SciPy 2008

Proceedings of the 7th Python in Science Conference (2008)

There are 0 articles published in this collection

SciPy 2009

Proceedings of the 8th Python in Science Conference (2009)

There are 0 articles published in this collection

SciPy 2010

Proceedings of the 9th Python in Science Conference (2010)

There are 18 articles published in this collection
SciPy 2010 | Article
Statsmodels: Econometric and Statistical Modeling with Python
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Jun 28, 2010

Statsmodels is a library for statistical and econometric analysis in Python. This paper discusses the current relationship between statistics and Python and open source more generally, outlining how the statsmodels package fills a gap in this relationship.

SciPy 2010 | Article
Audio-Visual Speech Recognition using SciPy
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Jun 28, 2010

In audio-visual automatic speech recognition (AVASR) both acoustic and visual modalities of speech are used to identify what a person is saying. In this paper we propose a basic AVASR system implemented using SciPy, an open source Python library for scientific computing.

SciPy 2010 | Article
PySPH: A Python Framework for Smoothed Particle Hydrodynamics
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Jun 28, 2010

PySPH is a Python-based open source parallel framework for Smoothed Particle Hydrodynamics (SPH) simulations. It is distributed under a BSD license. The performance critical parts are implemented in Cython.

SciPy 2010 | Article
A Programmatic Interface for Particle Plasma Simulation in Python
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Jun 28, 2010

Particle-in-Cell (PIC) simulations are a popular approach to plasma physics problems in a variety of applications. These simulations range from interactive to very large, and are well suited to parallel architectures, such as GPUs.

SciPy 2010 | Article
Numerical Pyromaniacs: The Use of Python in Fire Research
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Jun 28, 2010

Python along with various numerical and scientific libraries was used to create tools that enable fire protection engineers to perform various calculations and tasks including educational instruction, experimental work, and data visualization.

SciPy 2010 | Article
SpacePy - A Python-based Library of Tools for the Space Sciences
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Jun 28, 2010

Space science deals with the bodies within the solar system and the interplanetary medium; the primary focus is on atmospheres and above—at Earth the short timescale variation in the the geomagnetic field, the Van Allen radiation belts and the deposition of energy into the upper atmosphere are key areas of investigation.

SciPy 2010 | Article
Protein Folding with Python on Supercomputers
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Jun 28, 2010

Today's supercomputers have hundreds of thousands of compute cores and this number is likely to grow. Many of today's algorithms will have to be rethought to take advantage of such large systems. New algorithms must provide fine grained parallelism and excellent scalability.

SciPy 2010 | Article
Data Structures for Statistical Computing in Python
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Jun 28, 2010

In this paper we are concerned with the practical issues of working with data sets common to finance, statistics, and other related fields. pandas is a new library which aims to facilitate working with these data sets and to provide a set of fundamental building blocks for implementing statistical models.

SciPy 2010 | Article
Modeling Sudoku Puzzles with Python
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Jun 28, 2010

The popular Sudoku puzzles which appear daily in newspapers the world over have, lately, attracted the attention of mathematicians and computer scientists. There are many, difficult, unsolved problems about Sudoku puzzles and their generalizations which make them especially interesting to mathematicians.

SciPy 2010 | Article
Using Python with Smoke and JWST Mirrors
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Jun 28, 2010

We will describe how the Space Telescope Science Institute is using Python in support of the next large space telescope, the James Webb Space Telescope (JWST). We will briefly describe the 6.5 meter segmented-mirror infra-red telescope, currently planned for a 2014 launch, and its science goals.

SciPy 2010 | Article
Rebuilding the Hubble Exposure Time Calculator
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Jun 28, 2010

An Exposure Time Calculator (ETC) is an invaluable web tool for astronomers wishing to submit proposals to use the Hubble Space Telescope (HST). It provide a means of estimating how much telescope time will be needed to observe a specified source to the required accuracy.

SciPy 2010 | Article
Weather Forecast Accuracy Analysis
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Jun 28, 2010

ForecastWatch is a weather forecast verification and accuracy analysis system that collects over 70,000 weather forecasts per day. The system consists of data capture, verification, aggregation, audit and display components.

SciPy 2010 | Article
Unusual Relationships: Python and Weaver Birds
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Jun 28, 2010

As colonial birds, weaver birds nest in groups in very particular trees and face specific challenges in the selection and establishment of their nests. Socially-living individuals may organize themselves in particular configurations to decrease the probability of events that could be detrimental to their own fitness.

SciPy 2010 | Article
A High Performance Robot Vision Algorithm Implemented in Python
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Jun 28, 2010

A crucial behavior for assistive robots that operate in unstructured domestic settings is the ability to efficiently reconstruct the 3D geometry of novel objects at run time using no a priori knowledge of the object.

SciPy 2010 | Article
Theano: A CPU and GPU Math Compiler in Python
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Jun 28, 2010

Theano is a compiler for mathematical expressions in Python that combines the convenience of NumPy's syntax with the speed of optimized native machine language. The user composes mathematical expressions in a high-level description that mimics NumPy's syntax and semantics, while being statically typed and functional (as opposed to imperative).

SciPy 2010 | Article
Divisi: Learning from Semantic Networks and Sparse SVD
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Jun 28, 2010

Singular value decomposition (SVD) is a powerful technique for finding similarities and patterns in large data sets. SVD has applications in text analysis, bioinformatics, and recommender systems, and in particular was used in many of the top entries to the Netflix Challenge.

SciPy 2010 | Article
Astrodata
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Jun 28, 2010

The astrodata package is a part of the Gemini Telescope's python-based Data Reduction Suite. It is designed to help us deal in a normalized way with data from a variety of instruments and instrument-modes.

SciPy 2010 | Article
Keeping the Chandra Satellite Cool with Python
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Jun 28, 2010

The Chandra X-ray Observatory has been providing groundbreaking astronomical data since its launch by NASA in July of 1999. Now starting the second decade of science the Chandra operations team has been using Python to create predictive thermal models of key spacecraft components.

SciPy 2011

Proceedings of the 10th Python in Science Conference (2011)

There are 20 articles published in this collection
SciPy 2011 | Article
Improving efficiency and repeatability of lake volume estimates using Python
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Jul 11, 2011

With increasing population and water use demands in Texas, accurate estimates of lake volumes is a critical part of planning for future water supply needs. Lakes are large and surveying them is expensive in terms of labor, time and cost.

SciPy 2011 | Article
Time Series Analysis in Python with statsmodels
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Jul 11, 2011

We introduce the new time series analysis features of scikits.statsmodels. This includes descriptive statistics, statistical tests and several linear model classes, autoregressive, AR, autoregressive moving-average, ARMA, and vector autoregressive models VAR.

SciPy 2011 | Article
Google App Engine Python
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Jul 11, 2011

In recent years, one of the fastest growing trends in information technology has been the move towards cloud computing. The scalable concept of computing resources on demand allows applications to dynamically react to increased usage instead of having to keep resources in reserve that are often not in use but are still paid for.

SciPy 2011 | Article
N-th-order Accurate, Distributed Interpolation Library
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Jul 11, 2011

The research contained herein yielded an open source interpolation library implemented in and designed for use with the Python programming language. This library, named smbinterp, yields an interpolation to an arbitrary degree of accuracy.

SciPy 2011 | Article
Bringing Parallel Performance to Python with Domain-Specific Selective Embedded Just-in-Time Specialization
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Jul 11, 2011

Today's productivity programmers, such as scientists who need to write code to do science, are typically forced to choose between productive and maintainable code with modest performance (e.g. Python plus native libraries such as SciPy SciPy) or complex, brittle, hardware-specific code that entangles application logic with performance concerns but runs two to three orders of magnitude faster (e.

SciPy 2011 | Article
PyStream: Compiling Python onto the GPU
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Jul 11, 2011

PyStream is a static compiler that can radically transform Python code and run it on a Graphics Processing Unit (GPU). Python compiled to run on the GPU is \textasciitilde{}100,000x faster than when interpreted on the CPU.

SciPy 2011 | Article
Building a Framework for Predictive Science
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Jul 11, 2011

Key questions that scientists and engineers typically want to address can be formulated in terms of predictive science. Questions such as: "How well does my computational model represent reality?", "What are the most important parameters in the problem?", and "What is the best next experiment to perform?" are fundamental in solving scientific problems.

SciPy 2011 | Article
Using Python to Construct a Scalable Parallel Nonlinear Wave Solver
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Jul 11, 2011

Computational scientists seek to provide efficient, easy-to-use tools and frameworks that enable application scientists within a specific discipline to build and/or apply numerical models with up-to-date computing technologies that can be executed on all available computing systems.

SciPy 2011 | Article
IMUSim - Simulating inertial and magnetic sensor systems in Python
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Jul 11, 2011

IMUSim is a new simulation package developed in Python to model Inertial Measurement Units, i.e. devices which include accelerometers, gyroscopes and magnetometers. It was developed in the course of our research into algorithms for IMU-based motion capture, and has now been released under the GPL for the benefit of other researchers and users.

SciPy 2011 | Article
Hurricane Prediction with Python
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Jul 11, 2011

The National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS) is a global spectral model used for aviation weather forecast. It produces forecasts of wind speed and direction, temperature, humidity and precipitation out to 192 hr every 6 hours over the entire globe.

SciPy 2011 | Article
Automation of Inertial Fusion Target Design with Python
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Jul 11, 2011

The process of tuning an inertial confinement fusion pulse shape to a specific target design is highly iterative process. When done manually, each iteration has large latency and is consequently time consuming.

SciPy 2011 | Article
PyModel: Model-based testing in Python
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Jul 11, 2011

In unit testing, the programmer codes the test cases, and also codes assertions that check whether each test case passed. In model-based testing, the programmer codes a "model" that generates as many test cases as desired and also acts as the oracle that checks the cases.

SciPy 2011 | Article
Using Python, Partnerships, Standards and Web Services to provide Water Data for Texans
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Jul 11, 2011

Obtaining time-series monitoring data in a particular region often requires a significant effort involving visiting multiple websites, contacting multiple organizations and dealing with a variety of data formats.

SciPy 2011 | Article
Constructing scientific programs using SymPy
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Jul 11, 2011

We describe a method for constructing scientific programs where SymPy is used to model the mathematical steps in the derivation. With this workflow, each step in the process can be checked by machine, from the derivation of the equations to the generation of the source code.

SciPy 2011 | Article
Vision Spreadsheet: An Environment for Computer Vision
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Jul 11, 2011

Vision Spreadsheet is an environment for computer vision. It combines a spreadsheet with computer vision and scientific python. The cells in the spreadsheet are images, computations on images, measurements, and plots.

SciPy 2011 | Article
Using the Global Arrays Toolkit to Reimplement NumPy for Distributed Computation
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Jul 11, 2011

Global Arrays (GA) is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate distributed dense arrays.

SciPy 2011 | Article
gpustats: GPU Library for Statistical Computing in Python
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Jul 11, 2011

In this work we discuss gpustats, a new Python library for assisting in "big data" statistical computing applications, particularly Monte Carlo-based inference algorithms. The library provides a general code generation / metaprogramming framework for easily implementing discrete and continuous probability density functions and random variable samplers.

SciPy 2011 | Article
Crab: A Recommendation Engine Framework for Python
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Jul 11, 2011

Crab is a flexible, fast recommender engine for Python that integrates classic information filtering recommendation algorithms in the world of scientific Python packages (NumPy,SciPy, Matplotlib). The engine aims to provide a rich set of components from which you can construct a customized recommender system from a set of algorithms.

SciPy 2011 | Article
Fitting and Estimating Parameter Confidence Limits with Sherpa
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Jul 11, 2011

Sherpa is a generalized modeling and fitting package. Primarily developed for the Chandra Interactive Analysis of Observations (CIAO) package by the Chandra X-ray Center, Sherpa provides an Object-Oriented Programming (OOP) API for parametric data modeling.

SciPy 2011 | Article
A Technical Anatomy of SPM.Python, a Scalable, Parallel Version of Python
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Jul 11, 2011

SPM.Python is a scalable, parallel fault-tolerant version of the serial Python language, and can be deployed to create parallel capabilities to solve problems in domains spanning finance, life sciences, electronic design, IT, visualization, and research.

