135 Works

Machine Learning Techniques for Detecting Identifying Linguistic Patterns in the News Media

A Samuel Pottinger
Code and reference configurations used in research for https://whowrotethis.com and "Machine Learning Techniques for Detecting Identifying Linguistic Patterns in the News Media" by A. Samuel Pottinger. Released under the MIT license. For data, please see https://whowrotethis.com.

Frequency Estimation of a real sinusoid by three new interpolators

Guo Bai
This code is for the paper "Frequency Estimation of a real sinusoid by three new interpolators"

Reanalysis of Gold et al. (2019), Figures 4A and 4B

Peter M. C. Harrison
This project provides a reproducible reanalysis of Figures 4A and 4B from Gold et al.'s (2019) paper, "Musical reward prediction errors engage the nucleus accumbens and motivate learning". The original paper reports a reinforcement-learning experiment where reward prediction errors were elicited by the consonance or dissonance of musical stimuli. In Figures 4A and 4B of the original paper, the authors correlate activity in the right nucleus accumbens to variation in participants' learning and scores in...

Cardiac pulsatility mapping and vessel type identification using laser speckle contrast imaging

Dmitry Postnov, Sefik Evren Erdener, Kivilcim Kilic & David A. Boas
Exemplary code and data for figures generation (figures may not fully correspond to the published version). Additional code details: https://github.com/BUNPC/laserSpeckleImaging (runPulsatilityBasedIdentification.m)

Frangi-Net on High-Resolution Fundus (HRF) image database

Weilin Fu
This capsule holds the code for Frangi-Net experiment on High-Resolution Fundus (HRF) Image Database. We reformulate the conventional multi-scale 2-D Frangi vesselness measure into a pre-weighted neural network ("Frangi-Net"). Without training, Frangi-Net is equivalent to the original Frangi filter. With further training, the segmentation performance of the network is increased.

A Distributed BLAST with a Data-Parallel Computational Model

Majid Hajibaba, Mohsen Sharifi & Saeid Gorgin
With the advent of high-throughput next-generation sequencing (NGS) technologies, the amount of available sequencing data is growing exponentially. Hence, processing and storing such huge volume of data has become a major challenge for modern genomic research. In order to alleviate these issues, in this paper we present a computational model for BLAST that is data-parallel. The suggested model has a master-worker parallel programming paradigm. The master splits the database according to the number of available...

INSTRON compression test analysis

Joseph Porter
This script processes force data collected using an INTRON compression test machine, analysing the curing rate of homemade silicone compound in moisture controlled conditions. The code extracts .csv files, separated individual trials, visualises both conditions (as in profile picture) and generates a table of peak force achieved for each trial. trials were conducted at 15 minute intervals from when the compound was first mixed.

Acclimatization of massive reef-building corals to consecutive heatwaves

Thomas DeCarlo
Data and code to reproduce statistical analyses and create figures for "Acclimatization of massive reef-building corals to consecutive heatwaves" published in Proceedings of the Royal Society B. The code analyzes "stress bands" that were observed within the skeletons of long-lived Porites corals collected from the Great Barrier Reef and Coral Sea. Tests performed within the code include analysis of stress band occurrence vs. time, stress band occurrence vs. heat stress during the 21st century, changes...

Sparse Wavenumber Analysis

Joel B. Harley
In this script, we show an example of applying sparse wavenumber analysis (SWA) to simulation data corrupted by multipath interference. This learns the dispersion curves (i.e., the frequency-wavenumber representation) of wave data. The variable 'xm' contains the multipath "measured" simulation data. The multipath data is used as the input to sparse wavenumber analysis (SWA). The variable 'xc' contains the ideal (no multipath) simulation data. This data is used to evaluate our sparse wavenumber denoising results...

LabPal Sorting Demo

Sylvain Hallé
Designing clean, reusable, and repeatable experiments for a research paper does not have to be difficult. We report on our efforts to create an integrated toolchain for running, processing, and including the results of computer experiments in scientific publications. This capsule shows how the LabPal library can be used to automate this process.

MATLAB Code---Fault diagnosis of power transformers with membership degree

Enwen LI
A reference fault set is provided, and the fault diagnosis is implemented by calculating the membership of the DGA data to the reference fault set.

Effectiveness and equity of Payments for Ecosystem Services: Insights from real-effort experiments with Vietnamese land users

Lasse Loft, Stefan Gehrig, Dung Ngoc Le & Jens Rommel
The capsule contains all data, analysis and results of the research article "Effectiveness and equity of Payments for Ecosystem Services: Insights from real-effort experiments with Vietnamese land users". Payments for Ecosystem Services (PES) are widespread in conservation policy. In PES, environmental effectiveness and social equity are often perceived as conflicting goals. Empirical studies on the relationship of popular design features like payment differentiation and payment conditionality with effectiveness and equity are scarce and struggle with...

ACHR.cu: GPU accelerated sampling of metabolic networks.

Marouen Ben Guebila
Metabolic models are mathematical depiction of biological systems formulated as linear programs. A tool of choice for the exploration of a large number of solution i.e., phenotypes of the system is the uniform sampling of the solution space. The use of sampling remains quite limited because it is computationally expensive. ACHR.cu leverages the power of modern GPU cards to launch thousands of sampling chains in the solution space. Finally, it allows a faster processing of...

