相关论文: Package models and the information crisis of prebi…

Integrating heterogeneous data sources and expert knowledge is essential for overcoming data scarcity and enhancing estimation accuracy. Two main frameworks naturally arise to perform the integration of these multiple sources: sequential…

In this demo, we present PackageBuilder, a system that extends database systems to support package queries. A package is a collection of tuples that individually satisfy base constraints and collectively satisfy global constraints. The need…

When components of a system exchange data, they need to serialise the data so that it can be sent over the network. Then, the recipient has to deserialise the data in order to be able to process it. These steps take time and have an impact…

We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly…

Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…

This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…

The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA World, self-replicating RNAs have yet to be identified in a natural context, leaving a key…

Natural Language Processing (NLP) has undergone transformative changes with the advent of deep learning methodologies. One challenge persistently confronting researchers is the scarcity of high-quality, annotated datasets that drive these…

The pre-trained large language models (LLMs) have shown their extraordinary capacity to solve reasoning tasks, even on tasks that require a complex process involving multiple sub-steps. However, given the vast possible generation space of…

In a neglected 2005 paper, Nobel Laureate Paul Lauterbur proposed that molecular imprinting in amorphous materials -- a phenomenon with an extensive experimental literature -- played a key role in abiogenesis. The present paper builds on…

In a recent paper, Newman surveys the literature on power law spectra in evolution, self-organised criticality and presents a model of his own to arrive at a conclusion that self-organised criticality is not necessary for evolution. Not…

Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…

Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…

We illustrate the use of tools (asymptotic theories of standard error quantification using appropriate statistical models, bootstrapping, model comparison techniques) in addition to sensitivity that may be employed to determine the…

Although there is always an interplay between the dynamics of information diffusion and disease spreading, the empirical research on the systemic coevolution mechanisms connecting these two spreading dynamics is still lacking. Here we…

Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…

The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive…

At an early stage in pre-biotic evolution, groups of replicating molecules must coordinate their reproduction to form aggregated units of selection. Mechanisms that enable this to occur are currently not well understood. In this paper we…

Large Language Models~(LLMs) struggle with providing current information due to the outdated pre-training data. Existing methods for updating LLMs, such as knowledge editing and continual fine-tuning, have significant drawbacks in…

Replicating systems sustained by error-prone enzymatic amplification can undergo critical transitions between persistence and extinction. In RNA viruses, such transitions are classically governed by mutation rates and fitness landscapes,…