SciPy 2012

Proceedings of the 11th Python in Science Conference (2012)

There are 13 articles published in this collection
SciPy 2012 | Article
OpenMG: A New Multigrid Implementation in Python
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Jul 16, 2012

In many large-scale computations, systems of equations arise in the form , where is a linear operation to be performed on the unknown data , producing the known right-hand side, , which represents some constraint of known or assumed behavior of the system being modeled.

SciPy 2012 | Article
cphVB: A System for Automated Runtime Optimization and Parallelization of Vectorized Applications
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Jul 16, 2012

Modern processor architectures, in addition to having still more cores, also require still more consideration to memory-layout in order to run at full capacity. The usefulness of most languages is deprecating as their abstractions, structures or objects are hard to map onto modern processor architectures efficiently.

SciPy 2012 | Article
QuTiP: A framework for the dynamics of open quantum systems using SciPy and Cython
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Jul 16, 2012

We present QuTiP (http://www.qutip.org), an object-oriented, open-source framework for solving the dynamics of open quantum systems. Written in Python, and using a combination of Cython, NumPy, SciPy, and matplotlib, QuTiP provides an environment for computational quantum mechanics that is both easy and efficient to use.

SciPy 2012 | Article
Uncertainty Modeling with SymPy Stats
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Jul 16, 2012

We add a random variable type to a mathematical modeling language. We demonstrate through examples how this is a highly separable way to introduce uncertainty and produce and query stochastic models. We motivate the use of symbolics and thin compilers in scientific computing.

SciPy 2012 | Article
Fcm - A python library for flow cytometry
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Jul 16, 2012

Flow cytometry has the ability to measure multiple parameters of a heterogeneous mix of cells at single cell resolution. This has lead flow cytometry to become an integral tool in immunology and biology.

SciPy 2012 | Article
The Reference Model for Disease Progression
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Jul 16, 2012

The Reference Model for disease progression is based on a modeling framework written in Python. It is a prototype that demonstrates the use of computing power to aid in chronic disease forecast. The model uses references to publicly available data as a source of information, hence the name for the model.

SciPy 2012 | Article
Self-driving Lego Mindstorms Robot
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Jul 16, 2012

In this paper, I describe the workings of my personal hobby project - a self-driving lego mindstorms robot. The body of the robot is built with Lego Mindstorms. An Android smartphone is used to capture the view in front of the robot.

SciPy 2012 | Article
PythonTeX: Fast Access to Python from within LaTeX
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Jul 16, 2012

PythonTeX is a new LaTeX package that provides access to the full power of Python from within LaTeX documents. It allows Python code entered within a LaTeX document to be executed, and provides access to the output.

SciPy 2012 | Article
Python's Role in VisIt
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Jul 16, 2012

VisIt is an open source, turnkey application for scientific data analysis and visualization that runs on a wide variety of platforms from desktops to petascale class supercomputers. VisIt's core software infrastructure is written in C++, however Python plays a vital role in enabling custom workflows.

SciPy 2012 | Article
Total Recall: flmake and the Quest for Reproducibility
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Jul 16, 2012

FLASH is a high-performance computing (HPC) multi-physics code which is used to perform astrophysical and high-energy density physics simulations. To run a FLASH simulation, the user must go through three basic steps: setup, build, and execution.

SciPy 2012 | Article
A Tale of Four Libraries
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Jul 16, 2012

This work describes the use some scientific Python tools to solve information gathering problems using Reinforcement Learning. In particular, we focus on the problem of designing an agent able to learn how to gather information in linked datasets.

SciPy 2012 | Article
A Computational Framework for Plasmonic Nanobiosensing
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Jul 16, 2012

Basic principles in biosensing and nanomaterials precede the introduction of a novel fiber optic sensor. Software limitations in the biosensing domain are presented, followed by the development of a Python-based simulation environment.

SciPy 2012 | Article
Parallel High Performance Bootstrapping in Python
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Jul 16, 2012

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SciPy 2013

roceedings of the 12th Python in Science Conference (2013)

There are 17 articles published in this collection
SciPy 2013 | Article
Modeling the Earth with Fatiando a Terra
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Jun 24, 2013

Geophysics is the science of using physical observations of the Earth to infer its inner structure. Generally, this is done with a variety of numerical modeling techniques and inverse problems. The development of new algorithms usually involves copy and pasting of code, which leads to errors and poor code reuse.

SciPy 2013 | Article
GraphTerm: A notebook-like graphical terminal interface for collaboration and inline data visualization
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Jun 24, 2013

The notebook interface, which blends text and graphics, has been in use for a number of years in commercial mathematical software and is now finding more widespread usage in scientific Python with the availability browser-based front-ends like the Sage and IPython notebooks.

SciPy 2013 | Article
lpEdit: an editor to facilitate reproducible analysis via literate programming
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Jun 24, 2013

There is evidence to suggest that a surprising proportion of published experiments in science are difficult if not impossible to reproduce. The concepts of data sharing, leaving an audit trail and extensive documentation are fundamental to reproducible research, whether it is in the laboratory or as part of an analysis.

SciPy 2013 | Article
Reproducible Documents with PythonTeX
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Jun 24, 2013

PythonTeX is a LaTeX package that allows Python code in a LaTeX document to be executed. This makes possible reproducible documents that combine analysis with the code required to perform it. Writing such documents can be more efficient because code is adjacent to its output.

SciPy 2013 | Article
SunPy: Python for Solar Physicists
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Jun 24, 2013

SunPy is a data analysis toolkit which provides the necessary software for analyzing solar and heliospheric datasets in Python. SunPy aims to provide a free and open-source alternative to the current standard, an IDL-based solar data analysis environment known as SolarSoft (SSW).

SciPy 2013 | Article
Exploring Collaborative HPC Visualization Workflows using VisIt and Python
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Jun 24, 2013

As High Performance Computing (HPC) environments expand to address the larger computational needs of massive simulations and specialized data analysis and visualization routines, the complexity of these environments brings many challenges for scientists hoping to capture and publish their work in a reproducible manner.

SciPy 2013 | Article
Ginga: an open-source astronomical image viewer and toolkit
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Jun 24, 2013

Ginga is a new astronomical image viewer written in Python. It uses and inter-operates with several key scientific Python packages: NumPy, Astropy, and SciPy. A key differentiator for this image viewer, compared to older-generation FITS viewers, is that all the key components are written as Python classes, allowing for the first time a powerful FITS image display widget to be directly embedded in, and tightly coupled with, Python code.

SciPy 2013 | Article
Adapted G-mode Clustering Method applied to Asteroid Taxonomy
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Jun 24, 2013

The original G-mode was a clustering method developed by A. I. Gavrishin in the late 60's for geochemical classification of rocks, but was also applied to asteroid photometry, cosmic rays, lunar sample and planetary science spectroscopy data.

SciPy 2013 | Article
Pythran: Enabling Static Optimization of Scientific Python Programs
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Jun 24, 2013

Pythran is a young open source static compiler that turns modules written in a subset of Python into native ones. Based on the fact that scientific modules do not rely much on the dynamic features of the language, it trades them in favor of powerful, eventually inter procedural, optimizations.

SciPy 2013 | Article
Detection and characterization of interactions of genetic risk factors in disease
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Jun 24, 2013

It is well known that two or more genes can interact so as to enhance or suppress incidence of disease, such that the observed phenotype differs from when the genes act independently. The effect of a gene allele at one locus can mask or modify the effect of alleles at one or more other loci.

SciPy 2013 | Article
Automating Quantitative Confocal Microscopy Analysis
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Jun 24, 2013

Quantitative confocal microscopy is a powerful analytical tool used to visualize the associations between cellular processes and anatomical structures. In our biological experiments, we use quantitative confocal microscopy to study the association of three cellular components: binding proteins, receptors, and organelles.

SciPy 2013 | Article
Using Python to Study Rotational Velocity Distributions of Hot Stars
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Jun 24, 2013

Stars are fundamental pieces that compose our Universe. By studying them we can better comprehend the environment in which we live. In this work, we have studied a sample of 350 nearby O and B stars and have characterized them in aspects of their multiplicity, temperature, spectral classifications, and projected rotational velocity.

SciPy 2013 | Article
SkData: Data Sets and Algorithm Evaluation Protocols in Python
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Jun 24, 2013

Machine learning benchmark data sets come in all shapes and sizes, whereas classification algorithms assume sanitized input, such as (x, y) pairs with vector-valued input x and integer class label y. Researchers and practitioners know all too well how tedious it can be to get from the URL of a new data set to a NumPy ndarray suitable for e.

SciPy 2013 | Article
Hyperopt: A Python Library for Optimizing the Hyperparameters of Machine Learning Algorithms
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Jun 24, 2013

Sequential model-based optimization (also known as Bayesian optimization) is one of the most efficient methods (per function evaluation) of function minimization. This efficiency makes it appropriate for optimizing the hyperparameters of machine learning algorithms that are slow to train.

SciPy 2013 | Article
Multidimensional Data Exploration with Glue
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Jun 24, 2013

Modern research projects incorporate data from several sources, and new insights are increasingly driven by the ability to interpret data in the context of other data. Glue is an interactive environment built on top of the standard Python science stack to visualize relationships within and between datasets.

SciPy 2013 | Article
DMTCP: Bringing Checkpoint-Restart to Python
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Jun 24, 2013

DMTCP (Distributed MultiThreaded CheckPointing) is a mature checkpoint-restart package. It operates in user-space without kernel privilege, and adapts to application-specific requirements through plugins.

SciPy 2013 | Article
Preface
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Jun 24, 2013

SciPy 2013, the twelfth annual Scientific Computing with Python conference, was held June 24th-29th 2013 in Austin, Texas, USA.

SciPy 2014

Proceedings of the 13th Python in Science Conference (2014)

There are 17 articles published in this collection
SciPy 2014 | Article
Simulating X-ray Observations with Python
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Jul 6, 2014

X-ray astronomy is an important tool in the astrophysicist's toolkit to investigate high-energy astrophysical phenomena. Theoretical numerical simulations of astrophysical sources are fully three-dimensional representations of physical quantities such as density, temperature, and pressure, whereas astronomical observations are two-dimensional projections of the emission generated via mechanisms dependent on these quantities.

SciPy 2014 | Article
Blaze: Building A Foundation for Array-Oriented Computing in Python
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Jul 6, 2014

We present the motivation and architecture of Blaze, a library for cross-backend data-oriented computation. Blaze provides a standard interface to connect users familiar with NumPy and Pandas to other data analytics libraries like SQLAlchemy and Spark.

SciPy 2014 | Article
Frequentism and Bayesianism: A Python-driven Primer
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Jul 6, 2014

This paper presents a brief, semi-technical comparison of the essential features of the frequentist and Bayesian approaches to statistical inference, with several illustrative examples implemented in Python.

SciPy 2014 | Article
TracPy: Wrapping the Fortran Lagrangian trajectory model TRACMASS
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Jul 6, 2014

Numerical Lagrangian trajectory modeling is a natural method of investigating transport in a circulation system and understanding the physics on the wide range of length scales that are actually experienced by a drifter.

SciPy 2014 | Article
Creating a browser-based virtual computer lab for classroom instruction
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Jul 6, 2014

With laptops and tablets becoming more powerful and more ubiquitous in the classroom, traditional computer labs with rows of expensive desktop computers are slowly beginning to lose their relevance. An alternative approach for teaching Python is to use a browser-based virtual computer lab, with a notebook interface.

SciPy 2014 | Article
Validated numerics with Python: the ValidiPy package
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Jul 6, 2014

We introduce the ValidiPy package for validated numerics in Python. This suite of tools, which includes interval arithmetic and automatic differentiation, enables rigorous and guaranteed results using floating-point arithmetic.

SciPy 2014 | Article
Python for research and teaching economics
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Jul 6, 2014

Together with theory and experimentation, computational modeling and simulation has become a “third pillar” of scientific inquiry. I am developing a curriculum for a three part, graduate level course on computational methods designed to increase the exposure of graduate students and researchers in the School of Economics at the University of Edinburgh to basic techniques used in computational modeling and simulation using the Python programming language.

SciPy 2014 | Article
Campaign for IT literacy through FOSS and Spoken Tutorials
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Jul 6, 2014

This article explains an approach to promote Information Technology (IT) literacy in India, which has evolved into a pyramid structure. We begin this article by explaining the design decisions, such as the use of FOSS and being a friendly interface between beginners and experts, in undertaking this activity.

