Reproducible Research in Computational Science

Reproducible Research in Computational Science

from: http://www.csee.wvu.edu/~xinl/source.html

 

“It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong” - Richard Feynman

 

"As a method for finding things out, science lives by its disdain for authority and its reliance on experimentation." - Chris Quigg

 

Welcome to this site about reproducible research in computational science (including signal processing, computer vision, machine learning and neural computation). This site is intended to share the source codes of the latest advances in various technical fields to the best of my knowledge. Only through Reproducible Research (RR), can we live up to the standard that hard-core science has established since Bacon and Newton. If you know of any release of the source codes that is missing from the list or any broken link, please kindly let me know.

Image denoising

• Bayesian Structured Sparse Coding (BSSC)
• Wavelet-basedsoft/hard thresholding and TI denoising Wavelab
• Spatiallyadaptive image denoising under overcomplete expansion  SA-OE
• Low-complexity image denoising based on statistical modeling of wavelet coefficientscode
• BayesianLeast-Square Gaussian Scalar Mixture BLS-GSM
• Wavelet-domainHMM for image denoising WHMT
• Fields ofexperts model for image denoising FoE
• Learningsparse representation for image denoisingK-SVD
• Shapeadaptive DCT based image denoising SA-DCT
• Nonlocal meanbased image denoisingcodecode2
• Blockmatching 3D (BM3D) image denoising BM3D
• Productof Edgeperts denoising PoEdges
• TotalLeast-Square (TLS) image denoising TLS
• AVMF colorimage denoising AVMF
• MultiscleLMMSE-based image denoising  code
• Kernelregression based image denoising code
• Beliefpropagation for image restoration code
• Gaussian Field-of-Expert(GFoE) denoising code
• Active random field learningcode
• Clustering-based Denoising using Locally Learned Dictionaries (K-LLD)
• Local Pixel Grouping (LPG)-PCA image denoising
• Leaning simultaneous sparsity coding (LSSC)code (only runs on 64-bit Linux machine with MATLAB)
• BM3D image denoising with shape - adaptive principal component analysis(BM3D-SAPCA) code
• Learning Non-Local Range Markov Random Field for Image Restorationcode
• Image denoising via dictionary learning and structural clustering
• From Learning Models of Natural Image Patches to Whole Image Restorationcode
• Image denoising: Can plain Neural Networks compete with BM3D?
• Patch-based Locally Optimal Wiener Filtering for Image Denoising
• Nonparametric Bayesian Dictionary Learning for Analysis of Noisy and Incomplete Imagescode
• Spatially adaptive iterative singular-value threshodlign (SAIST)code
• Image Denoising using the Higher Order Singular Value Decompositioncode
• Dual-Domain Image Denoisingcode
• Progressive image denoisingcode

Image coding

• JPEG-LS standardLOCO-I
• Context-Based,Adaptive, Lossless Image Coding CALIC
• Edge directedprediction for lossless image compression EDP
• TMWlossless image compressionDownloadCode (lost in cyberspace)
• Minimum rateprediction with DP-based optimization Code
• EmbeddedPredictive Wavelet Image Coder Code
• SPIHTimage codec SPIHTMATLABcodes (third-party implementation)
• Estimation Quantizationlossy image codecEQ
• Least-SquareEstionation Quantization CodecLS-EQ
• EBCOTcodec for JPEG2000 EBCOT
• Multiple description coding with prediction compensationcode
• Multiple description image coding based on lagrangian rate allocationcode

Image demosaicing

• Primary-consistentsoft-decision (PCSD)-based schemeexecutable
• Alternateprojection (AP)-based schemeAP
• AdaptiveHomogeneity-Directed (AHD) demosaicing AHD
• DLMMSEdemosaicing  DLMMSE
• Demosaicingby successive approximation SA
• Demosaicingby directional filtering and a posteriori decision dfapd
• LPA-ICI demosaicingLPA-ICI
• A Model of Retinal Local Adaptation for the Tone Mapping of Color Filter Array Images
• Leaning simultaneous sparsity coding (LSSC)code (only runs on 64-bit Linux machine with MATLAB)
• PCA-based Spatially Adaptive Denoising of CFA Images for Single-Sensor Digital Camerascode
• Self-similarity driven image demosaicing
• Color Demosaicking by Local Directional Interpolation and Non-local Adaptive Thresholdingcode
• Residual Interpolation for color image demosaicking
• Vector-Valued Image Processing by Parallel Level Sets
• Exploitation of Inter-color correlation for Color Image Demosaicing

