However, most existing methods can only encode single-scale short-term facial behaviors in the latent features for personality…
We present new fitting functions for the velocity divergence auto- and cross-power spectra, $P_{\theta\theta}(k)$ and $P_{\delta\theta}(k)$, calibrated on gravity-only $N$-body simulations. By applying the Evolution Mapping framework, we…
This work concerns the development of deep networks that are certifiably robust to adversarial attacks. Joint robust classification-detection was recently introduced as a certified defense mechanism, where adversarial examples are either…
Individuals of different types, may it be genetic, cultural, or else, with different levels of fitness often compete for reproduction and survival. A fitter type generally has higher chances of disseminating their copies to other…
Affinity maturation produces antibodies that bind antigens with high specificity by accumulating mutations in the antibody sequence. Mapping out the antibody-antigen affinity landscape can give us insight into the accessible paths during…