SciPy 2014 | Article
Scaling Polygon Adjacency Algorithms to Big Data Geospatial Analysis
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Jul 6, 2014

Adjacency and neighbor structures play an essential role in many spatial analytical tasks. The computation of adjacenecy structures is non-trivial and can form a significant processing bottleneck as the total number of observations increases.

SciPy 2014 | Article
Python Coding of Geospatial Processing in Web-based Mapping Applications
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Jul 6, 2014

Python has powerful capabilities for coding elements of Web-based mapping applications. This paper highlights examples of analytical geospatial processing services that we have implemented for several Open Source-based development projects, including the Eastern Interconnection States' Planning Council (EISPC) Energy Zones Mapping Tool (http://eispctools.

SciPy 2014 | Article
Hyperopt-Sklearn: Automatic Hyperparameter Configuration for Scikit-Learn
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Jul 6, 2014

Hyperopt-sklearn is a new software project that provides automatic algorithm configuration of the Scikit-learn machine learning library. Following Auto-Weka, we take the view that the choice of classifier and even the choice of preprocessing module can be taken together to represent a single large hyperparameter optimization problem.

SciPy 2014 | Article
Project-based introduction to scientific computing for physics majors
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Jul 6, 2014

This paper presents an overview of a project-based course in computing for physics majors using Python and the IPython Notebook that was developed at Cal Poly San Luis Obispo. The course materials are made freely available on GitHub as a project under the Computing4Physics C4P organization.

SciPy 2014 | Article
Teaching numerical methods with IPython notebooks and inquiry-based learning
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Jul 6, 2014

A course in numerical methods should teach both the mathematical theory of numerical analysis and the craft of implementing numerical algorithms. The IPython notebook provides a single medium in which mathematics, explanations, executable code, and visualizations can be combined, and with which the student can interact in order to learn both the theory and the craft of numerical methods.

SciPy 2014 | Article
Measuring rainshafts: Bringing Python to bear on remote sensing data
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Jul 6, 2014

Remote sensing data is complicated, very complicated! It is not only geometrically tricky but also, unlike in-situ methods, indirect as the sensor measures the interaction of the scattering media (eg raindrops) with the probing radiation, not the geophysics.

SciPy 2014 | Article
BCE: Berkeley's Common Scientific Compute Environment for Research and Education
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Jul 6, 2014

There are numerous barriers to the use of scientific computing toolsets. These barriers are becoming more apparent as we increasingly see mixing of different academic backgrounds, and compute ranging from laptops to cloud platforms.

SciPy 2014 | Article
Scientific Computing with SciPy for Undergraduate Physics Majors
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Jul 6, 2014

The physics community is working to improve the undergraduate curriculum to include computer skills that graduates will need in the workforce. At Penn State Erie, The Behrend College, we have added computational tools to our Junior/Senior physics laboratory, PHYS421w Research Methods.

SciPy 2014 | Article
Preface
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Jul 6, 2014

SciPy 2014, the thirteenth annual Scientific Computing with Python conference, was held July 6–12th in Austin, Texas. SciPyis a community dedicated to the advancement of scientific computing through open source Python software for mathematics,science, and engineering

SciPy 2015

Proceedings of the 14th Python in Science Conference (2015)

There are 30 articles published in this collection
SciPy 2015 | Article
Building a Cloud Service for Reproducible Simulation Management
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Jul 6, 2015

The notion of capturing each execution of a script and workflow and its associated metadata is enormously appealing and should be at the heart of any attempt to make scientific simulations repeatable and reproducible.

SciPy 2015 | Article
Visualizing physiological signals in real-time
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Jul 6, 2015

This article presents an open-source Python software package, dubbed RTGraph, to visualize, process and record physiological signals (electrocardiography, electromyography, etc.) in real-time. RTGraph has a multiprocess architecture.

SciPy 2015 | Article
Testing Generative Models of Online Collaboration with BigBang
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Jul 6, 2015

We introduce BigBang, a new Python toolkit for analyzing online collaborative communities such as those that build open source software. Mailing lists serve as critical communications infrastructure for many communities, including several of the open source software development communities that build scientific Python packages.

SciPy 2015 | Article
Relation: The Missing Container
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Jul 6, 2015

The humble mathematical relation, a fundamental (if implicit) component in computational algorithms, is conspicuously absent in most standard container collections, including Python’s. In this paper, we present the basics of a relation container, and why you might use it instead of other methods.

SciPy 2015 | Article
Python in Data Science Research and Education
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Jul 6, 2015

In this paper we demonstrate how Python can be used throughout the entire life cycle of a graduate program in Data Science. In interdisciplinary fields, such as Data Science, the students often come from a variety of different backgrounds where, for example, some students may have strong mathematical training but less experience in programming.

SciPy 2015 | Article
Qiita: report of progress towards an open access microbiome data analysis and visualization platform
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Jul 6, 2015

Advances in sequencing, proteomics, transcriptomics and metabolomics are giving us new insights into the microbial world and dramatically improving our ability to understand microbial community composition and function at high resolution.

SciPy 2015 | Article
Geodynamic simulations in HPC with Python
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Jul 6, 2015

The deformation of the Earth surface reflects the action of several forces that act inside the planet. To understand how the Earth surface evolves complex models must be built to reconcile observations with theoretical numerical simulations.

SciPy 2015 | Article
Causal Bayesian NetworkX
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Jul 6, 2015

Probabilistic graphical models are useful tools for modeling systems governed by probabilistic structure. Bayesian networks are one class of probabilistic graphical model that have proven useful for characterizing both formal systems and for reasoning with those systems.

SciPy 2015 | Article
TrendVis: an Elegant Interface for dense, sparkline-like, quantitative visualizations of multiple series using matplotlib
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Jul 6, 2015

TrendVis is a plotting package that uses matplotlib to create information-dense, sparkline-like, quantitative visualizations of multiple disparate data sets in a common plot area against a common variable.

SciPy 2015 | Article
PySPLIT: a Package for the Generation, Analysis, and Visualization of HYSPLIT Air Parcel Trajectories
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Jul 6, 2015

The National Oceanic and Atmospheric Administration (NOAA) Air Resources Laboratory's HYSPLIT (HYbrid Single Particle Lagrangian Transport) model Drax98, Drax97 uses a hybrid Langrangian and Eulerian calculation method to compute air parcel trajectories and particle dispersion and deposition simulations.

SciPy 2015 | Article
Dask: Parallel Computation with Blocked algorithms and Task Scheduling
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Jul 6, 2015

Dask enables parallel and out-of-core computation. We couple blocked algorithms with dynamic and memory aware task scheduling to achieve a parallel and out-of-core NumPy clone. We show how this extends the effective scale of modern hardware to larger datasets and discuss how these ideas can be more broadly applied to other parallel collections.

SciPy 2015 | Article
Widgets and Astropy: Accomplishing Productive Research with Undergraduates
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Jul 6, 2015

This paper describes a tool for astronomical research implemented as an IPython notebook with a widget interface. The notebook uses Astropy, a community-developed package of fundamental tools for astronomy, and Astropy affiliated packages, as the back end.

SciPy 2015 | Article
pyDEM: Global Digital Elevation Model Analysis
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Jul 6, 2015

Hydrological terrain analysis is important for applications such as environmental resource, agriculture, and flood risk management. It is based on processing of high-resolution, tiled digital elevation model (DEM) data for geographic regions of interest.

SciPy 2015 | Article
Signal Processing and Communications: Teaching and Research Using IPython Notebook
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Jul 6, 2015

This paper will take the audience through the story of how an electrical and computer engineering faculty member has come to embrace Python, in particular IPython Notebook (IPython kernel for Jupyter), as an analysis and simulation tool for both teaching and research in signal processing and communications.

SciPy 2015 | Article
White Noise Test: detecting autocorrelation and nonstationarities in long time series after ARIMA modeling
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Jul 6, 2015

Time series analysis has been a dominant technique for assessing relations within datasets collected over time and is becoming increasingly prevalent in the scientific community; for example, assessing brain networks by calculating pairwise correlations of time series generated from different areas of the brain.

SciPy 2015 | Article
VisPy: Harnessing The GPU For Fast, High-Level Visualization
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Jul 6, 2015

The growing availability of large, multidimensional data sets has created demand for high-performance, interactive visualization tools. VisPy leverages the GPU to provide fast, interactive, and beautiful visualizations in a high-level API.

SciPy 2015 | Article
PyRK: A Python Package For Nuclear Reactor Kinetics
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Jul 6, 2015

In this work, a new python package, PyRK (Python for Reactor Kinetics), is introduced. PyRK has been designed to simulate, in zero dimensions, the transient, coupled, thermal-hydraulics and neutronics of time-dependent behavior in nuclear reactors.

SciPy 2015 | Article
Automated Image Quality Monitoring with IQMon
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Jul 6, 2015

Automated telescopes are capable of generating images more quickly than they can be inspected by a human, but detailed information on the performance of the telescope is valuable for monitoring and tuning of their operation.

SciPy 2015 | Article
Structural Cohesion: Visualization and Heuristics for Fast Computation with NetworkX and matplotlib
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Jul 6, 2015

The structural cohesion model is a powerful sociological conception of cohesion in social groups, but its diffusion in empirical literature has been hampered by computational problems. We present useful heuristics for computing structural cohesion that allow a speed-up of one order of magnitude over the algorithms currently available.

SciPy 2015 | Article
HoloViews: Building Complex Visualizations Easily for Reproducible Science
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Jul 6, 2015

Scientific visualization typically requires large amounts of custom coding that obscures the underlying principles of the work and makes it difficult to reproduce the results. Here we describe how the new HoloViews Python package, when combined with the IPython Notebook and a plotting library, provides a rich, interactive interface for flexible and nearly code-free visualization of your results while storing a full record of the process for later reproduction.

SciPy 2015 | Article
Mesa: An Agent-Based Modeling Framework
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Jul 6, 2015

Agent-based modeling is a computational methodology used in social science, biology, and other fields, which involves simulating the behavior and interaction of many autonomous entities, or agents, over time.

SciPy 2015 | Article
Circumventing The Linker: Using SciPy's BLAS and LAPACK Within Cython
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Jul 6, 2015

BLAS, LAPACK, and other libraries like them have formed the underpinnings of much of the scientific stack in Python. Until now, the standard practice in many packages for using BLAS and LAPACK has been to link each Python extension directly against the libraries needed.

SciPy 2015 | Article
The James Webb Space Telescope Data Calibration Pipeline
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Jul 6, 2015

The James Webb Space Telescope (JWST) is the successor to the Hubble Space Telescope (HST) and is currently expected to be launched in late 2018. The Space Telescope Science Institute (STScI) is developing the software systems that will be used to provide routine calibration of the science data received from JWST.

SciPy 2015 | Article
Creating a Real-Time Recommendation Engine using Modified K-Means Clustering and Remote Sensing Signature Matching Algorithms
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Jul 6, 2015

Built on Google App Engine (GAE), RealMassive encountered challenges while attempting to scale its recommendation engine to match its nationwide, multi-market expansion. To address this problem, we borrowed a conceptual model from spectral data processing to transform our domain-specific problem into one that the GAE's search engine could solve.

SciPy 2015 | Article
Scientific Data Analysis and Visualization with Python, VTK, and ParaView
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Jul 6, 2015

VTK and ParaView are leading software packages for data analysis and visualization. Since their early years, Python has played an important role in each package. In many use cases, VTK and ParaView serve as modules used by Python applications.

SciPy 2015 | Article
PyEDA: Data Structures and Algorithms for Electronic Design Automation
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Jul 6, 2015

This paper introduces PyEDA, a Python library for electronic design automation (EDA). PyEDA provides both a high level interface to the representation of Boolean functions, and blazingly-fast C extensions for fundamental algorithms where performance is essential.

SciPy 2015 | Article
librosa: Audio and Music Signal Analysis in Python
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Jul 6, 2015

This document describes version 0.4.0 of librosa: a Python package for audio and music signal processing. At a high level, librosa provides implementations of a variety of common functions used throughout the field of music information retrieval.