Image interpolation and Superresolution

• Linear interpolation revitalized
• New edge directed interpolation (NEDI)code
• Signal Discrete Sinc-interpolation in DCT Domaincode
• Directionalfiltering and data fusion DFDF
• Wavelet-basedtexture image interpolation wt_interp
• Fast and robustsuperresolution (SR) toolbox UCSC-SR
• Superresolutionfor synthetic zooming syn_zoom
• EPFL'sfrequency-domain approach EPFL
• Support vectormachine based image superresolution  result
• Imageinterpolation using multiscale geometric representations Code
• Kriging-basedBest Linear Unbiased Estimator  Code
• Imageinterpolation by adaptive 2D autoregressive modeling and soft-decisionestimation  Executable
• Super-resolution GUI developedby Bahadir at LSU
• Multi-frame image super-resolution
• Super-resolutionvia sparse coding code
• Super-resolution through neighbor embeddingcode
• Super-resolutionwith sparse mixing estimators
• Machine learning in multi-frame SR
• Example-based learning for super-resolution
• Super Resolution using Edge Prior and Single Image Detail Synthesiscode
• Binary halftone image resolution increasing by decision tree learning
• Simultaneous motion deblurring and super-resolution
• Exploiting Self-Similarities for Single Frame Super-Resolutioncode
• Fast image/video upsampling (binary executables only)
• Image deblurring and supper-resolution by adaptive sparse domain selection and adaptive regularizationcode
• Image and video upsampling from local self-examplescode (third-party implementation)
• Semi-Coupled Dictionary Learning with Applications to Image Super-resolution and Photo-Sketch Synthesis
• Sparse Representation based Image Interpolation with Nonlocal Autoregressive Modeling
• Structured Face Hallucinationcode
• Anchored Neighborhood Regression for Fast Example-Based Super-Resolutioncode
• Fast direct super-resolution by simple functions
• A+: adjusted anchored neighborhood regression for fast super-resolution
• Image Super-Resolution Using Deep Convolutional Networks
• Hyperspectral Image Super-resolution via Non-negative Structured Sparse Representation

Hyperspectral/Multispectral image processing

• Hyperspectral and Multispectral Image Fusion based on a Sparse Representationcode
• Bayesian fusion of multi-band imagescode
• Hyperspectral pansharpening: a reviewcode
• Minimum Volume Simplex Analysis: A Fast Algorithm for Linear Hyperspectral Unmixingcode
• Multiple Feature Learning for Hyperspectral Image Classificationcode
• Generalized Composite Kernel Framework for Hyperspectral Image Classificationcode
• Spectral-Spatial Classification of Hyperspectral Data Using Loopy Belief Propagation and Active Learningcode
• Spectral-Spatial Hyperspectral Image Segmentation Using Subspace Multinomial Logistic Regression and Markov Random Fields code
• Hyperspectral Image Segmentation Using a New Bayesian Approach with Active Learningcode
• Semi-Supervised Hyperspectral Image Segmentation Using Multinomial Logistic Regression with Active Learningcode
• Hyperspectral Image Super-resolution via Non-negative Structured Sparse Representation

Image segmentation, parsing and matting

• Image segmentationby normalized cut Ncut
• Epitome-basedimage segmentation epitome
• Bayesianmultiscale image segmentationSMAP
• Graph-cutBased Image Segmentation segment Code2
• EDISONSystem EDISON Code2
• Pfindersystem Pfinder
• Aclosed form solution to image matting matting
• Spectralmatting code
• Levelset evolution without reinitialization Code
• Implicitactive contour driven by local binary fitting energy Code
• Snakes, Shapes, and GradientVector Flow Code
• Unsupervisedlearning of finite mixture model Code
• DDMCMCImage Segmentation
• Image Segmentationby Generalized SW-cuts
• A generalized model for scratch detection
• Biased normalized cut
• Power Watersheds (iccv'2009)code
• Global contrast based salient region detection
• Generalizing Swendsen-Wang to sampling arbitrary posterior probabilitiescode
• Interactive segmentation toolbox (GrabCut+LazySnap)
• Geodesic Star Convexity for Interactive Image Segmentation
• Distributed Cosegmentation via Submodular Optimization on Anisotropic Diffusioncode
• Segmenting Scenes by Matching Image Composites
• Automatic Image Segmentation by Dynamic Region Mergingcode
• Interactive Images: Cuboid Proxies for Smart Image Manipulation
• Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials
• Image Segmentation with Cascaded Hierarchical Models and Logistic Disjunctive Normal Networkscode
• Nonlocal Matting
• KNN matting
• Unsupervised Joint Object Discovery and Segmentation in Internet Images

