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Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
I introduce a new approach to semantic information based upon the influence of erasure operations (interventions) upon distributions of a system's future trajectories through its phase space. Semantic (meaningful) information is…
This paper proposes a reconciliation of two different theories of information. The first, originally proposed in a lesser-known work by Claude Shannon, describes how the information content of channels can be described qualitatively, but…
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
Semantic memory is the subsystem of human memory that stores knowledge of concepts or meanings, as opposed to life specific experiences. The organization of concepts within semantic memory can be understood as a semantic network, where the…
Reliable biomedical and clinical retrieval requires more than strong ranking performance: it requires a practical way to find systematic model failures and curate the training evidence needed to correct them. Late-interaction models such as…
The information in an individual finite object (like a binary string) is commonly measured by its Kolmogorov complexity. One can divide that information into two parts: the information accounting for the useful regularity present in the…
This monograph presents a modular cognitive architecture for artificial intelligence grounded in the formal modeling of belief as structured semantic state. Belief states are defined as dynamic ensembles of linguistic expressions embedded…
The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but…
A phenomenological model of self-organization explaining the emergence of a complexity with features that apparently satisfy the specific criteria usually required for recognizing the appearance of life in laboratory is presented. The…
Information theory provides powerful tools for understanding communication systems. This analysis can be applied to intercellular signal transduction, which is a means of chemical communication among cells and microbes. We discuss how to…
Clear and effective explanations are essential for human understanding and knowledge dissemination. The scope of scientific research aiming to understand the essence of explanations has recently expanded from the social sciences to machine…
We introduce PRISM (Predictive Reasoning in Sequential Medicine), a transformer-based architecture designed to model the sequential progression of clinical decision-making processes. Unlike traditional approaches that rely on isolated…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
This paper describes a method for creating structure from heterogeneous sources, as part of an information database, or more specifically, a 'concept base'. Structures called 'concept trees' can grow from the semi-structured sources when…
Humans possess the capability to reason at an abstract level and to structure information into abstract categories, but the underlying neural processes have remained unknown. Experimental evidence has recently emerged for the organization…
Culture involves the origination and transmission of ideas, but the conditions in which culture can emerge and evolve are unclear. We constructed and studied a highly simplified neural-network model of these processes. In this model ideas…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
Statistical prediction models are often trained on data from different probability distributions than their eventual use cases. One approach to proactively prepare for these shifts harnesses the intuition that causal mechanisms should…