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Recursive relational specifications are commonly used to describe the computational structure of formal systems. Recent research in proof theory has identified two features that facilitate direct, logic-based reasoning about such…
Large Language Models (LLMs) have become powerful tools for annotating unstructured data. However, most existing workflows rely on ad hoc scripts, making reproducibility, robustness, and systematic evaluation difficult. To address these…
There are several ways to formally represent families of data, such as lambda terms, in a type theory such as the dependent type theory of Coq. Mathematical representations are very compact ones and usually rely on the use of dependent…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
Automatic code transformation in which transformations are tuned for specific applications and contexts are difficult to achieve in an accessible manner. In this paper, we present an approach to build application specific code…
A novel adaptive binary decoding algorithm for LDPC codes is proposed, which reduces the decoding complexity while having a comparable or even better performance than corresponding non-adaptive alternatives. In each iteration the variable…
Exascale computing will feature novel and potentially disruptive hardware architectures. Exploiting these to their full potential is non-trivial. Numerical modelling frameworks involving finite difference methods are currently limited by…
We present the new software OpDiLib, a universal add-on for classical operator overloading AD tools that enables the automatic differentiation (AD) of OpenMP parallelized code. With it, we establish support for OpenMP features in a reverse…
Scientific documents often contain a large number of acronyms. Disambiguation of these acronyms will help researchers better understand the meaning of vocabulary in the documents. In the past, thanks to large amounts of data from English…
Text documents, including programs, typically have human-readable semantic structure. Historically, programmatic access to these semantics has required explicit in-document tagging. Especially in systems where the text has an execution…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
We present some lambda calculus with explicit substitutions and named variables. The characteristic feature of this calculus is as follows: renaming of bound variables when performing substitutions is done using special reductions and may…
We present PackLib^2, the first fully integrated benchmark library for multi-dimensional packing instances. PackLib^2 combines a systematic collection of all benchmark instances from previous literature with a well-organized set of new and…
A compiler's optimizer operates over abstract syntax trees (ASTs), continuously applying rewrite rules to replace subtrees of the AST with more efficient ones. Especially on large source repositories, even simply finding opportunities for a…
Vision encoders are increasingly used in modern applications, from vision-only models to multimodal systems such as vision-language models. Despite their remarkable success, it remains unclear how these architectures represent features…
Braidlab is a Matlab package for analyzing data using braids. It was designed to be fast, so it can be used on relatively large problems. It uses the object-oriented features of Matlab to provide a class for braids on punctured disks and a…
The accurate recovery of constituent-level optical properties from integrating sphere measurements is a central analytical challenge in pharmaceutical analysis, food science, and biomedical diagnostics. Neural network autoencoders can…
We describe an approach to the verified implementation of transformations on functional programs that exploits the higher-order representation of syntax. In this approach, transformations are specified using the logic of hereditary Harrop…
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
Word representations induced from models with discrete latent variables (e.g.\ HMMs) have been shown to be beneficial in many NLP applications. In this work, we exploit labeled syntactic dependency trees and formalize the induction problem…