Image deblurring

• Fourier-WaveletRegularized Deconvolution ForWard
• PointwiseSA-DCT regularized deconvolution SA-DCT
• Imagedeconvolution using a natural image prior Code
• Total-Variation(TV) based image deblurring Code
• Two-stepiterative shrinkage/thresholding algorithms for image restorationCode
• Iterativemethods for image restoration  Code
• ICA Toolbox for blindimage separation
• L0-AbSDeblur 1.0
• Regularized Kernel Regression-Based Deblurring (AKTV)
• Projection-baseddeblurring with fine-granularity and spatially adaptive regularization
• Fast Gradient-Based Algorithms for Constrained Total Variation Image Deblurringcode
• Image deblurring by adaptive sparse domain selection and adaptive regularizationcode
• Fast Image Deconvolution using Hyper-Laplacian Priors
• BM3D Frames and Variational Image Deblurringcode
• Centralized Sparse Representation for Image Restorationcode
• Bayesian Structured Sparse Coding (BSSC)
• Image Restoration Using Joint Statistical Modeling in Space-Transform Domain

Blind image deblurring

• Removing Camera Shake from a Single Image code_request_form
• High-quality blind motion deblurring (executables only)
• Quality measure for Blind deblurring methods
• Eficient Marginal Likelihood Optimization in Blind Deconvolutioncode
• Analyzing spatially varying blur
• Fast motion deblurring
• Two-phase kernel estimation for robust motion deblurring
• Blind deconvolution using a normalized sparsity measure
• Efficient Deblurring for Shaken and Partially Saturated Images
• Fast Removal of Non-uniform Camera Shake
• Multi-frame Blind Deconvolution with Super-resolution and Saturation Correction
• Robust Multichannel Blind Deconvolution via Fast Alternating Minimization
• Benchmarking blind deconvolution with a real-world database (dataset only)
• Frequency domain blind deconvolution in multiframe imaging using anisotropic spatially-adaptive denoising
• Handling Noise in Single Image Deblurring using Directional Filters

Texture synthesis

• Reaction-diffusion texturescode
• Texture synthesis via a noncausal nonparametric multiscale Markov random fieldcode
• Pyramid Based Texture Analysis/Synthesiscode
• Wavelet-domain parametric model code
• Texture synthesis by nonparametric sampling code (third-party implementation)
• Image quiltingcodecode2
• Synthesizing Natural Texturescode
• Texture Optimization for Example-based Synthesiscode (third-party implementation)
• Parallel controllable texture synthesiscode
• Graphcut Textures: Image and Video Synthesis Using Graph Cutscode (third-party implementation)
• Random Phase Textures: Theory and Synthesiscode
• Higher Order SVD Analysis for Dynamic Texture Synthesis
• Symmetry-Guided Texture Synthesis and Manipulation

Physics-based image processing

• Single Image Haze Removalcode (third-party implementation)
• Efficient Image Dehazing with Boundary Constraint and Contextual Regularizationcode
• Singel image dehazing (only toy example included)
• Single Image Visibility Restoration Comparison
• Automatic single-frame-based rain streak removal via image decompositioncode
• Removing Atmospheric Turbulence via Space-Invariant Deconvolution
• Automatic Recovery of the Atmospheric Light in Hazy Images
• Blind Separation of Superimposed Moving Images Using Image Statisticscode
• 
  

Image inpainting

• Exemplar-basedimage inpainting code
• Fields ofexperts model for image inpainting FoE
• Imagerecovery via adaptive sparse representationcode
• Least-Squarebased sequential error concealment nsec
• Patch-basednonlocal error concealment
• Image recovery via hybrid sparse representation
• Higher Order SVD Analysis for Dynamic Texture Synthesis
• TV-based image inpaintingcode code2
• Robust Locally Linear Analysis with Applications to Image Denoising and Blind Inpaintingcode
• Non-Parametric Bayesian dictionary learning for sparse image representationscode
• Hierarchical super-resolustion-based inpainting

PDE-based image processing

• Perona-Malik nonlinear diffusion code code2
• Total variation based image denoisingcode code2
• Curvature-Driven Diffusion based image inpaintingcode
• Shock filter for image enhancement  code
• Weickert's anisotropic diffusion code
• Mean curvature diffusion (MCD)  code
• A variational method for image recoverycode
• Speckle reducing anisotropic diffusioncode
• Parametric Maximum Flow Algorithmsfor Fast Total Variation Minimizationcode
• An Algorithm for Nonlocal TV Minimization
• Vector-Valued Image Processing by Parallel Level Sets

Image quality assessment

• Universal image quality index  code
• Structural SIMilarity (SSIM) index  code
• Degradation model code
• FSIM: A Feature Similarity Index for Image Quality Assessmentcode
• A No-Reference Objective Image Sharpness Metric Based on the Notion of Just Noticeable Blurcode
• An Improved No-Reference Sharpness Metric Based on the Probability of Blur Detectioncode
• Gradient Magnitude Similarity Deviation: A Highly Efficient Perceptual Image Quality Index

