Related papers: Package models and the information crisis of prebi…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
We study the problem of determining what data is required to solve a decision-making task when only partial information about the state of the world is available. Focusing on linear programs, we introduce a decision-focused notion of data…
The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper,…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
The problem of evolutionary complexification of life is considered one of the fundamental aspects in contemporary evolutionary theory. Parasitism is ubiquitous, inevitable, and arises as soon as the first replicators appear, even during the…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…
Explaining how competing species coexist remains a central question in ecology. The well-known competitive exclusion principle (CEP) states that two species competing for the same resource cannot stably coexist, and more generally, that the…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these…
Deep learning-based food image classification enables precise identification of food categories, further facilitating accurate nutritional analysis. However, real-world food images often show a skewed distribution, with some food types…
New technologies and equipment allow for mass treatment of samples and research teams share acquired data on an always larger scale. In this context scientists are facing a major data exploitation problem. More precisely, using these data…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
We consider a stochastic model for a pathogen population in the presence of an immune response, in which pathogen types are partially ordered by ancestry and the immune system must eliminate ancestor types before it can eliminate their…
In this work, we introduce InfoDisent, a hybrid approach to explainability based on the information bottleneck principle. InfoDisent enables the disentanglement of information in the final layer of any pretrained model into atomic concepts,…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Accurate predictions of when a component will fail are crucial when planning maintenance, and by modeling the distribution of these failure times, survival models have shown to be particularly useful in this context. The presented…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
Real food web data available in the literature presents us with the relations between various species, sizes of these species, metabolic types of the species and other useful information, which allows us to define parameters for the…
Building a deep learning model for a Question-Answering (QA) task requires a lot of human effort, it may need several months to carefully tune various model architectures and find a best one. It's even harder to find different excellent…
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and…