20 papers · ranked by Valyu relevance
Bocirnea, Sean, Bowman, William J.
Macro embedding is a popular approach to defining extensible shallow embeddings of object languages in Schemelike host languages. While macro embedding has even been shown to enable implementing extensible typed languages in systems like Racket, it comes at a cost: compile-time performance. In this paper, we revisit…
Leif Percival Andersen, Michael Ballantyne, Matthias Felleisen
Many programming problems call for turning geometrical thoughts into code: tables, hierarchical structures, nests of objects, trees, forests, graphs, and so on. Linear text does not do justice to such thoughts. But, it has been the dominant programming medium for the past and will remain so for the foreseeable future.
Kazuhiro Ichikawa, Shigeru Chiba
One promising approach uses user-defined operators. A user-defined operator is a function with userdefined syntax. It can be regarded as a syntax extension implemented without macros. An advantage of userdefined operators is that an operator can be statically typed. The compiler can find type errors in the definition…
Tetsuro Matsumura, Kimio Kuramitsu
Parsing Expression Grammars are a popular foundation for describing syntax. Unfortunately, several syntax of programming languages are still hard to recognize with pure PEGs. Notorious cases appears: typedef-defined names in C/C++, indentation-based code layout in Python, and HERE document in many scripting languages.…
Frederic von Wegner, Gesine Hermann, Inken Tödt, Inga Karin Todtenhaupt + 1 more
Higher-order syntax properties of EEG microstate sequences offer insight into the transition dynamics of functional brain networks. We here define higher-order syntax as microstate sequence properties that are not explained by the first-order transition matrix, and we postulate three requirements that surrogate data…
Kaisa Helttunen, Heikki Kainulainen, J. M. García-Ruiz
The design and features of the CIF extension for Visual Studio Code are presented.
Noel O'Boyle, Andrew Dalke
Background There has been increasing interest in the use of deep neural networks for de novo design of molecules with desired properties. A common approach is to train a generative model on SMILES strings and then use this to generate SMILES strings for molecules with a desired property. Unfortunately, these SMILES…
David Thompson, Johan Gielis
Our understanding of quantum phenomena often begins with simple particle-in-a-box style problems, the solutions of which introduce the student to foundational quantum concepts such as degeneracy and quantization. Simple model geometries of confinement afford analytic solutions, which are readily derivable, easily…
Lei Yu, Yang Xu
The lexicon is an evolving symbolic system that expresses an unbounded set of emerging meanings with a limited vocabulary. As a result, words often extend to new meanings. Decades of research have suggested that word meaning extension is non-arbitrary, and recent work formalizes this process as cognitive models of…
Benjamin P. Kellman, Yujie Zhang, Emma Logomasini, Eric Meinhardt + 14 more
Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable…
Stephanie L. Mason, Sarah L. Walsh, Amanda R. Ridley
Recent evidence of extensive call sequence use in non-human primates has led to the theory that syntax evolved to mitigate the constraints of their genetically fixed repertoires, before vocal production learning later emerged in humans. However, evidence of similarly extensive sequence repertoires in an open-ended…
Adam M. Morgan, Orrin Devinsky, Werner K. Doyle, Patricia Dugan + 2 more
Syntax, the abstract structure of language, is a hallmark of human cognition. Despite its importance, its neural underpinnings remain obscured by inherent limitations of non-invasive brain measures and a near total focus on comprehension paradigms. Here, we address these limitations with high-resolution neurosurgical…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko
Background We study the adaptation of Link Grammar Parser to the biomedical sublanguage with a focus on domain terms not found in a general parser lexicon. Using two biomedical corpora, we implement and evaluate three approaches to addressing unknown words: automatic lexicon expansion, the use of morphological clues…
Kuba Nowak, Paweł Błażej, Małgorzata Wnetrzak, Dorota Mackiewicz + 1 more
Reprogramming of the standard genetic code in order to include non-canonical amino acids (ncAAs) opens a new perspective in medicine, industry and biotechnology. There are several methods of engineering the code, which allow us for storing new genetic information in DNA sequences and transmitting it into the protein…
Catia Pesquita, Francisco M. Couto, K. Bretonnel Cohen
Developing and extending a biomedical ontology is a very demanding task that can never be considered complete given our ever-evolving understanding of the life sciences. Extension in particular can benefit from the automation of some of its steps, thus releasing experts to focus on harder tasks. Here we present a…
Andreas Trotzke
This article presents a perspective on syntactic cyclicity in minimalism that is compatible with fundamental ideas in construction-grammar approaches. In particular, I outline the minimalist approach to syntactic structure building and highlight that units of potentially any phrasal size can be atomic items in the…
Rémi Segretain, Sergiu Ivanov, Laurent Trilling, Nicolas Glade
Formal interaction networks are well suited for representing complex biological systems and have been used to model signalling pathways, gene regulatory networks, interaction within ecosystems, etc. In this paper, we introduce Sign Boolean Networks (SBNs), which are a uniform variant of Threshold Boolean Networks…
Authors not listed
While virtual libraries of synthetically accessible compounds have exploded in size to many billions, our capacity to extract valuable drug leads from these vast databases remains limited by computational resources. To overcome this, we developed SLICE SMARTS and Logic In ChEmistry), a powerful new tool designed for…
Michael A. Boemo, Luca Cardelli, Conrad A. Nieduszynski
Biological systems are made up of components that change their actions (and interactions) over time and coordinate with other components nearby. Together with a large state space, the complexity of this behaviour can make it difficult to create concise mathematical models that can be easily extended or modified. This…