Related papers: New insights on the Dynamic Cellular Metabolism
Recent advances at the intersection of control theory, neuroscience, and machine learning have revealed novel mechanisms by which dynamical systems perform computation. These advances encompass a wide range of conceptual, mathematical, and…
Krotov and Hopfield (2021) proposed a biologically plausible two-layer associative memory network with memory storage capacity exponential in the number of visible neurons. However, the capacity was only linear in the number of hidden…
Associative memory, a form of content-addressable memory, facilitates information storage and retrieval in many biological and physical systems. In statistical mechanics models, associative memory at equilibrium is represented through…
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at biochemical and morphological levels. A…
Recent research has established a connection between modern Hopfield networks (HNs) and transformer attention heads, with guarantees of exponential storage capacity. However, these models still face challenges scaling storage efficiently.…
Hopfield networks are artificial neural networks which store memory patterns on the states of their neurons by choosing recurrent connection weights and update rules such that the energy landscape of the network forms attractors around the…
Dense Associative Memories or modern Hopfield networks permit storage and reliable retrieval of an exponentially large (in the dimension of feature space) number of memories. At the same time, their naive implementation is non-biological,…
Working memory is a cognitive function involving the storage and manipulation of latent information over brief intervals of time, thus making it crucial for context-dependent computation. Here, we use a top-down modeling approach to examine…
The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…
This paper proposes an extension of the traditional Central Dogma of molecular biology to a more dynamic model termed the Central Dogma Cycle (CDC) and a broader network called the Central Dogma Cyclic Network (CDCN). While the Central…
Neural network models capable of storing memory have been extensively studied in computer science and computational neuroscience. The Hopfield network is a prototypical example of a model designed for associative, or content-addressable,…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
The classic paradigms for learning and memory recall focus on strengths of synaptic couplings and how these can be modulated to encode memories. In a previous paper [A. K. Behera, M. Rao, S. Sastry, and S. Vaikuntanathan, Physical Review X…
The Hopfield model describes a neural network that stores memories using all-to-all-coupled spins. Memory patterns are recalled under equilibrium dynamics. Storing too many patterns breaks the associative recall process because frustration…
We present a Hopfield-like autoassociative network for memories representing examples of concepts. Each memory is encoded by two activity patterns with complementary properties. The first is dense and correlated across examples within…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
Neural circuits in the brain perform a variety of essential functions, including input classification, pattern completion, and the generation of rhythms and oscillations that support processes such as breathing and locomotion. There is also…
Non-equilibrium molecular-scale dynamics, where fast electron transport couples with slow chemical state evolution, underpins the complex behaviors of molecular memristors, yet a general model linking these dynamics to neuromorphic…
Epigenetic cell memory, the inheritance of gene expression patterns across subsequent cell divisions, is a critical property of multi-cellular organisms. In recent work [10], a subset of the authors observed in a simulation study how the…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…