SciPy 2015 | Article
Python as a First Programming Language for Biomedical Scientists
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Jul 6, 2015

We have been involved with teaching Python to biomedical scientists since 2005. In all, seven courses have been taught: 5 at the University of Pittsburgh, as a required course for biomedical informatics graduate students.

SciPy 2015 | Article
pgmpy: Probabilistic Graphical Models using Python
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Jul 6, 2015

Probabilistic Graphical Models (PGM) is a technique of compactly representing a joint distribution by exploiting dependencies between the random variables. It also allows us to do inference on joint distributions in a computationally cheaper way than the traditional methods.

SciPy 2015 | Article
Will Millennials Ever Get Married?
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Jul 6, 2015

Using data from the National Survey of Family Growth (NSFG), we investigate marriage patterns among women in the United States We describe and predict age at first marriage for successive generations based on decade of birth.

SciPy 2016

Proceedings of the 15th Python in Science Conference (2016)

There are 20 articles published in this collection
SciPy 2016 | Article
Launching Python Applications on Peta-scale Massively Parallel Systems
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Jul 11, 2016

We introduce a method to launch Python applications at near native speed on large high performance computing systems. The Python run-time and other dependencies are bundled and delivered to computing nodes via a broadcast operation.

SciPy 2016 | Article
An Ecological Approach to Software Supply Chain Risk Management
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Jul 11, 2016

We approach the problem of software assurance in a novel way inspired by an analytic framework used in natural hazard risk mitigation. Existing approaches to software assurance focus on evaluating individual software projects in isolation.

SciPy 2016 | Article
PySPH: a reproducible and high-performance framework for smoothed particle hydrodynamics
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Jul 11, 2016

Smoothed Particle Hydrodynamics (SPH) is a general purpose technique to numerically compute the solutions to partial differential equations such as those used to simulate fluid and solid mechanics. The method is grid-free and uses particles to discretize the various properties of interest (such as density, fluid velocity, pressure etc.

SciPy 2016 | Article
Spreading the Adoption of Python in India: the FOSSEE Python Project
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Jul 11, 2016

The FOSSEE (Free Open Source Software for Science and Engineering Education) project (http://fossee.in) is funded by the Ministry of Human Resources and Development, MHRD, (http://mhrd.gov.in) of the Government of India.

SciPy 2016 | Article
Validating Function Arguments in Python Signal Processing Applications
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Jul 11, 2016

Python does not have a built-in mechanism to validate the value of function arguments. This can lead to nonsensical exceptions, unexpected behaviour, erroneous results and the like. In the present paper, we define the concept of so-called application-driven data types which place a layer of abstraction on top of Python data types.

SciPy 2016 | Article
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
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Jul 11, 2016

MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function.

SciPy 2016 | Article
Linting science prose and the science of prose linting
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Jul 11, 2016

The craft of writing is hard despite the abundance of thoughtful advice available in usage guides and other sources. This is partly a problem of medium: amassing advice is not enough to improve writing.

SciPy 2016 | Article
PyTeCK: a Python-based automatic testing package for chemical kinetic models
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Jul 11, 2016

Combustion simulations require detailed chemical kinetic models to predict fuel oxidation, heat release, and pollutant emissions. These models are typically validated using qualitative rather than quantitative comparisons with limited sets of experimental data.

SciPy 2016 | Article
Tell Me Something I Don't Know: Analyzing OkCupid Profiles
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Jul 11, 2016

In this paper, we present an analysis of 59,000 OkCupid user profiles that examines online self-presentation by combining natural language processing (NLP) with machine learning. We analyze word usage patterns by self-reported sex and drug usage status.

SciPy 2016 | Article
The Climate Modelling Toolkit
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Jul 11, 2016

The Climate Modelling Toolkit (CliMT) is a Python-based software component toolkit providing a flexible problem-solving environment for climate science problems. It aims to simplify the development of models of complexity 'appropriate' to the scientific question at hand.

SciPy 2016 | Article
MONTE Python for Deep Space Navigation
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Jul 11, 2016

The Mission Analysis, Operations, and Navigation Toolkit Environment (MONTE) is the Jet Propulsion Laboratory's (JPL) signature astrodynamic computing platform. It was built to support JPL's deep space exploration program, and has been used to fly robotic spacecraft to Mars, Jupiter, Saturn, Ceres, and many solar system small bodies.

SciPy 2016 | Article
Comparison of machine learning methods applied to birdsong element classification
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Jul 11, 2016

Songbirds provide neuroscience with a model system for understanding how the brain learns and produces a motor skill similar to speech. Much like humans, songbirds learn their vocalizations from social interactions during a critical period in development.

SciPy 2016 | Article
datreant: persistent, Pythonic trees for heterogeneous data
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Jul 11, 2016

In science the filesystem often serves as a de facto database, with directory trees being the zeroth-order scientific data structure. But it can be tedious and error prone to work directly with the filesystem to retrieve and store heterogeneous datasets.

SciPy 2016 | Article
Storing Reproducible Results from Computational Experiments using Scientific Python Packages
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Jul 11, 2016

Computational methods have become a prime branch of modern science. Unfortunately, retractions of papers in high-ranked journals due to erroneous computations as well as a general lack of reproducibility of results have led to a so-called credibility crisis.

SciPy 2016 | Article
UConnRCMPy: Python-based data analysis for Rapid Compression Machines
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Jul 11, 2016

The ignition delay of a fuel/air mixture is an important quantity in designing combustion devices, and these data are also used to validate computational kinetic models for combustion. One of the typical experimental devices used to measure the ignition delay is called a Rapid Compression Machine (RCM).

SciPy 2016 | Article
cesium: Open-Source Platform for Time-Series Inference
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Jul 11, 2016

Inference on time series data is a common requirement in many scientific disciplines and internet of things (IoT) applications, yet there are few resources available to domain scientists to easily, robustly, and repeatably build such complex inference workflows: traditional statistical models of time series are often too rigid to explain complex time domain behavior, while popular machine learning packages require already-featurized dataset inputs.

SciPy 2016 | Article
Generalized earthquake classification
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Jul 11, 2016

We characterize the source of an earthquake based on identifying the nodal lines of the radiation pattern it produces. These characteristics are the mode of failure of the rock (shear or tensile), the orientation of the fault plane and direction of slip.

SciPy 2016 | Article
Composable Multi-Threading for Python Libraries
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Jul 11, 2016

Python is popular among numeric communities that value it for easy to use number crunching modules like NumPy, SciPy, Dask, Numba, and many others. These modules often use multi-threading for efficient multi-core parallelism in order to utilize all the available CPU cores.

SciPy 2016 | Article
Functional Uncertainty Constrained by Law and Experiment
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Jul 11, 2016

Many physical processes are modeled by unspecified functions. Here, we introduce the F_UNCLE project which uses the Python ecosystem of scientific software to develop and explore techniques for estimating such unknown functions and our uncertainty about them.

SciPy 2016 | Article
Fitting Human Decision Making Models using Python
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Jul 11, 2016

A topic of interest in experimental psychology and cognitive neuroscience is to understand how humans make decisions. A common approach involves using computational models to represent the decision making process, and use the model parameters to analyze brain imaging data.

SciPy 2017

Proceedings of the 16th Python in Science Conference (2017)

There are 17 articles published in this collection
SciPy 2017 | Article
ChiantiPy: a Python package for Astrophysical Spectroscopy
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Jul 10, 2017

ChiantiPy is an interface to the CHIANTI atomic database for astrophysical spectroscopy. The highly-cited CHIANTI project, now in its 20th year, is an invaluable resource to the solar physics community.

SciPy 2017 | Article
NEXT: A system to easily connect crowdsourcing and adaptive data collection
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Jul 10, 2017

Obtaining useful crowdsourcing results often requires more responses than can be easily collected. Reducing the number of responses required can be done by adapting to previous responses with "adaptive" sampling algorithms, but these algorithms present a fundamental challenge when paired with crowdsourcing.

SciPy 2017 | Article
Accelerating Scientific Python with Intel Optimizations
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Jul 10, 2017

It is well-known that the performance difference between Python and basic C code can be up 200x, but for numerically intensive code another speed-up factor of 240x or even greater is possible. The performance comes from software's ability to take advantage of CPU's multiple cores, single instruction multiple data (SIMD) instructions, and high performance caches.

SciPy 2017 | Article
Python meets systems neuroscience: affordable, scalable and open-source electrophysiology in awake, behaving rodents
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Jul 10, 2017

In-vivo electrophysiology, the recording of neurons in the brains of awake, behaving animals, is currently undergoing paradigm shifts. There is a push towards moving to open-source technologies that can: 1) be adjusted to specific experiments; 2) be shared with ease; and 3) more affordably record from larger numbers of electrodes simultaneously.

SciPy 2017 | Article
Optimised finite difference computation from symbolic equations
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Jul 10, 2017

Domain-specific high-productivity environments are playing an increasingly important role in scientific computing due to the levels of abstraction and automation they provide. In this paper we introduce Devito, an open-source domain-specific framework for solving partial differential equations from symbolic problem definitions by the finite difference method.

SciPy 2017 | Article
pulse2percept: A Python-based simulation framework for bionic vision
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Jul 10, 2017

By 2020 roughly 200 million people worldwide will suffer from photoreceptor diseases such as retinitis pigmentosa and age-related macular degeneration, and a variety of retinal sight restoration technologies are being developed to target these diseases.

SciPy 2017 | Article
MatchPy: A Pattern Matching Library
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Jul 10, 2017

Pattern matching is a powerful tool for symbolic computations, based on the well-defined theory of term rewriting systems. Application domains include algebraic expressions, abstract syntax trees, and XML and JSON data.

SciPy 2017 | Article
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library
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Jul 10, 2017

The analysis of biomolecular computer simulations has become a challenge because the amount of output data is now routinely in the terabyte range. We evaluated if this challenge can be met by a parallel map-reduce approach with the Dask parallel computing library for task-graph based computing coupled with our MDAnalysis Python library for the analysis of molecular dynamics (MD) simulations.

SciPy 2017 | Article
FigureFirst: A Layout-first Approach for Scientific Figures
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Jul 10, 2017

One major reason that Python has been widely adopted as a scientific computing platform is the availability of powerful visualization libraries. Although these tools facilitate discovery and data exploration, they are difficult to use when constructing the sometimes-intricate figures required to advance the narrative of a scientific manuscript.

SciPy 2017 | Article
The Sacred Infrastructure for Computational Research
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Jul 10, 2017

We present a toolchain for computational research consisting of Sacred and two supporting tools. Sacred is an open source Python framework which aims to provide basic infrastructure for running computational experiments independent of the methods and libraries used.

SciPy 2017 | Article
SciSheets: Providing the Power of Programming With The Simplicity of Spreadsheets
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Jul 10, 2017

Digital spreadsheets are arguably the most pervasive environment for end user programming on the planet. Although spreadsheets simplify many calculations, they fail to address requirements for expressivity, reuse, complex data, and performance.

SciPy 2017 | Article
PyHRF: A Python Library for the Analysis of fMRI Data Based on Local Estimation of the Hemodynamic Response Function
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Jul 10, 2017

Functional Magnetic Resonance Imaging (fMRI) is a neuroimaging technique that allows the non-invasive study of brain function. It is based on the hemodynamic variations induced by changes in cerebral synaptic activity following sensory or cognitive stimulation.

SciPy 2017 | Article
pyMolDyn: Identification, structure, and properties of cavities in condensed matter and molecules
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Jul 10, 2017

pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center).

SciPy 2017 | Article
LabbookDB: A Wet-Work-Tracking Database Application Framework
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Jul 10, 2017

LabbookDB is a relational database application framework for life sciences—providing an extendable schema and functions to conveniently add and retrieve information, and generate summaries. The core concept of LabbookDB is that wet work metadata commonly tracked in lab books or spreadsheets is more efficiently and more reliably stored in a relational database, and more flexibly queried.

SciPy 2017 | Article
BespON: Extensible config files with multiline strings, lossless round-tripping, and hex floats
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Jul 10, 2017

BespON is a human-editable data format focused on expressive syntax, lossless round-tripping, and advanced features for scientific and technical tasks. Nested data structures can be represented concisely without multiple levels of either brackets or significant whitespace.

SciPy 2017 | Article
Software Transactional Memory in Pure Python
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Jul 10, 2017

There has been a growing interest in programming models for concurrency. Strategies for dealing with shared data amongst parallel threads of execution include immutable (as in Erlang) and locked (as in Python) data structures.

