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Predicting the effects of chemical and genetic perturbations on quantitative cell states is a central challenge in computational biology, molecular medicine and drug discovery. Recent work has leveraged large-scale single-cell data and…
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
I discuss several aspects of information theory and its relationship to physics and neuroscience. The unifying thread of this somewhat chaotic essay is the concept of Kolmogorov or algorithmic complexity (Kolmogorov Complexity, for short).…
Ontologies represent the conceptual knowledge of a domain. At the core of an ontology is the taxonomy of concepts and subconcepts that represent specific entities, which can be complex to build. In many cases, information is available in…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physico-chemical…
Recently, we proposed polycontextural networks as a model of evolving systems of interacting beliefs. Here, we present an analysis of the phase transition as well as the scaling properties. The model contains interacting agents that strive…
The emergence of large language models offers new possibilities for structured exploration of scientific knowledge. Rather than viewing scientific discovery as isolated ideas or content, we propose a structured approach that emphasizes the…
The mechanisms of comprehension during language processing remains an open question. Classically, building the meaning of a linguistic utterance is said to be incremental, step-by-step, based on a compositional process. However, many…
Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability…
In this paper, we observe that semi-structured tabulated text is ubiquitous; understanding them requires not only comprehending the meaning of text fragments, but also implicit relationships between them. We argue that such data can prove…
Experiments in cognitive science and decision theory show that the ways in which people combine concepts and make decisions cannot be described by classical logic and probability theory. This has serious implications for applied disciplines…
Memory is inherently entangled with prediction and planning. Flexible behavior in biological and artificial agents depends on the interplay of learning from the past and predicting the future in ever-changing environments. This chapter…
This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other…
Large language models often reason beyond surface tokens, but the internal stage at which token-level information becomes abstract relational structure remains unclear. We investigate this question by analyzing how attention heads and…
This work examines the interconnections between logic, epistemology, and sciences within the Naturalist tradition. It presents a scheme that connects logic, mathematics, physics, chemistry, biology, and cognition, emphasizing…
The recent availability of larger typological databases such as Haspelmath et al. (2005) has brought the linguistics community closer to having a solid, empirical foundation for making actual claims about prehistoric migrations, deep…
Any search for present or past life beyond Earth should consider the initial processes and related environmental controls that might have led to its start. As on Earth, such an understanding lies well beyond how simple organic molecules…