Verification of the Multi-Physics Problems (MPP) library

Gautam Bisht & William J. Riley
This capsule reproduces verification of an open source numerical library for solving global terrestrial multi-physics process that includes a flexible coupling framework (Bisht and Riley, in review). Robust numerical solution for linear and nonlinear equations is provided via the PETSc library. The verification the numerical library using methods of manufactured solutions (MMS) for a range of problems comprising of single and multi-physics steady-state problems that are applied in one or multiple physical domains. The verification...

Deriving Neural Networks

Christopher Syben
CAPSULE: Compute Capsule for deriving neural networks and new algorithms. PAPER: 'Deriving neural network architectures using precision learning: parallel-to-fan beam conversion' ABSTRACT: n this paper, we derive a neural network architecture based on an analytical formulation of the parallel-to-fan beam conversion problem following the concept of precision learning. The network allows to learn the unknown operators in this conversion in a data-driven manner avoiding interpolation and potential loss of resolution. Integration of known operators results...

Delta-Ramp Encoder for Amplitude Sampling and its Interpretation as Time Encoding (codes)

Pablo Martinez-Nuevo, Hsin-Yu Lai & Alan V. Oppenheim
These are the codes to generate Figure 8-11 in the paper, P. Martınez-Nuevo, H.-Y. Lai, A.V. Oppenheim, "Delta-Ramp Encoder for Amplitude Sampling and its Interpretation as Time Encoding", IEEE Transactions on Signal Processing, 2019.

Revisiting Antarctic ice loss due to marine ice cliff instability

Tamsin Edwards
This Code Ocean capsule reproduces the main analysis of the below paper, which emulates and recalibrates the Antarctic ice sheet model ensemble projections of DeConto and Pollard (2016), Nature. Tamsin L. Edwards, Mark Brandon, Gael Durand, Neil R. Edwards, Nicholas R. Golledge, Philip B. Holden, Isabel Nias, Antony J. Payne, Catherine Ritz and Andreas Wernecke (2019), Revisiting Antarctic ice loss due to marine ice cliff instability, Nature.

Tutorial for the FMI++ Python Interface

Edmund Widl
This capsule provides simple test cases for exporting ns-3 scripts as FMUs for Co-Simulation. The usage of the exported FMUs is demonstrated with the help of simple Python scripts.

Supplementary code for: Simple Generation of Gamma, Gamma-Gamma and K Distributions with Exponential Autocorrelation Function

Dima Bykhovsky
This code provides an example of numerical generation of random process with gamma distribution and exponential auto-correlation function.

Improving contig binning of metagenomic data using d2S oligonucleotide frequency dissimilarity

Ying Wang, Kun Wang, Yang Young Lu & Fengzhu Sun
d2SBin is easy-to-use contig-binning improving tool, which adjusted the contigs among bins based on the output of any existing binning tools. The tool is taxonomy-free only on the k-tuples for single metagenomic sample. d2SBin is based on the mechanism that relative sequence compositions are similar across different regions of the same genome, but differ between genomes. Current tools generally used the normalized frequency of k-tuple directly, which actually is the absolute instead of relative sequence...

Minimal transparency is undermining the credibility of the social sciences

Tom Hardwicke, Joshua Wallach, Mallory Kidwell & John Ioannidis
Policy decisions based on flawed research can have substantial economic, social, and individual costs. Recently there have been calls for improved transparency in the social sciences to ensure that a robust evidence base is available to policy makers. New initiatives such as the Transparency and Openness Promotion (TOP) Guidelines have been launched in an effort to improve the transparency and credibility of the scientific literature. However, the cumulative effect of these initiatives is currently unknown....

Comparative Metatranscriptomics Workflow (CoMW)

Muhammad Zohaib Anwar, Anders Lanzen, Toke Bang-Andreasen & Carsten Suhr Jacobsen
Comparative Metatranscriptomics Workflow is a standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. CoMW is used for classification of these reads using assembled contigs to the reference databases provided and cited.

Sampling Clustering

Tarn Yeong Ching
We propose an efficient linear-time graph-based divisive cluster analysis approach called Sampling Clustering. It constructs a lite informative dendrogram by recursively dividing a graph into subgraphs. In each recursive call, a graph is sampled first with a set of vertices being removed to disconnect latent clusters, then condensed by adding edges to the remaining vertices to avoid graph fragmentation caused by vertex removals. We also present some sampling and condensing methods and discuss the effectiveness...

SReachTools: Controller synthesis for safe spacecraft rendezvous under uncertainty

Abraham P. Vinod, Joseph Gleason & Meeko Oishi
This Code Ocean capsule synthesizes controllers for the spacecraft rendezvous problem --- the problem of driving a spacecraft to meet another spacecraft in space while satisfying line-of-sight cone constraints as well as hard actuation limits. SReachTools provide multiple ways to generate lower bounds on probability of achieving this specification as well as controllers to obtain these guarantees.

Calibration Code based on Multi-Projection-Center Model

Qi Zhang
Light field cameras can capture both spatial and angular information of light rays, enabling 3D reconstruction by a single exposure. The geometry of 3D reconstruction is affected by intrinsic parameters of a light field camera significantly. In the paper, we propose a multi-projection-center (MPC) model with 6 intrinsic parameters to characterize light field cameras based on traditional two-parallel-plane (TPP) representation. The MPC model can generally parameterize light field in different imaging formations, including conventional and...

Registration Year

  • 2019

Resource Types

  • Software

Data Centers

  • Code Ocean