SciPy 2017 | Article
SPORCO: A Python package for standard and convolutional sparse representations
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Jul 10, 2017

SParse Optimization Research COde (SPORCO) is an open-source Python package for solving optimization problems with sparsity-inducing regularization, consisting primarily of sparse coding and dictionary learning, for both standard and convolutional forms of sparse representation.

SciPy 2018

Proceedings of the Python in Science Conference 2018

There are 24 articles published in this collection
SciPy 2018 | Article
Yaksh: Facilitating Learning by Doing
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Jul 9, 2018

Yaksh is a free and open-source online evaluation platform. At its core, Yaksh focuses on problem-based learning and lets teachers create practice exercises and quizzes which are evaluated in real-time.

SciPy 2018 | Article
signac: A Python framework for data and workflow management
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Jul 9, 2018

Computational research requires versatile data and workflow management tools that can easily adapt to the highly dynamic requirements of scientific investigations. Many existing tools require strict adherence to a particular usage pattern, so researchers often use less robust ad hoc solutions that they find easier to adopt.

SciPy 2018 | Article
Scalable Feature Extraction with Aerial and Satellite Imagery
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Jul 9, 2018

Deep learning techniques have greatly advanced the performance of the already rapidly developing field of computer vision, which powers a variety of emerging technologies—from facial recognition to augmented reality to self-driving cars.

SciPy 2018 | Article
A Bayesian’s journey to a better research workflow
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Jul 9, 2018

This work began when the two authors met at a software development meeting. Konstantinos was building Bayesian models in his research and wanted to learn how to better manage his research process. Marianne was working on data analysis workflows in industry and wanted to learn more about Bayesian statistics.

SciPy 2018 | Article
Design and Implementation of pyPRISM: A Polymer Liquid-State Theory Framework
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Jul 9, 2018

In this work, we describe the code structure, implementation, and usage of a Python-based, open-source framework, pyPRISM, for conducting polymer liquid-state theory calculations. Polymer Reference Interaction Site Model (PRISM) theory describes the equilibrium spatial-correlations, thermodynamics, and structure of liquid-like polymer systems and macromolecular materials.

SciPy 2018 | Article
Spatio-temporal analysis of socioeconomic neighborhoods: The Open Source Longitudinal Neighborhood Analysis Package (OSLNAP)
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Jul 9, 2018

The neighborhood effects literature represents a wide span of the social sciences broadly concerned with the influence of spatial context on social processes. From the study of segregation dynamics, the relationships between the built environment and health outcomes, to the impact of concentrated poverty on social efficacy, neighborhoods are a central construct in empirical work.

SciPy 2018 | Article
Binder 2.0 - Reproducible, interactive, sharable environments for science at scale
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Jul 9, 2018

Binder is an open source web service that lets users create sharable, interactive, reproducible environments in the cloud. It is powered by other core projects in the open source ecosystem, including JupyterHub and Kubernetes for managing cloud resources.

SciPy 2018 | Article
Harnessing the Power of Scientific Python to Investigate Biogeochemistry and Metaproteomes of the Central Pacific Ocean
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Jul 9, 2018

Oceanographic expeditions commonly generate millions of data points for various chemical, biological, and physical features, all in different formats. Scientific Python tools are extremely useful for synthesizing this data to make sense of major trends in the changing ocean environment.

SciPy 2018 | Article
Organic Molecules in Space: Insights from the NASA Ames Molecular Database in the era of the James Webb Space Telescope
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Jul 9, 2018

We present the software tool pyPAHdb to the scientific astronomical community, which is used to characterize emission from one of the most prevalent types of organic molecules in space, namely polycyclic aromatic hydrocarbons (PAHs).

SciPy 2018 | Article
Real-Time Digital Signal Processing Using pyaudio_helper and the ipywidgets
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Jul 9, 2018

The focus of this paper is on teaching real-time digital signal processing to electrical and computer engineers using the Jupyter notebook and the code module `pyaudio_helper`, which is a component of the package scikit-dsp-comm.

SciPy 2018 | Article
Exploring the Extended Kalman Filter for GPS Positioning Using Simulated User and Satellite Track Data
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Jul 9, 2018

This paper describes a Python computational tool for exploring the use of the extended Kalman filter (EKF) for position estimation using the Global Positioning System (GPS) pseudorange measurements. The development was motivated by the need for an example generator in a training class on Kalman filtering, with emphasis on GPS.

SciPy 2018 | Article
WrightSim: Using PyCUDA to Simulate Multidimensional Spectra
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Jul 9, 2018

Nonlinear multidimensional spectroscopy (MDS) is a powerful experimental technique used to interrogate complex chemical systems. MDS promises to reveal energetics, dynamics, and coupling features of and between the many quantum-mechanical states that these systems contain.

SciPy 2018 | Article
Bringing ipywidgets Support to plotly.py
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Jul 9, 2018

Plotly.js is a declarative JavaScript data visualization library built on D3 and WebGL that supports a wide range of statistical, scientific, financial, geographic, and 3-dimensional visualizations. Support for creating Plotly.

SciPy 2018 | Article
Sparse: A more modern sparse array library
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Jul 9, 2018

This paper is about sparse multi-dimensional arrays in Python. We discuss their applications, layouts, and current implementations in the SciPy ecosystem along with strengths and weaknesses. We then introduce a new package for sparse arrays that builds on the legacy of the scipy.

SciPy 2018 | Article
Text and data mining scientific articles with allofplos
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Jul 9, 2018

Mining scientific articles is hard when many of them are inaccessible behind paywalls. The Public Library of Science (PLOS) is a non-profit Open Access science publisher of the single largest journal (PLOS ONE), whose articles are all freely available to read and re-use.

SciPy 2018 | Article
Safe handling instructions for missing data
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Jul 9, 2018

In machine learning tasks, it is common to handle missing data by removing observations with missing values, or replacing missing data with the mean value for its feature. To show why this is problematic, we use listwise deletion and mean imputing to recover missing values from artificially created datasets, and we compare those models against ones with full information.

SciPy 2018 | Article
EarthSim: Flexible Environmental Simulation Workflows Entirely Within Jupyter Notebooks
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Jul 9, 2018

Building environmental simulation workflows is typically a slow process involving multiple proprietary desktop tools that do not interoperate well. In this work, we demonstrate building flexible, lightweight workflows entirely in Jupyter notebooks.

SciPy 2018 | Article
Practical Applications of Astropy
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Jul 9, 2018

Packages developed under the auspices of the Astropy Project (astropy2013, astropy2018) address many common problems faced by astronomers in their computational projects. In this paper we describe how capabilities provided by Astropy have been employed in two current projects.

SciPy 2018 | Article
Developing a Start-to-Finish Pipeline for Accelerometer-Based Activity Recognition Using Long Short-Term Memory Recurrent Neural Networks
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Jul 9, 2018

Increased prevalence of smartphones and wearable devices has facilitated the collection of triaxial accelerometer data for numerous Human Activity Recognition (HAR) tasks. Concurrently, advances in the theory and implementation of long short-term memory (LSTM) recurrent neural networks (RNNs) has made it possible to process this data in its raw form, enabling on-device online analysis.

SciPy 2018 | Article
The Econ-ARK and HARK: Open Source Tools for Computational Economics
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Jul 9, 2018

The Economics Algorithmic Repository and toolKit (Econ-ARK) aims to become a focal resource for computational economics. Its first ‘framework,’ the Heterogeneous Agent Resources and Toolkit (HARK), provides a modern, robust, transparent set of tools to solve a class of macroeconomic models whose usefulness has become increasingly apparent both for economic policy and for research purposes, but whose adoption has been limited because the existing literature derives from idiosyncratic, hand-crafted, and often impenetrable legacy code.

SciPy 2018 | Article
Composable Multi-Threading and Multi-Processing for Numeric Libraries
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Jul 9, 2018

Python is popular among scientific communities that value its simplicity and power, especially as it comes along with numeric libraries such as NumPy, SciPy, Dask, and Numba. As CPU core counts keep increasing, these modules can make use of many cores via multi-threading for efficient multi-core parallelism.

SciPy 2018 | Article
Equity, Scalability, and Sustainability of Data Science Infrastructure
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Jul 9, 2018

We seek to understand the current state of equity, scalability, and sustainability of data science education infrastructure in both the U.S. and Canada. Our analysis of the technological, funding, and organizational structure of four types of institutions shows an increasing divergence in the ability of universities across the United States to provide students with accessible data science education infrastructure, primarily JupyterHub.

SciPy 2018 | Article
Dynamic Social Network Modeling of Diffuse Subcellular Morphologies
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Jul 9, 2018

The use of fluorescence microscopy has catalyzed new insights into biological function, and spurred the development of quantitative models from rich biomedical image datasets. While image processing in some capacity is commonplace for extracting and modeling quantitative knowledge from biological systems at varying scales, general-purpose approaches for more advanced modeling are few.

SciPy 2018 | Article
Cloudknot: A Python Library to Run your Existing Code on AWS Batch
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Jul 9, 2018

We introduce Cloudknot, a software library that simplifies cloud-based distributed computing by programmatically executing user-defined functions (UDFs) in AWS Batch. It takes as input a Python function, packages it as a container, creates all the necessary AWS constituent resources to submit jobs, monitors their execution and gathers the results, all from within the Python environment.

SciPy 2019

Proceedings of the Python in Science Conference 2019

There are 20 articles published in this collection
SciPy 2019 | Article
PMDA - Parallel Molecular Dynamics Analysis
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Jul 8, 2019

MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. With the development of highly optimized MD software packages on high performance computing (HPC) resources, the size of simulation trajectories is growing up to many terabytes in size.

SciPy 2019 | Article
Visualization of Bioinformatics Data with Dash Bio
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Jul 8, 2019

Plotly's Dash is a library that empowers data scientists to create interactive web applications declaratively in Python. Dash Bio is a bioinformatics-oriented suite of components that are compatible with Dash.

SciPy 2019 | Article
Better and faster hyperparameter optimization with Dask
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Jul 8, 2019

Nearly every machine learning model requires hyperparameters, parameters that the user must specify before training begins and influence model performance. Finding the optimal set of hyperparameters is often a time- and resource-consuming process.

SciPy 2019 | Article
PyDDA: A new Pythonic Wind Retrieval Package
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Jul 8, 2019

PyDDA is a new community framework aimed at wind retrievals that depends only upon utilities in the SciPy ecosystem such as scipy, numpy, and dask. It can support retrievals of winds using information from weather radar networks constrained by high resolution forecast models over grids that cover thousands of kilometers at kilometer-scale resolution.

SciPy 2019 | Article
Parkinson's Classification and Feature Extraction from Diffusion Tensor Images
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Jul 8, 2019

Parkinson’s disease (PD) affects over 6.2 million people around the world. Despite its prevalence, there is still no cure, and diagnostic methods are extremely subjective, relying on observation of physical motor symptoms and response to treatment protocols.

SciPy 2019 | Article
PyLZJD: An Easy to Use Tool for Machine Learning
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Jul 8, 2019

As Machine Learning (ML) becomes more widely known and popular, so too does the desire for new users from other backgrounds to apply ML techniques to their own domains. A difficult prerequisite that often confounds new users is the feature creation and engineering process.

SciPy 2019 | Article
Parameter Estimation Using the Python Package pymcmcstat
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Jul 8, 2019

A Bayesian approach to solving inverse problems provides insight regarding model limitations as well as the underlying model and observation uncertainty. In this paper we introduce pymcmcstat, which provides a wide variety of tools for estimating unknown parameter distributions.

SciPy 2019 | Article
An intelligent shopping list based on the application of partitioning and machine learning algorithms
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Jul 8, 2019

A grocery list is an integral part of the shopping experience of many consumers. Several mobile retail studies of grocery apps indicate that potential customers place the highest priority on features that help them to create and manage personalized shopping lists.

SciPy 2019 | Article
A Real-Time 3D Audio Simulator for Cognitive Hearing Science
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Jul 8, 2019

This paper describes the development of a 3D audio simulator for use in cognitive hearing science studies and also for general 3D audio experimentation. The framework that the simulator is built upon is pyaudio\_helper, which is a module of the package scikit-dsp-comm.