Biometrics

• Fingerprint enhancement and matching
• Daugman's iris recognition algorithm implementation
• Photorealistic Models for Pupil Light Reflex and Iridal Pattern Deformation
• Gabor Feature based Sparse Representation for Face Recognitioncode
• Robust Sparse Coding for Face Recognitioncode
• Jialong He's Speaker Recognition (Identification) Tool
• Unsupervised Salience Learning for Person Re-identification
• Pose-free Facial Landmark Fitting via Optimized Part Mixtures and Deformable Shape Model
• Robust Sparse Coding for Face Recognitioncode
• Sparse Representation or Collaborative Representation: Which Helps Face Recognition?code

Gradient-domain image processing

• Distributed Gradient-Domain Processing of Planar and Spherical Images
• GradientShop:A Gradient-Domain Optimization Framework for Image and Video Filtering
• Local Laplacian Filters: Edge-aware Image Processing with a Laplacian Pyramid
• Domain Transform for Edge-Aware Image and Video Processing
• Image Smoothing via L 0 Gradient Minimization
• Guided image filtering
• Gaussian curvature filtering for spectrally regularized surfacescode

Video coding

• MPEG-1/2 reference software
• H.263/H.263+ reference software
• MPEG4 reference software (MoMuSys version)
• H.264/AVC reference software
• 3D SPIHT video codingcode
• DISCOVER video codec for DVC
• HEVC (H.265) Refence model in development

Texture/Shape/Image classification

• Wavelet-based GDD and KL-distancecode
• Local binary pattern (LBP) based
• Filter bank based at Visual Geometry Group
• A Completed Modeling of Local Binary Pattern Operator for Texture Classificationcode
• Shape Classification Using the Inner-Distancecode
• Deformed Lattice Detectorcode
• Ensemble Projection for Semi-supervised Image Classification

Object detection/recognition

• Adaboost method   code
• Biologically inspired object recognition code
• Hierarchical Models of Object Recognition in Cortex code
• Scalable recognition with a vocabulary treeCode
• Shock graphscode
• Shape contexts code
• Robust nonrigid point matching  Code
• Histograms of Oriented Gradients (HOG)code
• Pyramid histogram of oriented gradients (PHOG)
• Beyond Bag of featuresCode
• SuperParsingCode
• Aggregating Gradient Distributions into Intensity Orders
• Matching Local Self-Similarities across Images and Videoscode (third-party implementation)
• Deformed lattice detection in real-world images
• Feature-Centric Efficient Subwindow Searchcode
• Poselets: Body Part Detectors Trained Using 3D Human Pose Annotationscode
• Ensemble of Exemplar-SVMs for Object Detection and Beyond
• Discriminative Learning of Relaxed Hierarchy for Large-scale Visual Recognitioncode
• Multiple Kernels for Object Detection
• Ensemble of Exemplar-SVMs for Object Detection and Beyond
• Towards Total Scene Understanding: Classification, Annotation and Segmentation in an Automatic Framework
• Object Bank: A High-Level Image Representation for Scene Classification and Semantic Feature Sparsification
• Informative Feature Selection for Object Recognition via Sparse PCAcode
• Linear Spatial Pyramid Matching using Sparse Coding for Image Classificationcode
• Locality-constrained Linear Coding for Image Classificationcode
• MIT LabelMe Open Annotation tool
• Stream-based Joint Exploration-Exploitation Active Learningcode
• BoF meets HOG: Feature Extraction based on Histograms of Oriented p.d.f Gradients for Image Classificationcode
• Discriminatively trained deformable part models
• Joint Deep Learning for Pedestrian Detection

Image registration/mosaicing/OFE

• Affine SIFT (ASIFT) with online demo
• SIFT Flow: Dense Correspondence across scenes
• Lukas-Kanadealgorithm codecode2
• SIFT feature correspondencecode code2 code3
• Localbinary pattern (LBP)  code
• Speed up robust features (SURF)
• Compact And Real-time Descriptors (CARD)
• Maximallystable extremal regions (MSER) code
• Graph-cutbased  optical flow estimation  code
• Pyramid-basedhierarchical motion estimation Code
• AffineMotion Estimation for Medical Image Registration Code
• Afrequency-domain approach toward image registration Code
• Blended Intrinsic Maps
• An Efficient Earth Mover's Distance Algorithm for Robust Histogram Comparisoncode
• Diffusion Distance for Histogram Comparisoncode
• Coherency Sensitive Hashing
• Fast Template Matching in Non-Linear Tone-Mapped Imagescode
• BRIEF: Binary Robust Independent Elementary Features
• Autostitch developed for Apple iPhone
• Ztitch developed for Windows Phone
• Image Matching using Local Symmetry Features
• Secrets of optical flow estimation and their principles(Matlab code)
• Segmentation Based Variational Model for Accurate Optical Flow Estimation(Code)
• Total variation regularization of local-global optical flow
• Motion Detail Preserving Optical Flow Estimation
• Large displacement optical flow: descriptor matching in variational motion estimationcode
• FAsT-Match: Fast Affine Template Matching
• Pose-free Facial Landmark Fitting via Optimized Part Mixtures and Deformable Shape Model
• Deformable Spatial Pyramid Matching for Fast Dense Correspondences
• Nonlocal sparse and low-rank regularization for optical flow estimationcode

