Related papers: Optimal evolutionary decision-making to store immu…
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
Populations can evolve in order to adapt to external changes. The capacity to evolve and adapt makes successful treatment of infectious diseases and cancer difficult. Indeed, therapy resistance has quickly become a key challenge for global…
We present an end-to-end trained memory system that quickly adapts to new data and generates samples like them. Inspired by Kanerva's sparse distributed memory, it has a robust distributed reading and writing mechanism. The memory is…
Protein language models (PLMs) learn contextual representations from protein sequences and are profoundly impacting various scientific disciplines spanning protein design, drug discovery, and structural predictions. One particular research…
Animals often demonstrate a remarkable ability to adapt to their environments during their lifetime. They do so partly due to the evolution of morphological and neural structures. These structures capture features of environments shared…
A new age-distributed immuno-epidemiological model with information-based vaccine uptake suggested in this work represents a system of integro-differential equations for the numbers of susceptible individuals, infected individuals,…
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
Long-term memory is essential for LLM agents that operate across multiple sessions, yet existing memory systems treat retrieval infrastructure as fixed: stored content evolves while scoring functions, fusion strategies, and…
Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
The performance of evolutionary algorithms can be heavily undermined when constraints limit the feasible areas of the search space. For instance, while Covariance Matrix Adaptation Evolution Strategy is one of the most efficient algorithms…
It is widely believed that the perceptual system of an organism is optimized for the properties of the environment to which it is exposed. A specific instance of this principle known as the Infomax principle holds that the purpose of early…
Memory is fundamental to intelligence, enabling learning, reasoning, and adaptability across biological and artificial systems. While Transformer architectures excel at sequence modeling, they face critical limitations in long-range context…
We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as…
Direct reciprocity is a mechanism for the evolution of cooperation in repeated social interactions. According to this literature, individuals naturally learn to adopt conditionally cooperative strategies if they have multiple encounters…
Effective utilization of Multiple-Instruction-Multiple-Data (MIMD) parallel computers requires the application of good load balancing techniques. In this paper we show that heuristics derived from observation of complex natural systems,…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
Memory-one strategies are a set of Iterated Prisoner's Dilemma strategies that have been praised for their mathematical tractability and performance against single opponents. This manuscript investigates best response memory-one strategies…
When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen.…