SciPy 2019 | Article
Optimizing Python-Based Spectroscopic Data Processing on NERSC Supercomputers
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Jul 8, 2019

We present a case study of optimizing a Python-based cosmology data processing pipeline designed to run in parallel on thousands of cores using supercomputers at the National Energy Research Scientific Computing Center (NERSC).

SciPy 2019 | Article
Solving Polynomial Systems with phcpy
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Jul 8, 2019

The solutions of a system of polynomials in several variables are often needed, e.g.: in the design of mechanical systems, and in phase-space analyses of nonlinear biological dynamics. Reliable, accurate, and comprehensive numerical solutions are available through PHCpack, a FOSS package for solving polynomial systems with homotopy continuation.

SciPy 2019 | Article
Case study: Real-world machine learning application for hardware failure detection
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Jul 8, 2019

When designing microprocessors, engineers must verify whether the proposed design, defined in hardware description language, does what is intended. During this verification process, engineers run simulation tests and can fix bugs if the tests have failed.

SciPy 2019 | Article
Codebraid: Live Code in Pandoc Markdown
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Jul 8, 2019

Codebraid executes code blocks and inline code in Pandoc Markdown documents as part of the document build process. Code can be executed with a built-in system or Jupyter kernels. Either way, a single document can involve multiple programming languages, as well as multiple independent sessions or processes per language.

SciPy 2019 | Article
pyjanitor: A Cleaner API for Cleaning Data
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Jul 8, 2019

The pandas library has become the de facto library for data wrangling in the Python programming language. However, inconsistencies in the pandas application programming interface (API), while idiomatic due to historical use, prevent use of expressive, fluent programming idioms that enable self-documenting pandas code.

SciPy 2019 | Article
Developing a Graph Convolution-Based Analysis Pipeline for Multi-Modal Neuroimage Data: An Application to Parkinson's Disease
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Jul 8, 2019

Parkinson's disease (PD) is a highly prevalent neurodegenerative condition originating in subcortical areas of the brain and resulting in progressively worsening motor, cognitive, and psychiatric (e.g.

SciPy 2019 | Article
CAF Implementation on FPGA Using Python Tools
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Jul 8, 2019

The purpose of this project is to provide a real time geolocation solution by generating code for the complex ambiguity function (CAF) in a hardware description language (HDL) and the implementation on FPGA hardware.

SciPy 2019 | Article
Analyzing Particle Systems for Machine Learning and Data Visualization with freud
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Jul 8, 2019

The freud Python library analyzes particle data output from molecular dynamics simulations. The library's design and its variety of high-performance methods make it a powerful tool for many modern applications.

SciPy 2019 | Article
Accelerating the Advancement of Data Science Education
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Jul 8, 2019

We outline a synthesis of strategies created in collaboration with 35+ colleges and universities on how to advance undergraduate data science education on a national scale. The four core pillars of this strategy include the integration of data science education across all domains, establishing adoptable and scalable cyberinfrastructure, applying data science to non-traditional domains, and incorporating ethical content into data science curricula.

SciPy 2019 | Article
Deep and Ensemble Learning to Win the Army RCO AI Signal Classification Challenge
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Jul 8, 2019

Automatic modulation classification is a challenging problem with multiple applications including cognitive radio and signals intelligence. Most of the existing efforts to solve this problem are only applicable when the signal to noise ratio (SNR) is high and/or long observations of the signal are available.

SciPy 2019 | Article
Expert RF Feature Extraction to Win the Army RCO AI Signal Classification Challenge
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Jul 8, 2019

Automatic modulation classification is a challenging problem with multiple applications including cognitive radio and signals intelligence. Most of the existing efforts to solve this problem are only applicable when the signal to noise ratio (SNR) is high and/or long observations of the signal are available.

SciPy 2020

Proceedings of the Python in Science Conference 2020

There are 23 articles published in this collection
SciPy 2020 | Article
Towards an Unsupervised Spatiotemporal Representation of Cilia Video Using A Modular Generative Pipeline
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Jul 6, 2020

Motile cilia are a highly conserved organelle found on the exterior of many human cells. Cilia beat in rhythmic patterns to transport substances or generate signaling gradients. Disruption of these patterns is often indicative of diseases known as ciliopathies, whose consequences can include dysfunction of macroscopic structures within the lungs, kidneys, brain, and other organs.

SciPy 2020 | Article
Falsify your Software: validating scientific code with property-based testing
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Jul 6, 2020

Where traditional example-based tests check software using manually-specified input-output pairs, property-based tests exploit a general description of valid inputs and program behaviour to automatically search for falsifying examples.

SciPy 2020 | Article
Software Engineering as Research Method: Aligning Roles in Econ-ARK
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Jul 6, 2020

While general purpose scientific software has enjoyed great success in industry and academia, domain specific scientific software has not yet become well-established in many disciplines where it has potential.

SciPy 2020 | Article
SHADOW: A workflow scheduling algorithm reference and testing framework
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Jul 6, 2020

As the scale of science projects increase, so does the demand on computing infrastructures. The complexity of science processing pipelines, and the heterogeneity of the environments on which they are run, continues to increase; in order to deal with this, the algorithmic approaches to executing these applications must also be adapted and improved to deal with this increased complexity.

SciPy 2020 | Article
Leading magnetic fusion energy science into the big-and-fast data lane
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Jul 6, 2020

We present Delta, a Python framework that connects magnetic fusion experiments to high-performance computing (HPC) facilities in order leverage advanced data analysis for near real-time decisions. Using the ADIOS I/O framework, Delta streams measurement data with over 300 MByte/sec from a remote experimental site in Korea to Cori, a Cray XC-40 supercomputer at the National Energy Energy Research Scientific Computing Centre in California.

SciPy 2020 | Article
Pydra - a flexible and lightweight dataflow engine for scientific analyses
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Jul 6, 2020

This paper presents a new lightweight dataflow engine written in Python: Pydra. Pydra is developed as an open-source project in the neuroimaging community, but it is designed as a general-purpose dataflow engine to support any scientific domain.

SciPy 2020 | Article
Combining Physics-Based and Data-Driven Modeling for Pressure Prediction in Well Construction
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Jul 6, 2020

A framework for combining physics-based and data-driven models to improve well construction is presented in this study. Additionally, the proposed approach provides a more robust and accurate model that mitigates the disadvantages of using purely physics-based or data-driven models.

SciPy 2020 | Article
pandera: Statistical Data Validation of Pandas Dataframes
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Jul 6, 2020

pandas is an essential tool in the data scientist’s toolkit for modern data engineering, analysis, and modeling in the Python ecosystem. However, dataframes can often be difficult to reason about in terms of their data types and statistical properties as data is reshaped from its raw form to one that’s ready for analysis.

SciPy 2020 | Article
Having your cake and eating it: Exploiting Python for programmer productivity and performance on micro-core architectures using ePython
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Jul 6, 2020

Micro-core architectures combine many simple, low memory, low power computing cores together in a single package. These can be used as a co-processor or standalone but due to limited on-chip memory and esoteric nature of the hardware, writing efficient parallel codes for these chips is challenging.

SciPy 2020 | Article
Matched Filter Mismatch Losses in MPSK and MQAM Using Semi-Analytic BEP Modeling
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Jul 6, 2020

The focus of this paper is the bit error probability (BEP) performance degradation when the transmit and receive pulse shaping filters are mismatched. The modulation schemes considered are MPSK and MQAM.

SciPy 2020 | Article
Spectral Analysis of Mitochondrial Dynamics: A Graph-Theoretic Approach to Understanding Subcellular Pathology
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Jul 6, 2020

Perturbations of organellar structures within a cell are useful indicators of the cell’s response to viral or bacterial invaders. Of the various organelles, mitochondria are meaningful to model because they show distinct migration patterns in the presence of potentially fatal infections, such as tuberculosis.

SciPy 2020 | Article
High-performance operator evaluations with ease of use: libCEED's Python interface
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Jul 6, 2020

libCEED is a new lightweight, open-source library for high-performance matrix-free Finite Element computations. libCEED offers a portable interface to high-performance implementations, selectable at runtime, tuned for a variety of current and emerging computational architectures, including CPUs and GPUs.

SciPy 2020 | Article
Awkward Array: JSON-like data, NumPy-like idioms
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Jul 6, 2020

NumPy simplifies and accelerates mathematical calculations in Python, but only for rectilinear arrays of numbers. Awkward Array provides a similar interface for JSON-like data: slicing, masking, broadcasting, and performing vectorized math on the attributes of objects, unequal-length nested lists (i.

SciPy 2020 | Article
Learning from evolving data streams
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Jul 6, 2020

Ubiquitous data poses challenges on current machine learning systems to store, handle and analyze data at scale. Traditionally, this task is tackled by dividing the data into (large) batches. Models are trained on a data batch and then used to obtain predictions.

SciPy 2020 | Article
Boost-histogram: High-Performance Histograms as Objects
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Jul 6, 2020

Unlike arrays and tables, histograms in Python have usually been denied their own object, and have been represented as a single operation producing several arrays. Boost-histogram is a new Python library that provides histograms that can be filled, manipulated, sliced, and projected as objects.

SciPy 2020 | Article
Network visualizations with Pyvis and VisJS
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Jul 6, 2020

Pyvis is a Python module that enables visualizing and interactively manipulating network graphs in the Jupyter notebook, or as a standalone web application. Pyvis is built on top of the powerful and mature VisJS JavaScript library, which allows for fast and responsive interactions while also abstracting away the low-level JavaScript and HTML.

SciPy 2020 | Article
Introduction to Geometric Learning in Python with Geomstats
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Jul 6, 2020

There is a growing interest in leveraging differential geometry in the machine learning community. Yet, the adoption of the associated geometric computations has been inhibited by the lack of a reference implementation.

SciPy 2020 | Article
Netlist Analysis and Transformations Using SpyDrNet
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Jul 6, 2020

Digital hardware circuits (i.e., for application specific integrated circuits or field programmable gate array circuits) can contain a large number of discrete components and connections. These connections are defined by a data structure called a \textquotedbl{}netlist\textquotedbl{}.

SciPy 2020 | Article
Compyle: a Python package for parallel computing
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Jul 6, 2020

Compyle allows users to execute a restricted subset of Python on a variety of HPC platforms. It is an embedded domain-specific language (eDSL) for parallel computing. It currently supports multi-core execution using Cython, and OpenCL and CUDA for GPU devices.

SciPy 2020 | Article
HOOMD-blue version 3.0 A Modern, Extensible, Flexible, Object-Oriented API for Molecular Simulations
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Jul 6, 2020

HOOMD-blue is a library for running molecular dynamics and hard particle Monte Carlo simulations that uses pybind11 to provide a Python interface to fast C++ internals. The package is designed to scale from a single CPU core to thousands of NVIDIA or AMD GPUs.

SciPy 2020 | Article
Fluctuation X-ray Scattering real-time app
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Jul 6, 2020

The Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory is an X-ray Free Electron Laser (X-FEL) facility enabling scientists to take snapshots of single macromolecules to study their structure and dynamics.

SciPy 2020 | Article
Quasi-orthonormal Encoding for Machine Learning Applications
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Jul 6, 2020

Most machine learning models, especially artificial neural networks, require numerical, not categorical data. We briefly describe the advantages and disadvantages of common encoding schemes. For example, one-hot encoding is commonly used for attributes with a few unrelated categories and word embeddings for attributes with many related categories (e.

SciPy 2020 | Article
Securing Your Collaborative Jupyter Notebooks in the Cloud using Container and Load Balancing Services
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Jul 6, 2020

Jupyter has become the go-to platform for developing data applications but data and security concerns, especially when dealing with healthcare, have become paramount for many institutions and applications dealing with sensitive information.

SciPy 2021

Proceedings of the Python in Science Conference 2021

There are 20 articles published in this collection
SciPy 2021 | Article
PyBMRB: Data visualization tool for BioMagResBank
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Jul 12, 2021

The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB https://bmrb.io), founded in 1988, is the international, open archive for data generated by Nuclear Magnetic Resonance (NMR) spectroscopy of biological systems.

SciPy 2021 | Article
Social Media Analysis using Natural Language Processing Techniques
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Jul 12, 2021

Social media is very popularly used every day with daily content viewing and/or posting that in turn influences people around this world in a variety of ways. Social media platforms, such as YouTube, have a lot of activity that goes on every day in terms of video posting, watching and commenting.

