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Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based…
We introduce VAREX (VARied-schema EXtraction), a benchmark for evaluating multimodal foundation models on structured data extraction from government forms. VAREX employs a Reverse Annotation pipeline that programmatically fills PDF…
In recent times, it has been shown that one can use code as data to aid various applications such as automatic commit message generation, automatic generation of pull request descriptions and automatic program repair. Take for instance the…
We present KinetiX, a software toolkit to generate computationally efficient fuel-specific routines for the chemical source term, thermodynamic and mixture-averaged transport properties for use in combustion simulation codes. The C++…
A key feature of collaboration in science and software development is to have a {\em log} of what and how is being done - for private use and reuse and for sharing selected parts with collaborators, which most often today are distributed…
The CellxGene project has enabled access to single-cell data in the scientific community, providing tools for browsed-based no-code analysis of more than 500 annotated datasets. However, single-cell data requires dimensional reduction to…
Automatically generating function summaries for binaries is an extremely valuable but challenging task, since it involves translating the execution behavior and semantics of the low-level language (assembly code) into human-readable natural…
Representing source code in a generic input format is crucial to automate software engineering tasks, e.g., applying machine learning algorithms to extract information. Visualizing code representations can further enable human experts to…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
ixpeobssim is a simulation and analysis framework, based on the Python programming language and the associated scientific ecosystem, specifically developed for the Imaging X-ray Polarimetry Explorer (IXPE). Given a source model and the…
Open source projects are adopting faster release cycles that reflect various changes. Therefore, comprehending the effects of these changes on software's architecture over the releases becomes necessary. However, it is challenging to keep…
This paper describes a C code generator for ACL2 that recognizes ACL2 representations of C constructs, according to a shallow embedding of C in ACL2, and translates those representations to the represented C constructs. The code generator…
Binary code similarity detection is a core task in reverse engineering. It supports malware analysis and vulnerability discovery by identifying semantically similar code in different contexts. Modern methods have progressed from manually…
This paper proposes an open source visual analytics tool consisting of several views and perspectives on eye movement data collected during code reading tasks when writing computer programs. Hence the focus of this work is on code and…
Given an algorithm the quality of the output largely depends on a proper specification of the input parameters. A lot of work has been done to analyze tasks related to using a fixed model [25] and finding a good set of inputs. In this paper…
There are several approaches for encoding source code in the input vectors of neural models. These approaches attempt to include various syntactic and semantic features of input programs in their encoding. In this paper, we investigate…
Conformance checking is a major function of process mining, which allows organizations to identify and alleviate potential deviations from the intended process behavior. To fully leverage its benefits, it is important that conformance…
Binary similarity involves determining whether two binary programs exhibit similar functionality, often originating from the same source code. In this work, we propose VexIR2Vec, an approach for binary similarity using VEX-IR, an…
The past decade has seen rapid growth in the number of experimentally realized two-dimensional (2D) materials with diverse chemical and physical properties. However, information on their crystal structure, synthesis routes, and measured or…
Symmetry provides a powerful machinery to classify, interpret, and understand quantum-mechanical theories and results. However, most contemporary quantum chemistry packages lack the ability to handle degeneracy and symmetry breaking…