Chemical concrete machine

The chemical concrete machine is a graph rewriting system which uses only local moves (rewrites), seen as chemical reactions involving molecules which are graphs made up by 4 trivalent nodes. It is Turing complete, therefore it might be used as a model of computation in algorithmic chemistry

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

A Conceptual Framework for Adapation

This paper presents a white-box conceptual framework for adaptation that promotes a neat separation of the adaptation logic from the application logic through a clear identification of control data and their role in the adaptation logic. The framework provides an original perspective from which we survey archetypal approaches to (self-)adaptation ranging from programming languages and paradigms, to computational models, to engineering solutions

Graph AI in Medicine

In clinical artificial intelligence (AI), graph representation learning, mainly through graph neural networks (GNNs), stands out for its capability to capture intricate relationships within structured clinical datasets. With diverse data -- from patient records to imaging -- GNNs process data holistically by viewing modalities as nodes interconnected by their relationships. Graph AI facilitates model transfer across clinical tasks, enabling models to generalize across patient populations without additional parameters or minimal re-training. However, the importance of human-centered design and model interpretability in clinical decision-making cannot be overstated. Since graph AI models capture information through localized neural transformations defined on graph relationships, they offer both an opportunity and a challenge in elucidating model rationale. Knowledge graphs can enhance interpretability by aligning model-driven insights with medical knowledge. Emerging graph models integrate diverse data modalities through pre-training, facilitate interactive feedback loops, and foster human-AI collaboration, paving the way to clinically meaningful predictions

A Conceptual Framework for Adapation

We present a white-box conceptual framework for adaptation. We called it CODA, for COntrol Data Adaptation, since it is based on the notion of control data. CODA promotes a neat separation between application and adaptation logic through a clear identification of the set of data that is relevant for the latter. The framework provides an original perspective from which we survey a representative set of approaches to adaptation ranging from programming languages and paradigms, to computational models and architectural solutions

A Conceptual Framework for Adapation

This paper presents a white-box conceptual framework for adaptation that promotes a neat separation of the adaptation logic from the application logic through a clear identification of control data and their role in the adaptation logic. The framework provides an original perspective from which we survey archetypal approaches to (self-)adaptation ranging from programming languages and paradigms, to computational models, to engineering solutions