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Reconfigurable linear optical networks are a key component for the development of optical quantum information processing platforms in the NISQ era and beyond. We report the implementation of such a device based on an innovative design that…

Rule-based models are often used for data analysis as they combine interpretability with predictive power. We present RuleKit, a versatile tool for rule learning. Based on a sequential covering induction algorithm, it is suitable for…

Adapting small instruction-tuned models to specialized domains often relies on supervised fine-tuning (SFT) on curated instruction-response examples, which is expensive to collect at scale. Synthetic training examples generated by a teacher…

Large language models (LLMs) have been widely applied in various practical applications, typically comprising billions of parameters, with inference processes requiring substantial energy and computational resources. In contrast, the human…

Multiple Set Membership Testing (MSMT) is a well-known problem in a variety of search and query applications. Given a dataset of K different sets and a query q, it aims to find all of the sets containing the query. Trivially, an MSMT…

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…

Retrieval-Augmented Generation (RAG) quality depends on many interacting choices across retrieval, ranking, augmentation, prompting, and generation, so optimizing modules in isolation is brittle. We introduce RAGSmith, a modular framework…

We present KumQuat, a system for automatically generating data parallel implementations of Unix shell commands and pipelines. The generated parallel versions split input streams, execute multiple instantiations of the original pipeline…

Historically, Recurrent neural networks (RNNs) and its variants such as LSTM and GRU and more recently Transformers have been the standard go-to components when processing sequential data with neural networks. One notable issue is the…

Scientific and engineering verticals often suffer from data scarcity and strict executability requirements: models must generate not only fluent text, but also syntactically valid, tool-compilable scripts. We present a schema-first…

Graphical Processing Units (GPUs) have recently become a valuable computing tool for the acquisition of data at high rates and for a relatively low cost. The devices work by parallelizing the code into thousands of threads, each executing a…

Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…

We introduce Instruct-SkillMix, an automated approach for creating diverse, high quality SFT data for instruction-following. The pipeline involves two stages, each leveraging an existing powerful LLM: (1) Skill extraction: uses the LLM to…

Generative retrieval-based recommendation has emerged as a promising paradigm aiming at directly generating the identifiers of the target candidates. However, in large-scale recommendation systems, this approach becomes increasingly…

Data harmonization remains a major bottleneck for integrative analysis due to heterogeneity in schemas, value representations, and domain-specific conventions. BDI-Kit provides an extensible toolkit for schema and value matching. It exposes…

Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…

This paper introduces Fermihedral, a compiler framework focusing on discovering the optimal Fermion-to-qubit encoding for targeted Fermionic Hamiltonians. Fermion-to-qubit encoding is a crucial step in harnessing quantum computing for…

Performing massive data mining experiments with multiple datasets and methods is a common task faced by most bioinformatics and computational biology laboratories. WEKA is a machine learning package designed to facilitate this task by…

Data movement between memory and processors is a major bottleneck in modern computing systems. The processing-in-memory (PIM) paradigm aims to alleviate this bottleneck by performing computation inside memory chips. Real PIM hardware (e.g.,…

Minimum flow decomposition (MFD) (the problem of finding a minimum set of paths that perfectly decomposes a flow) is a classical problem in Computer Science, and variants of it are powerful models in multiassembly problems in Bioinformatics…