Code Ocean

United States

193 Works

A Hidden Markov Regime-Switching Smooth Transition Model

John W. Lau
This archive contains the data and the R code used for the simulation and the empirical application in "A Hidden Markov Regime-Switching Smooth Transition Model" by Robert J. Elliott, Tak Kuen Siu, and John W. Lau. We have developed a new class of parametric nonlinear time series models by combining two important classes of models, namely smooth transition models and hidden Markov regime-switching models. The class of models is general and flexible enough to incorporate...

DRAMSim2 - A cycle accurate DRAM simulator modified for row-buffer caching

Dave Wilkinson
Reproducibility experimentation for "A permutation-based page interleaving scheme to reduce row-buffer conflicts and exploit data locality" that uses a modified DRAMSim2 to simulate SPEC CPU benchmarks with an interleaved row-buffer addressing scheme.

Multiresolution Alignment for Multiple Unsynchronized Audio Sequences using Sequential Monte Carlo Samplers

Dogac Basaran
This project provides the implementation of the algorithm proposed in the article "Multiresolution alignment for multiple unsynchronized audio sequences using sequential Monte Carlo samplers" ( In order to give the users the ability to recreate the results in article, the audio dataset is also provided. For more information, you can consult README file. You may notice that the source codes are also provided on The difference between Code Ocean and GitHub is that the...

Genome Annotation Generator NCBI for submission

Scott Geib
Genome Annotation Generator A command line program to read, modify, annotate and output genomic data. Can write files to .gff3 or to the NCBI's .tbl format. Perfect if you're trying to submit a genome to NCBI.

LoRa interference simulator

Daniele Croce
This is a simulation tool for testing the performance of a LoRa link in case of collision between LoRa packets modulated with different spreading factors. You can use it for obtaining the results presented in Table 1 of our paper.

A Simple Soundness Proof for DOT

Marianna Rapoport
A simple Coq type safety proof for the DOT (Dependent Object Types) calculus

Blaschke Unwinding AFD Based ECG Compression

Liming Zhang
This code implements the ECG signal compression algorithm in the paper: C. Tan, L. Zhang and H. Wu, "A Novel Blaschke Unwinding Adaptive Fourier Decomposition based Signal Compression Algorithm with Application on ECG Signals," submitted in Journal of Biomedical and Health Informatics.

Double Line Image Rotation

Amir Hossein Ashtari
This code provides a fast algorithm for rotating images while preserving their quality. The new approach rotates images based on vertical or horizontal lines in the original image and their rotated equation in the target image. The proposed method is a one-pass method that determines a based-line equation in the target image and extracts all corresponding pixels on the base-line. Floating-point multiplications are performed to calculate the base-line in the target image, and other line...

ELMSeq: An Extended Linear Model for Joint Normalization and Differential Gene Expression Detection in RNA-Seq data

Kefei Liu
The RNA-sequencing (RNA-seq) is becoming increasingly popular for quantifying gene expression levels. Since the RNA-seq measurements are relative in nature, between-sample normalization of counts is an essential step in differential expression (DE) analysis. The normalization of existing DE detection algorithms is performed once at the outset prior to DE detection, which may not be adequate since ideally normalization should be based on non-DE genes only and thus coupled with DE detection. We propose a statistical...

Split FASTA files in different sizes

Majid Hajibaba
In this method, we split a fasta database to several bunch of chunks with different sizes. Each bunch has chunks with fixed size and equal to number_of_files. In each level of partitioning data is being split to a specific size (size_inc times larger than size of earlier level). For example, first bunch of chunks have 32MB, second bunch of chunks have 64MB, and third bunch of chunks have 128MB and so on.

A Distributed BLAST with a Data-Parallel Computational Model

Majid Hajibaba
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...

FingerNet: A Unified Deep Network for Fingerprint Minutiae Extraction

Yao Tang
FingerNet is a universal deep ConvNet for extracting fingerprint representations including orientation field, segmentation, enhanced fingerprint and minutiae. It can produce reliable results on both rolled/slap and latent fingerprints.

A Modularized Efficient Framework for Non-Markov Time Series Estimation

Gabriel Schamberg
This capsule provides a Python implementation of our ADMM framework for obtaining a maximum a-posteriori (MAP) estimate of a latent process with non-Gaussian observations and/or non-Markov dynamics. In addition to the framework implementation, we provide three iPython notebooks that are executed in parallel when running the capsule (estimated 2.5 hours to complete). The contents of the notebooks are as follows: "state_space_model_learning" details how to use the framework for the application described in Section IV.A, "state_space_model_learning_evaluation"...