SciPy 2021 | Article
PyCID: A Python Library for Causal Influence Diagrams
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Jul 12, 2021

Why did a decision maker select a certain decision? What behaviour does a certain objective incentivise? How can we improve this behaviour and ensure that a decision-maker chooses decisions with safer or fairer consequences? This paper introduces the Python package PyCID, built upon pgmpy, that implements (causal) influence diagrams, a widely used graphical modelling framework for decision-making problems.

SciPy 2021 | Article
CLAIMED, a visual and scalable component library for Trusted AI
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Jul 12, 2021

CLAIMED is a component library for artificial intelligence, machine learning, \textquotedbl{}extract, transform, load\textquotedbl{} processes and data science. The goal is to enable low-code/no-code rapid prototyping by providing ready-made components for various business domains, supporting various computer languages, working on various data flow editors and running on diverse execution engines.

SciPy 2021 | Article
Natural Language Processing with Pandas DataFrames
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Jul 12, 2021

Most areas of Python data science have standardized on using Pandas DataFrames for representing and manipulating structured data in memory. Natural Language Processing (NLP), not so much. We believe that Pandas has the potential to serve as a universal data structure for NLP data.

SciPy 2021 | Article
MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package
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Jul 12, 2021

Molecular dynamics (MD) computer simulations help elucidate details of the molecular processes in complex biological systems, from protein dynamics to drug discovery. One major issue is that these MD simulation files are now commonly terabytes in size, which means analyzing the data from these files becomes a painstakingly expensive task.

SciPy 2021 | Article
Accelerating Spectroscopic Data Processing Using Python and GPUs on NERSC Supercomputers
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Jul 12, 2021

The Dark Energy Spectroscopic Instrument (DESI) will create the most detailed 3D map of the Universe to date by measuring redshifts in light spectra of over 30 million galaxies. The extraction of 1D spectra from 2D spectrograph traces in the instrument output is one of the main computational bottlenecks of DESI data processing pipeline, which is predominantly implemented in Python.

SciPy 2021 | Article
signac: Data Management and Workflows for Computational Researchers
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Jul 12, 2021

The signac data management framework (https://signac.io) helps researchers execute reproducible computational studies, scales workflows from laptops to supercomputers, and emphasizes portability and fast prototyping.

SciPy 2021 | Article
Modernizing computing by structural biologists with Jupyter and Colab
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Jul 12, 2021

Protein crystallography produces most of the protein structures used in structure-based drug design. The process of protein structure determination is computationally intensive and error-prone because many software packages are involved.

SciPy 2021 | Article
Using Python for Analysis and Verification of Mixed-mode Signal Chains
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Jul 12, 2021

Any application involving sensitive measurements of the physical world starts with accurate, precise, and low-noise signal chain. Modern, highly integrated data acquisition devices can often be directly connected to sensor outputs, performing analog signal conditioning, digitization, and digital filtering on a single silicon device, greatly simplifying system electronics.

SciPy 2021 | Article
How PDFrw and fillable forms improves throughput at a Covid-19 Vaccine Clinic
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Jul 12, 2021

PDFrw was used to prepopulate Covid-19 vaccination forms to improve the efficiency and integrity of the vaccination process in terms of federal and state privacy requirements. We will describe the vaccination process from the initial appointment, through the vaccination delivery, to the creation of subsequent required documentation.

SciPy 2021 | Article
Cell Tracking in 3D using deep learning segmentations
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Jul 12, 2021

Live-cell imaging is a highly used technique to study cell migration and dynamics over time. Although many computational tools have been developed during the past years to automatically detect and track cells, they are optimized to detect cell nuclei with similar shapes and/or cells not clustering together.

SciPy 2021 | Article
CNN Based ToF Image Processing
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Jul 12, 2021

In this paper a Time of Flight (ToF) camera specific data processing pipeline is presented, followed by real life applications using artificial intelligence. These applications include use cases such as gesture recognition, movement direction estimation or physical exercises monitoring.

SciPy 2021 | Article
Multithreaded parallel Python through OpenMP support in Numba
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Jul 12, 2021

A modern CPU delivers performance through parallelism. A program that exploits the performance available from a CPU must run in parallel on multiple cores. This is usually best done through multithreading.

SciPy 2021 | Article
Training machine learning models faster with Dask
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Jul 12, 2021

Machine learning (ML) relies on stochastic algorithms, all of which rely on gradient approximations with \textquotedbl{}batch size\textquotedbl{} examples. Growing the batch size as the optimization proceeds is a simple and usable method to reduce the training time, provided that the number of workers grows with the batch size.

SciPy 2021 | Article
Monitoring Scientific Python Usage on a Supercomputer
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Jul 12, 2021

In 2021, more than 30\% of users at the National Energy Research Scientific Computing Center (NERSC) used Python on the Cori supercomputer. To determine this we have developed and open-sourced a simple, minimally invasive monitoring framework that leverages standard Python features to capture Python imports and other job data via a package called \textquotedbl{}Customs\textquotedbl{}.

SciPy 2021 | Article
Classification of Diffuse Subcellular Morphologies
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Jul 12, 2021

Characterizing dynamic sub-cellular morphologies in response to perturbation remains a challenging and important problem. Many organelles are anisotropic and difficult to segment, and few methods exist for quantifying the shape, size, and quantity of these organelles.

SciPy 2021 | Article
PyRSB: Portable Performance on Multithreaded Sparse BLAS Operations
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Jul 12, 2021

This article introduces PyRSB, a Python interface to the LIBRSB library. LIBRSB is a portable performance library offering so called Sparse BLAS (Sparse Basic Linear Algebra Subprograms) operations for modern multicore CPUs.

SciPy 2021 | Article
Programmatically Identifying Cognitive Biases Present in Software Development
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Jul 12, 2021

Mitigating bias in AI-enabled systems is a topic of great concern within the research community. While efforts are underway to increase model interpretability and de-bias datasets, little attention has been given to identifying biases that are introduced by developers as part of the software engineering process.

SciPy 2021 | Article
Conformal Mappings with SymPy: Towards Python-driven Analytical Modeling in Physics
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Jul 12, 2021

This contribution shows how the symbolic computing Python library SymPy can be used to improve flow force modeling due to a Couette-type flow, i.e. a flow of viscous fluid in the region between two bodies, where one body is in tangential motion relative to the other.

SciPy 2024

Proceedings of the Python in Science Conference 2024

There are 0 articles published in this collection

SciPy 2022

Proceedings of the Python in Science Conference 2022

There are 39 articles published in this collection
SciPy 2022 | Article
Automatic random variate generation in Python
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Jul 11, 2022

The generation of random variates is an important tool that is required in many applications. Various software programs or packages contain generators for standard distributions like the normal, exponential or Gamma, e.g., the programming language R and the packages SciPy and NumPy in Python.

SciPy 2022 | Article
Global optimization software library for research and education
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Jul 11, 2022

Machine learning models are often represented by functions given by computer programs. Optimization of such functions is a challenging task because traditional derivative based optimization methods with guaranteed convergence properties cannot be used.

SciPy 2022 | Article
Search for Extraterrestrial Intelligence: GPU Accelerated TurboSETI
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Jul 11, 2022

A common technique adopted by the Search For Extraterrestrial Intelligence (SETI) community is monitoring electromagnetic radiation for signs of extraterrestrial technosignatures using ground-based radio observatories.

SciPy 2022 | Article
A New Python API for Webots Robotics Simulations
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Jul 11, 2022

Webots is a popular open-source package for 3D robotics simulations. It can also be used as a 3D interactive environment for other physics-based modeling, virtual reality, teaching or games. Webots has provided a simple API allowing Python programs to control robots and/or the simulated world, but this API is inefficient and does not provide many "pythonic" conveniences.

SciPy 2022 | Article
poliastro: a Python library for interactive astrodynamics
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Jul 11, 2022

Space is more popular than ever, with the growing public awareness of interplanetary scientific missions, as well as the increasingly large number of satellite companies planning to deploy satellite constellations.

SciPy 2022 | Article
Papyri: better documentation for the scientific ecosystem in Jupyter
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Jul 11, 2022

We present here the idea behind Papyri, a framework we are developing to provide a better documentation experience for the scientific ecosystem.

SciPy 2022 | Article
Experience report of physics-informed neural networks in fluid simulations: pitfalls and frustration
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Jul 11, 2022

Though PINNs (physics-informed neural networks) are now deemed as a complement to traditional CFD (computational fluid dynamics) solvers rather than a replacement, their ability to solve the Navier-Stokes equations without given data is still of great interest.

SciPy 2022 | Article
Low Level Feature Extraction for Cilia Segmentation
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Jul 11, 2022

Cilia are organelles found on the surface of some cells in the human body that sweep rhythmically to transport substances. Dysfunction of ciliary motion is often indicative of diseases known as ciliopathies, which disrupt the functionality of macroscopic structures within the lungs, kidneys and other organs.

SciPy 2022 | Article
Enabling Active Learning Pedagogy and Insight Mining with a Grammar of Model Analysis
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Jul 11, 2022

Modern engineering models are complex, with dozens of inputs, uncertainties arising from simplifying assumptions, and dense output data. While major strides have been made in the computational scalability of complex models, relatively less attention has been paid to user-friendly, reusable tools to explore and make sense of these models.

SciPy 2022 | Article
atoMEC: An open-source average-atom Python code
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Jul 11, 2022

Average-atom models are an important tool in studying matter under extreme conditions, such as those conditions experienced in planetary cores, brown and white dwarfs, and during inertial confinement fusion.

SciPy 2022 | Article
Monaco: A Monte Carlo Library for Performing Uncertainty and Sensitivity Analyses
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Jul 11, 2022

This paper introduces *monaco*, a Python library for conducting Monte Carlo simulations of computational models, and performing uncertainty analysis (UA) and sensitivity analysis (SA) on the results.

SciPy 2022 | Article
A Python Pipeline for Rapid Application Development (RAD)
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Jul 11, 2022

Rapid Application Development (RAD) is the ability to rapidly prototype an interactive interface through frequent feedback, so that it can be quickly deployed and delivered to stakeholders and customers.

SciPy 2022 | Article
Variational Autoencoders For Semi-Supervised Deep Metric Learning
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Jul 11, 2022

Deep metric learning (DML) methods generally do not incorporate unlabelled data. We propose borrowing components of the variational autoencoder (VAE) methodology to extend DML methods to train on semi-supervised datasets.

SciPy 2022 | Article
Wailord: Parsers and Reproducibility for Quantum Chemistry
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Jul 11, 2022

Data driven advances dominate the applied sciences landscape, with quantum chemistry being no exception to the rule. Dataset biases and human error are key bottlenecks in the development of reproducible and generalized insights.

SciPy 2022 | Article
RocketPy: Combining Open-Source and Scientific Libraries to Make the Space Sector More Modern and Accessible
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Jul 11, 2022

In recent years we are seeing exponential growth in the space sector, with new companies emerging in it. On top of that more people are becoming fascinated to participate in the aerospace revolution, which motivates students and hobbyists to build more High Powered and Sounding Rockets.

SciPy 2022 | Article
Improving PyDDA's atmospheric wind retrievals using automatic differentiation and Augmented Lagrangian methods
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Jul 11, 2022

Meteorologists require information about the spatiotemporal distribution of winds in thunderstorms in order to analyze how physical and dynamical processes govern thunderstorm evolution. Knowledge of such processes is vital for predicting severe and hazardous weather events.

SciPy 2022 | Article
pyDAMPF: a Python package for modeling mechanical properties of hygroscopic materials under interaction with a nanoprobe
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Jul 11, 2022

SciPy 2022 | Article
popmon: Analysis Package for Dataset Shift Detection
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Jul 11, 2022

popmon is an open-source Python package to check the stability of a tabular dataset.

SciPy 2022 | Article
The Geoscience Community Analysis Toolkit: An Open Development, Community Driven Toolkit in the Scientific Python Ecosystem
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Jul 11, 2022

The Geoscience Community Analysis Toolkit (GeoCAT) team develops and maintains data analysis and visualization tools on structured and unstructured grids for the geosciences community in the Scientific Python Ecosystem (SPE).

