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A mechanism of the replication of proto-RNAs in oligomer world is proposed. The replication is carried out by a minimum cycle which is sustained by a ligase and a helicase. We expect that such a cycle actually worked in the primordial soup…

Biomolecules · Quantitative Biology 2013-06-04 Daisuke Sato , Osamu Narikiyo

Based on the oligomer-world hypothesis we propose an abstract model where the molecular recognition among oligomers is described in the shape space. The origin of life in the oligomer world is regarded as the establishment of a metabolic…

Subcellular Processes · Quantitative Biology 2012-09-21 Tomoaki Nishio , Osamu Narikiyo

Foundation models exhibit significant capabilities in decision-making and logical deductions. Nonetheless, a continuing discourse persists regarding their genuine understanding of the world as opposed to mere stochastic mimicry. This paper…

Machine Learning · Computer Science 2023-10-24 Dean S. Hazineh , Zechen Zhang , Jeffery Chiu

Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…

Cell Behavior · Quantitative Biology 2007-05-23 Javier Macia , Ricard V. Sole

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…

Biological Physics · Physics 2025-08-01 Arvind Murugan , David Zwicker , Charlotta Lorenz , Eric R. Dufresne

In this paper, the application of a cycle accurate binary translator for rapid prototyping of SoCs will be presented. This translator generates code to run on a rapid prototyping system consisting of a VLIW processor and FPGAs. The…

Hardware Architecture · Computer Science 2011-11-09 Jurgen Schnerr , Oliver Bringmann , Wolfgang Rosenstiel

As a result of the rapid changes in information and communication technology (ICT), the world has become a small village where people from all over the world connect with each other in dialogue and communication via the Internet. Also,…

Computation and Language · Computer Science 2017-09-15 Nabeel T. Alsohybe , Neama Abdulaziz Dahan , Fadl Mutaher Ba-Alwi

Transformers have proven highly effective across various applications, especially in handling sequential data such as natural languages and time series. However, transformer models often lack clear interpretability, and the success of…

Machine Learning · Computer Science 2025-12-01 Wei Shi , Yuan Cao

Do transformers, when trained on sequential reasoning traces, build internal models of the underlying task? And if so, does the structure of those internal representations mirror the structure of the domain? We train an 8-layer transformer…

Machine Learning · Computer Science 2026-05-20 Roman Kniazev , Nathanaël Fijalkow

The field of machine translation has progressed tremendously in recent years. Even though the translation quality has improved significantly, current systems are still unable to produce uniformly acceptable machine translations for the…

Computation and Language · Computer Science 2020-05-11 Meng Zhang , Xin Jiang , Yang Liu , Qun Liu

Predicting future events, and their order, is important for efficient planning. We propose a neural mechanism to non-destructively translate the current state of memory into the future, so as to construct an ordered set of future…

Neurons and Cognition · Quantitative Biology 2017-03-28 Karthik H. Shankar , Inder Singh , Marc W. Howard

The transformers have achieved significant accomplishments in the natural language processing as its outstanding parallel processing capabilities and highly flexible attention mechanism. In addition, increasing studies based on transformers…

Computation and Language · Computer Science 2024-07-19 Wei Lan , Guohang He , Mingyang Liu , Qingfeng Chen , Junyue Cao , Wei Peng

We introduce a proof recommender system for the HOL4 theorem prover. Our tool is built upon a transformer-based model [2] designed specifically to provide proof assistance in HOL4. The model is trained to discern theorem proving patterns…

Logic in Computer Science · Computer Science 2025-01-13 Nour Dekhil , Adnan Rashid , Sofiene Tahar

In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…

Physics and Society · Physics 2018-10-10 S. S. Chanda , B. McKelvey

Neural machine translation is a recently proposed approach to machine translation. Unlike the traditional statistical machine translation, the neural machine translation aims at building a single neural network that can be jointly tuned to…

Computation and Language · Computer Science 2016-05-23 Dzmitry Bahdanau , Kyunghyun Cho , Yoshua Bengio

The transformer is a state-of-the-art neural translation model that uses attention to iteratively refine lexical representations with information drawn from the surrounding context. Lexical features are fed into the first layer and…

Computation and Language · Computer Science 2019-07-01 Denis Emelin , Ivan Titov , Rico Sennrich

Due to its effectiveness and performance, the Transformer translation model has attracted wide attention, most recently in terms of probing-based approaches. Previous work focuses on using or probing source linguistic features in the…

Computation and Language · Computer Science 2021-04-21 Hongfei Xu , Josef van Genabith , Qiuhui Liu , Deyi Xiong

The transformer is a neural network component that can be used to learn useful representations of sequences or sets of data-points. The transformer has driven recent advances in natural language processing, computer vision, and…

Machine Learning · Computer Science 2026-01-21 Richard E. Turner

Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…

Computational Engineering, Finance, and Science · Computer Science 2012-08-21 Vincent Noel , Dima Grigoriev , Sergei Vakulenko , Ovidiu Radulescu

The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…

Cell Behavior · Quantitative Biology 2009-09-29 Harold Fellermann , Ricard V. Solé
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