Speckle Reduction by Selective Spatial-Domain Mask in Digital Holography

Mingda Liang
We report on an improved method of using a selective spatial-domain mask to reduce speckle noise in digital holography. Multiple sub-reconstructed images with different speckle patterns are obtained by shifting the rectangular apertures in the hologram. The speckle noise is suppressed with averaging the favorable sub-images which are selected based on the pixel gradient of the hologram. This is significant because all of the sub-images are accumulated without any selective standard, will leading to the...

MIMO-NOMA based VLC with NGDPA power allocation

Chen Chen
MATLAB code calculating the sum rate of a MIMO-NOMA based VLC system using our proposed NGDPA power allocation method is presented. To ensure efficient and low-complexity power allocation in indoor MIMO-NOMA based VLC systems, a normalized gain difference power allocation (NGDPA) method is firstly proposed by exploiting users’ channel conditions. We investigate the performance of an indoor 2×2 MIMO-NOMA based multi-user VLC system through numerical simulations. The obtained results show that the achievable sum rate...

RS-Feature Matching Evaluation Platform Based on An Orbital Optical Pushbroom Stereo Imaging System

Wen-Liang Du
This code is for simulating correspondences of remote sensing. Researchers could evaluate their feature-matching algorithms on the simulated correspondences. Copyright (c) 2018 by Wenliang Du (, Faculty of Information and Technology, Macau University of Science and Technology Last Modified October 2018/01/12

BLAST output MERGE - eValue sorted

We have extended blastmerge to sort the results according to e-values. At last, master delivers the results to the user as a file similar to the BLAST output. blastmerge sort the results according to score.

Schema Perception

Christopher Baldassano
This capsule demonstrates the analyses described in "Representation of real-world event schemas during narrative perception" by Baldassano, Hasson, and Norman.

Millimeter Wave Beam-Selection Using Out-of-Band Spatial Information

Millimeter wave (mmWave) communication is one feasible solution for high data-rate applications like vehicle-to-everything communication and next generation cellular communication. Configuring mmWave links, which can be done through channel estimation or beam-selection, however, is a source of significant overhead. In this paper, we propose to use spatial information extracted at sub-6 GHz to help establish the mmWave link. Assuming a fully digital architecture at sub-6 GHz; and an analog architecture at mmWave, we outline a...

Frequency-Partitioning Fitting

Taku Noda
It is often the case that the frequency response data of a system or a network is available and one wants to identify a linear equivalent from the frequency response data for time-domain simulations and other purposes. To this end, a variety of methods have been proposed, and the vector fitting (VF) method and the frequency-partitioning fitting (FpF) method are often used for electromagnetic transient (EMT) simulations of power systems. The main applications are frequency-dependent...

Preprocessing Acceleration Data and Applying Deep Learning for Human Activity Recognition

Xiaochen Zheng
This algorithm is designed to preprocess acceleration data with different methods and classify human activities using deep convolutional neural networks based on the preprocessed data. The algorithm contains two general sections: the data preprocessing section (written in R language) and deep convolutional neural networks training and testing section (written in Python language). Four public datasets are used in this algorithm: RealWorld-2016 (Timo, Skoda (P. Zappi, WISDM v1.1 (Jennifer and WISDM v2.0 (Gary...

A filtered-x affine projection sign algorithm for multichannel system

JunWoong Hur
A filtered-x affine projection sign algorithm for multichannel system ensures the enhancement of ANC performance in the aspect of the steady-state estimation error and convergence rate with impulsive noises and colored inputs.

Sparsity Within and Across Overlapping Groups

Ilker Bayram
Recently, penalties promoting signals that are sparse within and across groups have been proposed. This software demonstrates the use of a generalized penalty function, that is more flexible in defining groups, in a simple inverse problem formulation. Specifically, the software reproduces the experiment in the associated article below.

Gershgorin radii and centers ratio (GRCR) and other detectors

Dayan Adionel Guimarães
This is a Matlab code for simulating the performance of several data fusion cooperative spectrum sensing techniques for cognitive radio applications, under uniform or nonuniform noise condition. The configurable system parameters are the number of primary user (PU) transmitters, the number of secondary user (SU) receivers, the average signal-to-noise ratio (SNR) across all SUs, the number of Monte Carlo events, the number of samples collected by each SU, the type of PU signal (Gaussian or...

Nonintrusive Vital Signs Monitoring for Sleep Apnea Patients: A Preliminary Study

Ibrahim Sadek
The purpose of the provided manuscripts is to assess the capability of the microbend fiber optic sensor for nonintrusive monitoring of vital signs, i.e., heart rate and respiration in a clinical setting. Besides, assessing the capacity of the sensor for nonintrusive sleep apnea detection.

Resource Types

  • Software

Publication Year

  • 2018
  • 2017
  • 2016

Registration Year

  • 2018
  • 2017

Data Centers

  • Code Ocean