Related papers: Package models and the information crisis of prebi…
Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…
In this paper we present a modification of the usual Proteus mirabilis swarm model. For the obtained model (which is a two phase model with a non-linear diffusion term containing memory) we set up a collection of a priori estimates. Those…
Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources…
Data preprocessing is often paid little attention in machine learning, despite its potentially significant impact on model performance. While automated machine learning pipelines are starting to recognize and integrate data preprocessing…
The longevity R package provides provide maximum likelihood estimation routine for modelling of survival data that are subject to non-informative censoring and truncation mechanisms. It includes a selection of 12 parametric models of…
Under the paradigm of caching, partial data is delivered before the actual requests of users are known. In this paper, this problem is modeled as a canonical distributed source coding problem with side information, where the side…
We study a spatial, one-shot prisoner's dilemma (PD) model in which selection operates on both an organism's behavioral strategy (cooperate or defect) and its choice of when to implement that strategy across a set of discrete time slots.…
The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…
Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit…
When a small number of individuals of organism of single species is confined in a closed space with limited amount of indispensable resources, their breading may start initially under suitable conditions, and after peaking, the population…
We consider a spatial stochastic model for a pathogen population growing inside a host that attempts to eliminate the pathogens through its immune system. The pathogen population is divided into different types. A pathogen can either…
Large language models internalize enormous parametric knowledge during pre-training. Concurrently, realistic applications necessitate external contextual knowledge to aid models on the underlying tasks. This raises a crucial dilemma known…
Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
This paper introduces the R package INLAjoint, designed as a toolbox for fitting a diverse range of regression models addressing both longitudinal and survival outcomes. INLAjoint relies on the computational efficiency of the integrated…
With the rise of the fine-tuned-pretrained paradigm, storing numerous fine-tuned models for multi-tasking creates significant storage overhead. Delta compression alleviates this by storing only the pretrained model and the highly compressed…
Intelligent agents must be able to articulate its own uncertainty. In this work, we show that pre-trained sequence models are naturally capable of probabilistic reasoning over exchangeable data points -- forming informed beliefs and…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
The now classical replicator equation describes a wide variety of biological phenomena, including those in theoretical genetics, evolutionary game theory, or in the theories of the origin of life. Among other questions, the permanence of…
Humans continuously make new discoveries, and understanding temporal sequence of events leading to these breakthroughs is essential for advancing science and society. This ability to reason over time allows us to identify future steps and…
Replication is a key technique in the design of efficient and reliable distributed systems. As information grows, it becomes difficult or even impossible to store all information at every replica. A common approach to deal with this problem…