Related papers: Inferring differentiation order in adaptive immune…
Inference-time computation is a powerful paradigm to enhance the performance of large language models (LLMs), with Best-of-N sampling being a widely used technique. However, this method is computationally expensive, requiring both (1) an…
High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals. However, quantitative comparison between…
Memory has a great impact on the evolution of every process related to human societies. Among them, the evolution of an epidemic is directly related to the individuals' experiences. Indeed, any real epidemic process is clearly sustained by…
Adaptive response to a varying environment is a common feature of biological organisms. Reproducing such features in electronic systems and circuits is of great importance for a variety of applications. Here, we consider memory models…
We introduce a new approach to learning in hierarchical latent-variable generative models called the "distributed distributional code Helmholtz machine", which emphasises flexibility and accuracy in the inferential process. In common with…
The adaptive immune system relies on the diversity of receptors expressed on the surface of B and T-cells to protect the organism from a vast amount of pathogenic threats. The proliferation and degradation dynamics of different cell types…
Biological neural networks are shaped both by evolution across generations and by individual learning within an organism's lifetime, whereas standard artificial neural networks undergo a single, large training procedure without inherited…
Recent methods have been developed to map single-cell lineage statistics to population growth. Because population growth selects for exponentially rare phenotypes, these methods inherently depend on sampling large deviations from finite…
Lymphocyte selection is a fundamental operation of adaptive immunity. In order to produce B-lymphocytes with a desired antigenic profile, a process of mutation-selection occurs in the germinal center, which is part of the lymph nodes. We…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
Progressive diseases worsen over time and are characterised by monotonic change in features that track disease progression. Here we connect ideas from two formerly separate methodologies -- event-based and hidden Markov modelling -- to…
Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens…
Growth and shape formation in crowded multicellular assemblies arise from the interplay of chemical gradients, single-cell expansion and mechanical interactions, making it essential to understand how these processes jointly shape collective…
Associative memory models are content-addressable memory systems fundamental to biological intelligence and are notable for their high interpretability. However, existing models evaluate the quality of retrieval based on proximity, which…
Machine learning algorithms can be fooled by small well-designed adversarial perturbations. This is reminiscent of cellular decision-making where ligands (called antagonists) prevent correct signalling, like in early immune recognition. We…
Adaptive therapy (AT) is designed to postpone the emergence of drug resistance by exploiting evolutionary competition among tumor subclones. Most mathematical models of AT assume a binary population structure of drug-sensitive and…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
We consider the mutual interactions, via cytokine exchanges, among helper lymphocytes, B lymphocytes and killer lymphocytes, and we model them as a unique system by means of a tripartite network. Each part includes all the different clones…
During an epidemic outbreak, individuals often modify their behavior in response to global prevalence cues, using spatially mediated adaptations such as reduced mobility or transmission range. In this work, we investigate the impact of…
Adaptive subgroup enrichment design is an efficient design framework that allows accelerated development for investigational treatments while also having flexibility in population selection within the course of the trial. The adaptive…