Action/event/scene recognition

• Human Activity Detection from RGBD Images
• Action MACH: a spatio-temporal maximum average correlation height filter for action recognition
• Evaluation of local spatio-temporal features for action recognition
• 2D Action Recognition Serves 3D Human Pose Estimation
• Hierarchical Mean Shift, Space-Time Segmentation and Action Recognition
• Human Activity Recognition with Metric Learning
• A Hough Transform-Based Voting Framework for Action Recognition
• Learning hierarchical spatio-temporal features for action recognition with independent subspace analysis
• Recognizing Scene Viewpoint using Panoramic Place Representation
• Multimodal Decomposable Models for Human Pose Estimation

Visual tracking

• Object detection and tracking in motion sequence
• Incremental Learning for Robust Visual Trackingcode
• Online Visual Tracking with Histograms and Articulating Blockscode

• Kanade-Lucas-Tomasi Feature Tracker

• SIFT keypoint detectorcode2code3
• Speeded-Up Robust Features (SURF)
• Histogram of oriented gradients (HOG) based human detection
• HOGgles: Visualizing Object Detection Features
• Visual tracking using appearance model and particle filters
• Video Object Segmentation by Tracking Regionscode
• Visual tracking decomposition
• Robust Visual Tracking using L1 Minimizationcode
• Visual Tracking via Adaptive Structural Local Sparse Appearance Model
• Robust Object Tracking via Sparsity-based Collaborative Model
• Discrete-Continuous Optimization for Multi-Target Tracking
• Multi-Target Tracking by Continuous Energy Minimization
• Distribution Fields for Tracking
• Least Soft-threshold Squares Trackingcode
• HOGgles: Visualizing Object Detection Features
• Online Robust Non-negative Dictionary Learning for Visual Tracking
• The Way They Move: Tracking Targets with Similar Appearance
• Real-time compressive tracking

Saliency/Objectness Detection

• Learning to Detect A Salient Objectcode (third-party implementation)
• Dynamic visual attention: searching for coding length incrementscode
• What is an object?
• Saliency Detection: A Spectral Residual Approach
• Image Classification: An Integration of Randomization and Discrimination
  in A Dense Feature Representation
• Saliency filters: contrast based filtering for salient region detectioncode
• Global Contrast based Salient Region Detection
• Frequency-tuned salient region detection
• Saliency, attention, and visual search: An information theoretic approach
• Saliency detection using maximum symmetric surround
• Segmenting salient objects from images and videos
• Static and space-time visual saliency detection by self-resemblance
• SUN: A bayesian framework for saliency using natural statistics
• Saliency estimation using a non-parametric low-level vision model
• model of saliency-based visual attention for rapid scene analysis
• Graph-based visual saliency
• Context-aware saliency detection
• Salient region detection and segmentation
• Automatic salient object segmentation based on context and shape prior
• Saliency Detection via Graph-based Manifold Ranking
• Kernel Null Space Methods for Novelty Detection
• Efficient Salient Region Detection with Soft Image Abstraction
• A Unified Approach to Salient Object Detection via Low Rank Matrix Recovery
• Saliency Optimization from Robust Background Detectioncode

 

Low rank methods

• Efficient Computation of Robust Low-Rank Matrix Approximations in the Presence of Missing Data using the L1 Normcode
• Low-Rank Matrix Recovery and Completion via Convex Optimization
• Predictive low-rank decomposition for kernel methods
• Improved Nyström Low-rank Approximation forScalable Manifold Learning
• RASL: Robust Batch Alignment of Images by Sparse and Low-Rank Decomposition
• TILT: Transform Invariant Low-rank Textures
• Nonlocal sparsity regularized image restoration: a low-rank approachcode
• Bayesian Robust Matrix Factorization for Image and Video Processing
• Motion Saliency Detection Using Low-rank and Sparse Decompositioncode
• Low-rank Modeling and its Applications in Image Analysis
• Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation

Deep Learning

• DeepLearnToolbox
• Deep Belief Networks
• Convolutional deep belief network
• Learning Deep Boltzmann Machines
• Conditional RBMs/DBNs
• Neocognitron
• Convolutional/Deconvolutional networks
• Invariant scattering convolution network
• Marginalized Stacked Denoising Autoencoders
• Joint Deep Learning for Pedestrian Detection
• Pedestrian Parsing via Deep Decompositional Neural Network
• Deep Learning Identity Preserving Face Space
• Deep Convolutional Network Cascade for Facial Point Detection

