相关论文: pgMAP: a pipeline to enable guide RNA read mapping…
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the…
Motivation: Usefulness of analysis derived from Affymetrix microarrays depends largely upon the reliability of files describing the correspondence between probe sets, genes and transcripts. In particular, in case a gene is targeted by two…
We present MapReader, a free, open-source software library written in Python for analyzing large map collections (scanned or born-digital). This library transforms the way historians can use maps by turning extensive, homogeneous map sets…
While Multimodal Large Language Models have achieved human-like performance on many visual and textual reasoning tasks, their proficiency in fine-grained spatial understanding, such as route tracing on maps remains limited. Unlike humans,…
The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Graph kernels have recently emerged as a promising approach to this problem. There are now many kernels, each…
We present a convenient, all-in-one framework for the scientific analysis of fully reduced, (integral-field) spectroscopic data. The GIST pipeline (Galaxy IFU Spectroscopy Tool) is entirely written in Python3 and conducts all steps from the…
Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…
We present a pipeline for unbiased and robust multimodal registration of neuroimaging modalities with minimal pre-processing. While typical multimodal studies need to use multiple independent processing pipelines, with diverse options and…
Modern machine learning systems are increasingly realised as multistage pipelines, yet existing transparency mechanisms typically operate at a model level: they describe what a system is and why it behaves as it does, but not how individual…
Fully automated astronomical data calibration and imaging pipelines are difficult to develop without a good prototyping method which permits to bridge the time between observatory commissioning and the moment when the special features and…
Retrieval-Augmented Generation (RAG) systems couple large language models with external knowledge, yet most evaluation methods report aggregate scores that reveal whether a pipeline underperforms but not where or why. We introduce…
We consider the task of grasping a target object based on a natural language command query. Previous work primarily focused on localizing the object given the query, which requires a separate grasp detection module to grasp it. The cascaded…
PHOTOMETRYPIPELINE (PP) is an automated pipeline that produces calibrated photometry from imaging data through image registration, aperture photometry, photometric calibration, and target identification with only minimal human interaction.…
Performance analysis is a critical step in the oft-repeated, iterative process of performance tuning of parallel programs. Per-process, per-thread traces (detailed logs of events with timestamps) enable in-depth analysis of parallel program…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
Spatial join is a fundamental operation in spatial databases. With the rapid growth of 3D data in applications such as LiDAR-based object detection and 3D digital pathology, there is an increasing need to support spatial join over 3D…
Cancer survival prediction is an active area of research that can help prevent unnecessary therapies and improve patient's quality of life. Gene expression profiling is being widely used in cancer studies to discover informative biomarkers…
Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of…
Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale.…
The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for…