Related papers: Supporting Workflow Reproducibility by Linking Bio…
One of the challenges in machine learning research is to ensure that presented and published results are sound and reliable. Reproducibility, that is obtaining similar results as presented in a paper or talk, using the same code and data…
We propose an autoregressive entity linking model, that is trained with two auxiliary tasks, and learns to re-rank generated samples at inference time. Our proposed novelties address two weaknesses in the literature. First, a recent method…
Objective: The aim of this study was to build an effective co-reference resolution system tailored for the biomedical domain. Materials and Methods: Experiment materials used in this study is provided by the 2011 i2b2 Natural Language…
Scientific workflows are powerful tools for management of scalable experiments, often composed of complex tasks running on distributed resources. Existing cyberinfrastructure provides components that can be utilized within repeatable…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…
Discovering authoritative links between publications and the datasets that they use can be a labor-intensive process. We introduce a natural language processing pipeline that retrieves and reviews publications for informal references to…
Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…
Efficient reproduction of research papers is pivotal to accelerating scientific progress. However, the increasing complexity of proposed methods often renders reproduction a labor-intensive endeavor, necessitating profound domain expertise.…
Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…
We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
Background: Empirical studies on widely used model-based development tools such as MATLAB/Simulink are limited despite the tools' importance in various industries. Aims: The aim of this paper is to investigate the reproducibility of…
The integration of Large Language Models (LLMs) into scientific workflows presents exciting opportunities to accelerate biomedical discovery. However, the reactive nature of LLMs, which respond only when prompted, limits their effectiveness…
This registered report introduces the largest, and for the first time, reproducible experimental survey on biomedical sentence similarity with the following aims: (1) to elucidate the state of the art of the problem; (2) to solve some…
Entity linking (EL) is the task of automatically identifying entity mentions in text and resolving them to a corresponding entity in a reference knowledge base like Wikipedia. Throughout the past decade, a plethora of EL systems and…
Computational notebooks, widely used for ad-hoc analysis and often shared with others, can be difficult to understand because the standard linear layout is not optimized for reading. In particular, related text, code, and outputs may be…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several…
One of the foundations of science is that researchers must publish the methodology used to achieve their results so that others can attempt to reproduce them. This has the added benefit of allowing methods to be adopted and adapted for…