Manifold learning and embedding

• A Global Geometric Framework for Nonlinear Dimensionality Reduction   code
• Nonlinear Dimensionality Reduction by Locally Linear Embedding  code
• Laplacian Eigenmaps code
• Diffusion mapscode
• Manifold learning toolbox&demo
• Learning distance metric
• Diffusion processes for retrieval

Wavelets and frames

• Emergence of simple-cell receptive field properties by learning a sparse code for natural imagescode
• A Wavelet Tour of Signal Processing Wavelab
• Steerable PyramidmatlabPyrtools.tar.gz
• Rice Wavelet Toolboxrwt.zip
• Contourlet and Ridgelet Toolbox   download
• Beamlet and Curvelet Toolbox   Beamlab
• Complex wavelet Toolbox   download
• Wavelet/bandelet Toolbox at Matlab Central
• MCALab
• Differentiation of discrete multidimensional signalscode
• The finite ridgelet transform for image representationcode
• Framing pyramidscode
• Contourlet transform: an efficient directional multiresolution image representationcode
• Directional multiscale modeling of images using the contourlet transformcode
• The nonsubsampled contourlet transform: Theory, design, and applicationscode
• Multidimensional directional filter banks and surfaceletscode
• 3D Discrete Shearlet Transform and Video Processingcode

Compressed Sensing

• l1-Magic
• SparseLab
• GPSR
• ell-1 LS: Simple Matlab Solver for ell-1-Regularized Least Squares Problems
• sparsify
• MPTK: Matching Pursuit Toolkit
• Bayesian Compressive Sensing
• SPGL1: A solver for large scale sparse reconstruction
• sparseMRI
• FPC
• CVX
• Chaining Pursuit
• Regularized OMP
• SPARCO: A toolbox for testing sparse reconstruction algorithms
• TwIST
• Compressed Sensing Codes
• Fast CS using SRM
• FPC_AS
• Fast Bayesian Matching Pursuit (FBMP)
• SL0
• Sparse recovery using sparse matrices
• PPPA
• Compressive sensing via belief propagation
• SpaRSA
• KF-CS: Kalman Filtered CS (and other sequential CS algorithms)
• Fast Bayesian CS with Laplace Priors
• YALL1
• TVAL3
• RecPF
• Basis Pursuit DeQuantization (BPDQ)
• k-t FOCUSS
• Sub-Nyquist sampling: The Modulated Wideband Converter
• Threshold-ISD
• A Sparse Learning Package
• Model-based Compressive Sensing Toolbox
• Sparse Modeling Software
• Spectral Compressive Sensing Toolbox
• CS-CHEST: A MATLAB Toolbox for Compressive Channel Estimation
• DictLearn: A MATLAB Implementation for Dictionary Learning
• SPAMS
• Peformance benchmark of l1-optimization algorithms
• BM3D-based compressed sensing
• Compressed sensing using belief propagation
• Model-based Compressed Sensing
• Bayesian Compressive Sensing
• Latent Variable Graphical Model Selection via Convex Optimizationcode

HDR/RGBD imaging

• HDR image rendering using a retinex-based adaptive filter
• Digital Camera Workflow for HDR Images Using a Model of Retinal Processing
• HDR image rendering by iCAM06 model
• Rafal Mantiuk's research on HDR imaging
• Binocular Tone Mapping
• High dynamic range imaging and tonemapping
• Indoor Segmentation and Support Inference from RGBD Images
• Unsupervised Feature Learning for RGB-D Based Object Recognition
• Image Guided Depth Map Upsampling

Biomedical Imaging

• SparseMRI Toolbox
• Image reconstruction toolbox
• medical image registration
• Level set based medical image segmentation
• Gradient vector flow
• Compressed sensing image reconstruction via recursive spatially adaptive filtering
• multiresolution celluar image classification
• multirate fluorescence microscopy image acquisition
• Nonlocal MRI Upsampling
• Joint image reconstruction and sensitivity estimation in SENSE (JSENSE)code
• Nonlinear GRAPPA: a kernel approach to parallel MRI reconstructioncode
• MR image reconstruction from highly undersampled k-space data by dictionary learning
• k-t FOCUSS
• k-t SLR: Accelerated dynamic MRI using low rank and sparse penalties
• Low-Rank Modeling of Local k-Space Neighborhoods (LORAKS) for Constrained MRI
• k-t SPARSE SENSE
• ESPIRiT: Programming Library and Software Toolbox for Compressed Sensing and Parallel Imaging

2D Phase Unwrapping

• Graph cut based 2D Phase unwrapping  code
• Unwrapping MR phase images by a Markov random field modelcode
• Satellite radar interferometry - Two - dimensional phase unwrappingcode
• Phase unwrapping algorithmsfor radar interferometry: residue-cut,least-squares, and synthesis algorithms code

