27 papers · ranked by Valyu relevance
Johanna Bebout, Eva Belke
Gender induction has been claimed to be virtually impossible unless nouns provide reliable semantic or phonological gender-relevant cues. However, learners might exploit syntactic cues, such as definite articles, to infer the gender of gender-unmarked nouns. In children’s poems and songs, such syntactic cues are…
Chabin, Jacques, Ferrari, Mirian Halfeld + 2 more
We introduce an automated method for structuring textual data into a model-agnostic schema, enabling alignment with any database model. It generates both a schema and its instance. Initially, textual data is represented as semantically enriched syntax trees, which are then refined through iterative tree rewriting and…
Jacques Chabin, Mírian Halfeld Ferrari, Nicolas Hiot
We present a general methodology for structuring textual data, represented as syntax trees enriched with semantic information, guided by a meta-model G defined as an attribute grammar. The method involves an evolution process where both the instance and its grammar evolve, with instance transformations guided by…
Jérémie Cabessa, Tao Song
In neural computation, the essential information is generally encoded into the neurons via their spiking configurations, activation values or (attractor) dynamics. The synapses and their associated plasticity mechanisms are, by contrast, mainly used to process this information and implement the crucial learning…
Alexander Gress, Sanjay K Srikakulam, Sebastian Keller, Vasily Ramensky + 1 more
Size and complexity of inputs given to StructMAn can vary a lot. This results in various scaling issues that had to be solved in a way considering the resources provided by the underlying system architecture. We provide several solutions to optimally balance the core load and memory usage. The major mechanism to…
Victoria Siegrist, Rui Mata, Wolf Langewitz, Heike Gerger + 4 more
The need to communicate effectively is pervasive in healthcare , and it is of utmost importance in the acute care setting such as the emergency department (ED) . Patients are typically discharged within few hours once life-threatening conditions have been excluded, but serious conditions may still be under…
Shani Alkoby, Ron S. Hirschprung
Introduction Privacy has become a significant concern in the digital world, especially concerning the personal data collected by websites and other service providers on the World Wide Web network. One of the significant approaches to enable the individual to control privacy is the privacy policy document, which…
Apuã C. M. Paquola, Jennifer A. Erwin, Fred H. Gage
Analysis of high troughput biological data often involves the use of many software packages and in-house written code. For each analysis step there are multiple options of software tools available, each with its own capabilities, limitations and assumptions on the input and output data. The development of…
Geoff Langdale, Daniel Lemire
Despite the maturity of the problem of JSON parsing, we show that substantial speedups are possible. We present the first standard-compliant JSON parser to process gigabytes of data per second on a single core, using commodity processors. We can use a quarter or fewer instructions than a state-of-the-art reference…
Somesh Mohapatra, Daniel Griffin
Identification and control of impurities play a critical role in chemical process development for drug substance synthesis. Most chemical reactions result in a number of by-products and side-products, along with the intended major product. While chemists can predict many of the main process impurities, it remains…
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…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Peter Ford Dominey, Timothy M. Ellmore, Jocelyne Ventre-Dominey
Computational models of language are having an increasing impact in understanding the neural bases of language processing in humans. A recent model of cortical dynamics based on reservoir computing was able to account for temporal aspects of human narrative processing as revealed by fMRI. In this context the current…
Emanuel Diamant
—"Information Processing" is a recently launched buzzword whose meaning is vague and obscure even for the majority of its users. The reason for this is the lack of a suitable definition for the term "information". In my attempt to amend this bizarre situation, I have realized that, following the insights of…
Philippe Blache
Most architectures and models of language processing have been built upon a restricted view of language, which is limited to sentence processing. These approaches fail to capture one primordial characteristic: efficiency. Many facilitation effects are known to be at play in natural situations such as conversation…
Elias Stehle, Hans‐Arno Jacobsen
Parsing is essential for a wide range of use cases, such as stream processing, bulk loading, and in-situ querying of raw data. Yet, the compute-intense step often constitutes a major bottleneck in the data ingestion pipeline, since parsing of inputs that require more involved parsing rules is challenging to…
Sami Mollard, Catherine Wacongne, Sander M. Bohte, Pieter R. Roelfsema
Many cognitive problems can be decomposed into series of subproblems that are solved sequentially by the brain. When subproblems are solved, relevant intermediate results need to be stored by neurons and propagated to the next subproblem, until the overarching goal has been completed. We will here consider visual…
Daniele Oboe, Luca Colombo, Claudio Sbarufatti, Marco Giglio + 1 more
'Marco Gherlone'] The inverse Finite Element Method (iFEM) is receiving more attention for shape sensing due to its independence from the material properties and the external load. However, a proper definition of the model geometry with its boundary conditions is required, together with the acquisition of the…
Cas W. Coopmans, Helen de Hoop, Filiz Tezcan, Peter Hagoort + 1 more
Studies of perception have long shown that the brain adds information to its sensory analysis of the physical environment. A touchstone example for humans is language use: to comprehend a physical signal like speech, the brain must add linguistic knowledge, including syntax. Yet, syntactic rules and representations are…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Giorgio Gonnella, M. Sohel Rahman
Text formats are common in bioinformatics, as they allow for editing and filtering using standard tools, as well as, since text formats are often human readable, manual inspection and evaluation of the data. Bioinformatics is a rapidly evolving field, hence, new techniques, new software tools, new kinds of data often…
Hendrik Folmer
Field-Programmable Gate Arrays (FPGAs) provide highly parallel and customizable hardware solutions but are traditionally programmed using low-level Hardware Description Languages (HDLs) like VHDL and Verilog. These languages have a low level of abstraction and require engineers to manage control and scheduling…
Łukasz Szeremeta
The use of computers to store and process different types of data is growing every day. The same applies to chemical data. SDF and Open Babel are recognized solutions in this field. However, each solution has its drawbacks, which are revealed in specific applications. It is important to be able to easily convert the…
Felix Bänsch, Jonas Schaub, Betül Sevindik, Samuel Behr + 3 more
Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the…
Charlotte Neidiger, Tarek Saier, Kai Kühn, Victor Larignon + 12 more
In this work, a concept for an open chemistry knowledge base was developed to integrate chemical research results into a collaboratively usable platform. To achieve this, we enhanced Semantic MediaWiki (SMW) to support the collection and structured summary of chemical data contained in publications. We implemented…
Jakob Schuster, Kathleen Zeglinski, Lucinda Xiao, Olivia Voulgaris + 5 more
The wide variety of protocols and applications for DNA and RNA sequencing makes flexible tools for read processing an important step in sequence analysis. Beyond trimming and demultiplexing, custom read-level processing is commonly required for data exploration, QC and analysis. Existing tools are often task-specific…
Eric Raman, Larry Shupe, Ryan Eaton, Eberhard Fetz
The activity and connectivity of neurons in the primate brain underlying behavior cannot yet be completely specified, but neural networks provide complete models of the connectivity and activity that performs specific tasks and provide insight into the neural computations performed by the primate brain (5). Studies of…