SciPy 2022 | Article
Design of a Scientific Data Analysis Support Platform
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Jul 11, 2022

Software data analytic workflows are a critical aspect of modern scientific research and play a crucial role in testing scientific hypotheses.

SciPy 2022 | Article
Temporal Word Embeddings Analysis for Disease Prevention
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Jul 11, 2022

Human languages' semantics and structure constantly change over time through mediums such as culturally significant events. By viewing the semantic changes of words during notable events, contexts of existing and novel words can be predicted for similar, current events.

SciPy 2022 | Article
Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2
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Jul 11, 2022

Due to the fact that the SARS-CoV-2 pandemic reaches its peak, researchers around the globe are combining efforts to investigate the genetics of different variants to better deal with its distribution. This paper discusses phylogeographic approaches to examine how patterns of divergence within SARS-CoV-2 coincide with geographic features, such as climatic features.

SciPy 2022 | Article
pyAudioProcessing: Audio Processing, Feature Extraction, and Machine Learning Modeling
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Jul 11, 2022

pyAudioProcessing is a Python based library for processing audio data, constructing and extracting numerical features from audio, building and testing machine learning models, and classifying data with existing pre-trained audio classification models or custom user-built models.

SciPy 2022 | Article
Likeness: a toolkit for connecting the social fabric of place to human dynamics
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Jul 11, 2022

The ability to produce richly-attributed synthetic populations is key for understanding human dynamics, responding to emergencies, and preparing for future events, all while protecting individual privacy. The Likeness toolkit accomplishes these goals.

SciPy 2022 | Article
Keeping your Jupyter notebook code quality bar high (and production ready) with Ploomber
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Jul 11, 2022

This paper walks through the ploomber interactive tutorial.

SciPy 2022 | Article
Awkward Packaging: building Scikit-HEP
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Jul 11, 2022

Scikit-HEP has grown rapidly over the last few years, not just to serve the needs of the High Energy Physics (HEP) community, but in many ways, the Python ecosystem at large. AwkwardArray, boost-histogram/hist, and iminuit are examples of libraries that are used beyond the original HEP focus. In this paper we will look at key packages in the ecosystem.

SciPy 2022 | Article
Incorporating Task-Agnostic Information in Task-Based Active Learning Using a Variational Autoencoder
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Jul 11, 2022

It is often much easier and less expensive to collect data than to label it. Active learning (AL) responds to this issue by selecting which unlabeled data are best to label next.

SciPy 2022 | Article
Codebraid Preview for VS Code: Pandoc Markdown Preview with Jupyter Kernels
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Jul 11, 2022

Codebraid Preview is a VS Code extension that provides a live preview of Pandoc Markdown documents with optional support for executing embedded code. Unlike typical Markdown previews, all Pandoc features are fully supported because Pandoc itself generates the preview.

SciPy 2022 | Article
Pylira: deconvolution of images in the presence of Poisson noise
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Jul 11, 2022

All physical and astronomical imaging observations are degraded by the finite angular resolution of the camera and telescope systems. The recovery of the true image is limited by both how well the instrument characteristics are known and by the magnitude of measurement noise.

SciPy 2022 | Article
Python vs. the pandemic: a case study in high-stakes software development
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Jul 11, 2022

When it became clear in early 2020 that COVID-19 was going to be a major public health threat, politicians and public health officials turned to academic disease modelers like us for urgent guidance.

SciPy 2022 | Article
Bayesian Estimation and Forecasting of Time Series in statsmodels
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Jul 11, 2022

Statsmodels, a Python library for statistical and econometric analysis, has traditionally focused on frequentist inference, including in its models for time series data.

SciPy 2022 | Article
USACE Coastal Engineering Toolkit and a Method of Creating a Web-Based Application
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Jul 11, 2022

In the early 1990s the Automated Coastal Engineering Systems, ACES, was created with the goal of providing state-of-the-art computer-based tools to increase the accuracy, reliability, and cost-effectiveness of Corps coastal engineering endeavors.

SciPy 2022 | Article
Python for Global Applications: teaching scientific Python in context to law and diplomacy students
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Jul 11, 2022

For students across domains and disciplines, the message has been communicated loud and clear: data skills are an essential qualification for today’s job market.

SciPy 2022 | Article
The myth of the normal curve and what to do about it
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Jul 11, 2022

Reliance on the normal curve as a tool for measurement is almost a given. It shapes our grading systems, our measures of intelligence, and importantly, it forms the mathematical backbone of many of our inferential statistical tests and algorithms.

SciPy 2022 | Article
A Novel Pipeline for Cell Instance Segmentation, Tracking and Motility Classification of Toxoplasma Gondii in 3D Space
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Jul 11, 2022

Toxoplasma gondii is the parasitic protozoan that causes disseminated toxoplasmosis, a disease that is estimated to infect around one-third of the world's population. TSeg is developed for segmenting, tracking, and classifying the motility phenotypes of T. gondii in 3D microscopic images.

SciPy 2022 | Article
Utilizing SciPy and other open source packages to provide a powerful API for materials manipulation in the Schrödinger Materials Suite
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Jul 11, 2022

The use of several open source scientific packages in the Schrödinger Materials Science Suite will be discussed.

SciPy 2022 | Article
Galyleo: A General-Purpose Extensible Visualization Solution
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Jul 11, 2022

Galyleo is an open-source, extensible dashboarding solution integrated with JupyterLab.

SciPy 2022 | Article
Semi-Supervised Semantic Annotator (S3A): Toward Efficient Semantic Labeling
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Jul 11, 2022

Most semantic image annotation platforms suffer severe bottlenecks when handling large images, complex regions of interest, or numerous distinct foreground regions in a single image. We have developed the Semi-Supervised Semantic Annotator (S3A) to address each of these issues and facilitate rapid collection of ground truth pixel-level labeled data.

SciPy 2022 | Article
The Advanced Scientific Data Format (ASDF): An Update
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Jul 11, 2022

We report on progress in developing and extending the new (ASDF) format we have developed for the data from the James Webb and Nancy Grace Roman Space Telescopes since we reported on it at a previous Scipy.

SciPy 2023

Proceedings of the Python in Science Conference 2023

There are 19 articles published in this collection
SciPy 2023 | Article
Data Reduction Network
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Jul 10, 2023

Multidimensional categorical data is widespread but not easily visualized using standard methods. For example, questionnaire data generally consists of questions with categorical responses. Popular methods of handling categorical data include one-hot encoding and enumeration, which applies an unwarranted and potentially misleading notional order to the data. To address this, we introduce a novel visualization method named Data Reduction Network.

SciPy 2023 | Article
libyt: a Tool for Parallel In Situ Analysis with yt
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Jul 10, 2023

In the era of exascale computing, storage and analysis of large scale data have become more important and difficult. We present libyt, an open source C++ library, that allows researchers to analyze and visualize data using yt or other Python packages in parallel during simulation runtime.

SciPy 2023 | Article
Pandera: Going Beyond Pandas Data Validation
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Jul 10, 2023

Data quality remains a core concern for practitioners in machine learning, data science, and data engineering, and many specialized packages have emerged to fulfill the need of validating and monitoring data and models. This paper outlines pandera’s motivation and challenges that took it from being a pandas-only data validation framework to one that is extensible to other non-pandas-compliant dataframe-like libraries.

SciPy 2023 | Article
aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake
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Jul 10, 2023

The gene sequencing data, along with the associated lineage tracing and research data generated throughout the Coronavirus disease 2019 (COVID-19) pandemic, constitute invaluable resources that profoundly empower phylogeography research. To optimize the utilization of these resources, we have developed an interactive analysis platform called aPhyloGeo-Covid.

SciPy 2023 | Article
PyQtGraph - High Performance Visualization for All Platforms
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Jul 10, 2023

PyQtGraph is a plotting library with high performance, cross-platform support and interactivity as its primary objectives. These goals are achieved by connecting the Qt GUI framework and the scientific Python ecosystem.

SciPy 2023 | Article
itk-elastix: Medical image registration in Python
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Jul 10, 2023

Image registration plays a vital role in understanding changes that occur in 2D and 3D scientific imaging datasets. In this paper, we introduce itk-elastix, a user-friendly Python wrapping of the mature elastix registration toolbox.

SciPy 2023 | Article
Spatial Microsimulation and Activity Allocation in Python: An Update on the Likeness Toolkit
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Jul 10, 2023

Understanding human security and social equity issues within human systems requires large-scale models of population dynamics that simulate high-fidelity representations of individuals and access to essential activities (work/school, social, errands, health). Likeness is a Python toolkit that provides spatial microsimulation project.

SciPy 2023 | Article
The Pandata Scalable Open-Source Analysis Stack
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Jul 10, 2023

As the scale of scientific data analysis continues to grow, traditional domain-specific tools often struggle with data of increasing size and complexity. We introduce the Pandata open-source software stack as a solution, emphasizing the use of domain-independent tools at critical stages of the data life cycle, without compromising the depth of domain-specific analyses.

SciPy 2023 | Article
MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis
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Jul 10, 2023

The reproducibility and transparency of scientific findings are widely recognized as crucial for promoting scientific progress. The MDAKits framework provides a cookiecutter template, best practices documentation, and a continually validated registry.

SciPy 2023 | Article
Using Blosc2 NDim As A Fast Explorer Of The Milky Way (Or Any Other NDim Dataset)
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Jul 10, 2023

Large multidimensional datasets are widely used in various engineering and scientific applications. We have added support for large dimensional datasets to Blosc2, a compression and format library.

SciPy 2023 | Article
Emukit: A Python toolkit for decision making under uncertainty
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Jul 10, 2023

Emukit is a highly flexible Python toolkit for enriching decision making under uncertainty with statistical emulation. It is particularly pertinent to complex processes and simulations where data are scarce or difficult to acquire.

SciPy 2023 | Article
vak: a neural network framework for researchers studying animal acoustic communication
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Jul 10, 2023

The study of acoustic communication is being revolutionized by deep neural network models. To address this need, we developed vak, a neural network framework designed for acoustic communication researchers.

SciPy 2023 | Article
EEG-to-fMRI Neuroimaging Cross Modal Synthesis in Python
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Jul 10, 2023

Electroencepholography and functional magnetic resonance imaging are two ways of recording brain activity. We developed a Python package, EEG-to-fMRI, which provides cross modal neuroimaging synthesis functionalities.

SciPy 2023 | Article
Using Numba for GPU acceleration of Neutron Beamline Digital Twins
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Jul 10, 2023

Digital twins of neutron instruments using Monte Carlo ray tracing have proven to be useful in neutron data analysis and verifying instrument and sample designs. In this paper, we present a GPU accelerated version of MCViNE using Python and Numba to balance user extensibility with performance.

SciPy 2023 | Article
Bayesian Statistics with Python, No Resampling Necessary
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Jul 10, 2023

TensorFlow Probability is a powerful library for statistical analysis in Python. Using TensorFlow Probability’s implementation of Bayesian methods, modelers can incorporate prior information and obtain parameter estimates and a quantified degree of belief in the results.

SciPy 2023 | Article
Biomolecular Crystallographic Computing with Jupyter
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Jul 10, 2023

To further advance this use of Jupyter, we developed a collection of code fragments that use the vast Computational Crystallography Toolbox (cctbx) library for novel analyses. We made versions of this library for use in JupyterLab and Colab.

SciPy 2023 | Article
An Accessible Python based Author Identification Process
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Jul 10, 2023

Author identification also known as ‘author attribution’ and more recently ‘forensic linguistics’ involves identifying true authors of anonymous texts. In this paper we replicate the analysis but in a much more accessible way using modern text mining methods and Python.

SciPy 2023 | Article
A Modified Strassen Algorithm to Accelerate Numpy Large Matrix Multiplication with Integer Entries
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Jul 10, 2023

We present a Strassen type algorithm for multiplying large matrices with integer entries. The algorithm is the standard Strassen divide and conquer algorithm but it crosses over to Numpy when either the row or column dimension of one of the matrices drops below 128.

SciPy 2023 | Article
Python Array API Standard: Toward Array Interoperability in the Scientific Python Ecosystem
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Jul 10, 2023

The Python array API standard specifies standardized application programming interfaces and behaviors for array and tensor objects and operations. The establishment and subsequent adoption of the standard aims to reduce ecosystem fragmentation and facilitate array library interoperability.

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