Related papers: Want Drugs? Use Python
Using a single tool to build and compare recommender systems significantly reduces the time to market for new models. In addition, the comparison results when using such tools look more consistent. This is why many different tools and…
The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this…
Similar to Open Data initiatives, data science as a community has launched initiatives for sharing not only data but entire pipelines, derivatives, artifacts, etc. (Open Data Science). However, the few efforts that exist focus on the…
Over the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major…
Python is rapidly becoming the lingua franca of machine learning and scientific computing. With the broad use of frameworks such as Numpy, SciPy, and TensorFlow, scientific computing and machine learning are seeing a productivity boost on…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Dynamically typed languages such as Python have become very popular. Among other strengths, Python's dynamic nature and its straightforward linking to native code have made it the de-facto language for many research areas such as Artificial…
Local governments, as part of 'smart city' initiatives and to promote interoperability, are increasingly incorporating open-source software into their data management, analysis, and visualisation workflows. Python, with its concise and…
Logical models offer a simple but powerful means to understand the complex dynamics of biochemical regulation, without the need to estimate kinetic parameters. However, even simple automata components can lead to collective dynamics that…
In this article we describe how we successfully incorporated data analysis in Python in a first-year laboratory course without significantly altering the course structure and without overburdening students. We show how we created and used…
How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead…
In this report, we introduce DocXChain, a powerful open-source toolchain for document parsing, which is designed and developed to automatically convert the rich information embodied in unstructured documents, such as text, tables and…
In today's software world with its cornucopia of reusable software libraries, when a programmer is faced with a programming task that they suspect can be completed through the use of a library, they often look for code examples using a…
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools…
Spreadsheets are widely used in various fields to do large numerical analysis. While several companies have relied on spreadsheets for decades, data scientists are going in the direction of using scientific programming languages such as…
Managing the data for Information Retrieval (IR) experiments can be challenging. Dataset documentation is scattered across the Internet and once one obtains a copy of the data, there are numerous different data formats to work with. Even…
PyTerrier provides a declarative framework for building and experimenting with Information Retrieval (IR) pipelines. In this demonstration, we highlight several recent pipeline operations that improve their ability to be programmatically…
Background: Data mining and analyzing of public Git software repositories is a growing research field. The tools used for studies that investigate a single project or a group of projects have been refined, but it is not clear whether the…
Everybody wants to analyse their data, but only few posses the data science expertise to to this. Motivated by this observation we introduce a novel framework and system \textsc{VisualSynth} for human-machine collaboration in data science.…
LensKit is an open-source toolkit for building, researching, and learning about recommender systems. First released in 2010 as a Java framework, it has supported diverse published research, small-scale production deployments, and education…