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The immune response is a dynamic process by which the body determines whether an antigen is self or nonself. The state of this dynamic process is defined by the relative balance and population of inflammatory and regulatory actors which…

Traditional vaccines against viruses are designed to target their surface proteins, i.e., antigens, which can trigger the immune system to produce specific antibodies to capture and neutralize the viruses. However, viruses often evolve…

Populations and Evolution · Quantitative Biology 2020-03-25 Rui Qiao , Ngoc Hieu Tran , Baozhen Shan , Ali Ghodsi , Ming Li

Cybersecurity attacks are a major and increasing burden to economic and social systems globally. Here we analyze the principles of security in different domains and demonstrate an architectural flaw in current cybersecurity. Cybersecurity…

Cryptography and Security · Computer Science 2013-03-13 Blake C. Stacey , Yaneer Bar-Yam

In this paper, we investigate the importance of a defense system's learning rates to fight against the self-propagating class of malware such as worms and bots. To this end, we introduce a new propagation model based on the interactions…

Cryptography and Security · Computer Science 2019-05-02 Saeed Valizadeh , Marten van Dijk

A central question in human immunology is how a patient's repertoire of T cells impacts disease. Here, we introduce a method to infer the causal effects of T cell receptor (TCR) sequences on patient outcomes using observational TCR…

Machine Learning · Statistics 2024-10-21 Eli N. Weinstein , Elizabeth B. Wood , David M. Blei

Modeling the immune system so that its essential functionalities stand out without the need for every molecular or cellular interaction to be taken into account has been challenging for many decades. Two competing approaches have been the…

Cellular Automata and Lattice Gases · Physics 2017-11-13 Kátia K. Cassiano , Valmir C. Barbosa

A new emerging paradigm of Uncertain Risk of Suspicion, Threat and Danger, observed across the field of information security, is described. Based on this paradigm a novel approach to anomaly detection is presented. Our approach is based on…

Artificial Intelligence · Computer Science 2010-07-05 Jan Feyereisl , Uwe Aickelin

As introduced by Bentley et al. (2005), artificial immune systems (AIS) are lacking tissue, which is present in one form or another in all living multi-cellular organisms. Some have argued that this concept in the context of AIS brings…

Artificial Intelligence · Computer Science 2010-07-05 Jan Feyereisl , Uwe Aickelin

Cultural algorithm is a kind of evolutionary algorithm inspired from societal evolution and is composed of a belief space, a population space and a protocol that enables exchange of knowledge between these sources. Knowledge created in the…

Neural and Evolutionary Computing · Computer Science 2012-09-14 Sujatha Srinivasan , Sivakumar Ramakrishnan

An essential feature of the adaptive immune system is the proliferation of antigen-specific lymphocytes during an immune reaction to form a large pool of effector cells. This proliferation must be regulated to ensure an effective response…

Populations and Evolution · Quantitative Biology 2021-01-06 Andreas Mayer , Yaojun Zhang , Alan S. Perelson , Ned S. Wingreen

Biologically inspired computing is an area of computer science which uses the advantageous properties of biological systems. It is the amalgamation of computational intelligence and collective intelligence. Biologically inspired mechanisms…

Neural and Evolutionary Computing · Computer Science 2009-10-22 Sabu M. Thampi

Oncolytic virotherapy - the use of viruses that specifically kill tumor cells - is an innovative and highly promising route for treating cancer. However, its therapeutic outcomes are mainly impaired by the host immune response to the viral…

Tissues and Organs · Quantitative Biology 2015-06-15 Leticia R Paiva , Hallan S Silva , Silvio C Ferreira , Marcelo L Martins

The Agentic Service Ecosystem consists of heterogeneous autonomous agents (e.g., intelligent machines, humans, and human-machine hybrid systems) that interact through resource exchange and service co-creation. These agents, with distinct…

Multiagent Systems · Computer Science 2025-08-12 Xuwen Zhang , Xiao Xue , Xia Xie , Qun Ma , Xiangning Yu , Deyu Zhou , Yifan Wang , Ming Zhang

As one of the solutions to intrusion detection problems, Artificial Immune Systems (AIS) have shown their advantages. Unlike genetic algorithms, there is no one archetypal AIS, instead there are four major paradigms. Among them, the…

Cryptography and Security · Computer Science 2013-06-03 Feng Gu , Julie Greensmith , Uwe Aickelin

We present a probabilistic T-cell model that includes negative selection and takes contrasting models of tissue-restricted antigen (TRA) expression in the thymus into account. We start from the basic model of van den Berg, Rand, and…

Cell Behavior · Quantitative Biology 2014-07-22 Corinna Ernst , Ellen Baake

We analyze a within-host model of virus infection with antibody and CD8+ cytotoxic T lymphocyte (CTL) responses proposed by Schwartz et al. (2013). The goal of this work is to gain an overview of the stability of the biologically-relevant…

Populations and Evolution · Quantitative Biology 2022-02-14 Tyler Meadows , Elissa J. Schwartz

Immune cells coordinate their efforts for the correct and efficient functioning of the immune system (IS). Each cell type plays a distinct role and communicates with other cell types through mediators such as cytokines, chemokines and…

Molecular Networks · Quantitative Biology 2007-05-23 Paolo Tieri , Silvana Valensin , Vito Latora , Gastone C. Castellani , Massimo Marchiori , Daniel Remondini , Claudio Franceschi

In this work we adopt a statistical mechanics approach to investigate basic, systemic features exhibited by adaptive immune systems. The lymphocyte network made by B-cells and T-cells is modeled by a bipartite spin-glass, where, following…

Cell Behavior · Quantitative Biology 2015-06-04 Elena Agliari , Adriano Barra , Silvia Bartolucci , Andrea Galluzzi , Francesco Guerra , Francesco Moauro

The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…

Populations and Evolution · Quantitative Biology 2015-04-28 Yuval Elhanati , Anand Murugan , Curtis G. Callan , Thierry Mora , Aleksandra M. Walczak

While prior red-teaming efforts have focused on eliciting harmful text outputs from large language models (LLMs), such approaches fail to capture agent-specific vulnerabilities that emerge through multi-step tool execution, particularly in…

Cryptography and Security · Computer Science 2026-03-25 Hyomin Lee , Sangwoo Park , Yumin Choi , Sohyun An , Seanie Lee , Sung Ju Hwang