DTI and fiber tractography

• DSI Studio
• FMRIB
• dtiQuery
• Camino
• NAMIC

Data Clustering

• Unsupervised learning of finite mixture modelscode
• Affinity propagation
• On Spectral Clustering: Analysis and an algorithmcodecode2 code3
• Nonnegative matrix factorization (NMF)code2code3
• Computing nonnegative tensor factorizations
• Fast kmeans via triangle inequality
• FastANN and FastCluster for approximate kmeans
• kdtree-based NN/kNN searchfast kNN search code2
• RANSAC toolbox for robust fitting
• Clustering Through Ranking On Manifoldscode
• Correlation clustering optimization
• Hybrid Linear Modeling via Local Best Flatscode

Stereo matching& Multiview geometry

• A taxonomy and evaluation of dense two-frame stereo correspondence algorithmscode
• Graph cut based stereo matching   code
• Belief propagation based stereo matchingcode
• A roadmap to the integration of early visual modules Code
• Adaptive support-weight approach Code
• Energy minization based stereo matching
• Energy Based Multiple Model Fitting for Non-Rigid Structure from Motioncode
• Recognizing Scene Viewpoint using Panoramic Place Representation
• A Closed-Form Solution to Uncalibrated Photometric Stereo via Diffuse Maxima
• Patch-based Multi-view Stereo (PMVS)
• Library for Efficient Large-scale Stereo Matching

Graphics, Cartoons,Motion&3D

• Apparent Layer Operations for the Manipulation of Deformable Objects

• 2.5D cartoon models
• 3D modeling with sihouettes
• Real-time Large-deformation Substructuring
• Generalized biped walking control
• Locomotion Skills for Simulated Quadrupeds
• Action Recognition from a Distributed Representation of Pose and Appearance
• RECON: Scale-Adaptive Robust Estimation via Residual Consensuscode
• How Do Humans Sketch Objects?
• Manifold Exploration: A Markov Chain Monte Carlo technique for rendering scenes with difficult specular transport
• Exploring Collections of 3D Models using Fuzzy Correspondences
• Illuminant Chromaticity from Image Sequences
• Network Principles for SfM: Disambiguating Repeated Structures with Local Context

 

Machine learning&Neural Networks

• Resource collection at UC-Merced
• Belief propagation/Sum-Product Algorithmcode
• Deep Boltzmann Machines
• Shape Boltzmann machine: a strong model of object shapes
• Support vector machine
• Liblinear for large linear classification
• Object detection with Boosting
• Convolutional/Deconvolutional networks
• Hopfield networkscode
• Self-organizing map (SOM) Toolbox
• Reservoir Computing Toolbox
• Polychronization: Computation With Spikes
• Slowly coupled oscillators: phase dynamics and sync
• Liquid State Machines(LSM)code
• Sparse Coding Neural Gascode
• Echo state networks for harnessing nonlinearitycode
• Fast Approximate Nearest Neighbors with Automatic Algorithm Configuration
• Sum-Product Networks: A New Deep Architecturecode
• Deformable graph matchingcode

Blind source separation

• Shiro Ikeda's page of Blind Source Separation
• Independent Component Analysis by JV Stone
• Blind source separation via Independent component analysis
• ICALab for image processing
• Separating a Real-Life Nonlinear Image Mixture

Camera calibration

• A toolbox containing several camera calibration techniques
• A flexible new technique for camera calibration
• Geometric Camera Calibration Using Circular Control Points
• A New Mirror-based Extrinsic Camera Calibration Using an Orthogonality Constraint

Sampling&Physics-based Simulation

• Poisson-disk sampling

• Filtering solid Gabor noise
• Gabor Noise by Example
• Guided Exploration of Physically Valid Shapes for Furniture Design
• Efficient Geometrically Exact Continuous Collision Detection
• Illuminant Chromaticity from Image Sequences

Evolutionary computing/Optimization

• Ant colony optimization
• Genetic algorithm toolbox
• Particle Swarm Optimization Toolbox
• Cache-efficient graph cuts on structured grids

Networking Research

• The network simulator (ns-2)
• NetSim at Tetcos
• LBNL's software releases

Miscellaneous

• Simple model of spiking neuronsspike train analysis
• Visual pattern recognition by moment invariantscode
• Direct LS-based ellipsis fitting code
• DACE: a MATLAB Kriging toolbox
• Inference packagefor undirected graphical models
• Kernel smoothingtoolbox
• CMUstatistics library collections
• Rice DSP software release
• Complexnetwork toolbox
• DistLearnKit: a MATLABToolkit for distance metric learning
• Subspace segmentationsource code distribution
• Multiview geometry and 3D reconstruction
• A probabilistic image jigsaw puzzle solver
• Non-Iterative Approach for Fast and Accurate Vanishing Point Detectioncode
• Affine registration of 2d point sets
• Rotation Invariant Nonrigid Point Set Matching in Cluttered Scenescode
• Tensor Product model transformation (for control design)
• N-way toolbox (more versatile than the above one but slower)
• Simple Formulas For Quasiconformal Plane Deformations
• An Analytic Model for Full Spectral Sky-Dome Radiance
• Implementation of a Low-Depth of Field Picture Classifier
• Decoding, Calibration and Rectification for Lenselet-Based Cameras

