Related papers: Package models and the information crisis of prebi…
Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…
Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic…
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal…
Due to their flexibility and superior performance, machine learning models frequently complement and outperform traditional statistical survival models. However, their widespread adoption is hindered by a lack of user-friendly tools to…
The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthesis of synthetic chemical complexes. Unlike the…
When complex Bayesian models exhibit implausible behaviour, one solution is to assemble available information into an informative prior. Challenges arise as prior information is often only available for the observable quantity, or some…
Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider…
We consider a two-type stochastic competition model on the integer lattice Z^d. The model describes the space evolution of two ``species'' competing for territory along their boundaries. Each site of the space may contain only one…
Through in-depth thinking and reasoning about the conditions required for cells to maintain unchanged material distribution, it is concluded that life metabolic reactions require high information content. However, the self-replication of a…
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution. We explored experimentally the effect of mutation supply and the strength of selective…
Diffusion large language models (dLLMs) theoretically permit token decoding in arbitrary order, a flexibility that could enable richer exploration of reasoning paths than autoregressive (AR) LLMs. In practice, however, random-order decoding…
We study open domain response generation with limited message-response pairs. The problem exists in real-world applications but is less explored by the existing work. Since the paired data now is no longer enough to train a neural…
Information theory is gaining popularity as a tool to characterize performance of biological systems. However, information is commonly quantified without reference to whether or how a system could extract and use it; as a result,…
Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the…
Model evolution in model libraries differs from general model evolution. It limits the scope to the manageable and allows to develop clear concepts, approaches, solutions, and methodologies. Looking at model quality in evolving model…
In reliability engineering, data about failure events is often scarce. To arrive at meaningful estimates for the reliability of a system, it is therefore often necessary to also include expert information in the analysis, which is…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
Explaining the black-box predictions of NLP models naturally and accurately is an important open problem in natural language generation. These free-text explanations are expected to contain sufficient and carefully-selected evidence to form…
Pre-trained language models derive substantial linguistic and factual knowledge from the massive corpora on which they are trained, and prompt engineering seeks to align these models to specific tasks. Unfortunately, existing prompt…
Synthetic data becomes crucial for large language model training, but its effectiveness is highly inconsistent. We provide an information-theoretic account of this inconsistency: synthetic data improves a model only when the…