Related papers: Modelling Immunological Memory
Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of…
Nowadays, the interpretability of machine learning models is becoming increasingly important, especially in the medical domain. Aiming to shed some light on how to rationalize medical relation prediction, we present a new interpretable…
Infectious diseases are caused by pathogenic microorganisms and can spread through different ways. Mathematical models and computational simulation have been used extensively to investigate the transmission and spread of infectious…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
To produce accurate predictions, language models (LMs) must balance between generalization and memorization. Yet, little is known about the mechanism by which transformer LMs employ their memorization capacity. When does a model decide to…
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…
Verhulst-like mathematical modeling has been used to investigate several complex biological issues, such as immune memory equilibrium and cell-mediated immunity in mammals. The regulation mechanisms of both these processes are still not…
Recently Quantum Computation has generated a lot of interest due to the discovery of a quantum algorithm which can factor large numbers in polynomial time. The usefulness of a quantum com puter is limited by the effect of errors. Simulation…
Stimulated by recent experimental results, we simulate ``temperature''-cycling experiments in a model for the compaction of granular media. We report on the existence of two types of memory effects: short-term dependence on the history of…
The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self-cells or non-self cells. It does this with the help…
In recent years, neural models have been repeatedly touted to exhibit state-of-the-art performance in recommendation. Nevertheless, multiple recent studies have revealed that the reported state-of-the-art results of many neural…
Computational models of complex systems are usually elaborate and sensitive to implementation details, characteristics which often affect their verification and validation. Model replication is a possible solution to this issue. It avoids…
We analyze different types of simulations that applied researchers can use to assess whether their inference methods reliably control false-positive rates. We show that different assessments involve trade-offs, varying in the types of…
Understanding the mental state of other people is an important skill for intelligent agents and robots to operate within social environments. However, the mental processes involved in `mind-reading' are complex. One explanation of such…
In the last decades, the interest to understand the connection between brain and body has grown notably. For example, in psychoneuroimmunology many studies associate stress, arising from many different sources and situations, to changes in…
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular…
A growing body of work has established the modelling of stochastic processes as a promising area of application for quantum techologies; it has been shown that quantum models are able to replicate the future statistics of a stochastic…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
When the body gets infected by a pathogen or receives a vaccine dose, the immune system develops pathogen-specific immunity. Induced immunity decays in time and years after recovery/vaccination the host might become susceptible again.…