Links to other communities' reproducible research effort

• Geostatistics toolboxmgstat DACE
• Error Correcting Codes (ECC)
• Face recognition software at face-rec.org
• Computer graphicsgraphics papers on the web
• Computer visionCV papers on the web
• Machine learning
• Google Sites on Compressed Sensing
• Google Sites on Matrix Factorization
• DMOZ Open Directory Project
• MATLAB toolbox collection at Plymouth
• Neurophysiological data analysis
• VLFeat library for open-source CV
• Algorithms and source code for Quality&Technology
• Video-based human action detection resources
• Data compression resources
• Deep learning (including DBM and RBM)
• Computational Topology
• Open Remote Sensing Website

Links to reproducible books/journals/tutorials

• Image Processing Online (IPOL)
• Gradient Domain Manipulation Techniques in Vision and Graphics
• Statistical and Structural Recognition of Human Actions
• Distance functions and metric learning
• Feature Learning for Image Classification
• Recognizing and Learning Object Categories
• Physics-Based Human Motion Modelling for People Tracking
• 3d Shape Reconstruction from Photographs: a Multi-View Stereo Approach
• Deblurring Images: Matrices, Spectra, and Filtering
• Natural image statistics
• Spikes, decisions & actions
• Multiple view geometry in computer vision
• Collective Animal Behavior
• Signal Processing Techniques for Spike Train Analysis using MatLab
• Image Processing Online (IPOL) (many excellent c-coded source codes)

Links to other individual's reproducible research

• Abhinav Gupta 's research code release
• Adrian Barbu's research codes release
• Al Hero's Lab and his reproducible research
• Alexei Efros' research codes release
• Allen Yang's research codes release
• Amir Beck's work on optimization theory and applications
• Amir Saffari'sreproducible reseach code releases
• Amit Agrawal's Matlab and C codes
• Anand Rangarajan 's matlab codes on hisreproducible research
• Anat Levin's matlab codes release
• Andrew Davison's work on Computational neuroscience
• Ann Lee's Diffusionmaps and treelet
• Andrew Zisserman'svisual geometry group source codes
• Antonio Torralba's research codes release
• Ashok Veeraraghavan'sreproducible research code release
• Ayan Chakrabarti'sreproducible research code release
• Bahadir Gunturk's research code release
• Bill Freeman's software release on his group'sreproducible research
• Bob Kass' research codes on neuronal data analysis
• Ce Liu's software release on hisreproducible research
• Chih-Chung Hsu's research code release
• Chih-Jian Lin's machine learning software release
• Chih-Yuan Yang's research code release
• Christopher Kanan'sreproducible research code release
• Chuck Anderson's matlab codes on NNs and reinforcement learning
• Chunming Li's research code release
• Claude Knaus' research codes release
• Dafeng Sun's matlab codes release
• Dan Ellis' MATLAB Audio Processing Examples
• Daniel DeMenthon's research code release
• Daniel Huttenlocher 's research code release
• Daniel Zoran's research code release
• Danny Harari's software release
• David Heeger's toolboxes
• Deqing Sun'sreproducible research code release
• Derek Hoiem's research software release
• Deva Ramanan's work on object recognition
• Dror Baron's research software release
• Dimitri Van De Ville 's research codes release
• Emmanuel Candes' software release
• Emanuel Todorov's research codes release
• EPFL CVLab's research codes release
• Eugene M. Izhikevich's matlab codes on NNs
• Fei-fei Li's research code release
• Gaofeng Meng's research code release
• Guoping Qiu's research codes release
• Graham Taylor's source codes release
• Guy Gilboa's matlab codes on PDE-based image processing
• Haibin Ling's research codes release
• Haichao Zhang's research codes release
• Hanchun Peng's software release
• Hao Jiang's research code release
• H.J. Seo's interesting collection of everything
• Honglak Lee's research code release
• Huchuan Lu's research codes release
• Huifung Poo's research codes release
• Human sensing @CMU's software release
• INRIA LEAR research codes release
• IPL (Politechnico di Torino)'s research codes release
• Jason Corso's research codes release
• Jalal Fadili's source codes on sparse representation
• James Hays' research code release
• Javier Portilla's research codes release
• Jelena Kovacevic's bimagicLab: Software
• Jeffrey A. Fessler's matlab codes release
• Jia-bin Huang's Awesome Computer Vision website
• Jian Sun's research code release
• Jian Zhang's research code release
• Jianbo Shi's software release
• JianChao Yang's sourcecodes on image classification and super-resolution
• Jianxiong Xiao's research codes release
• Jiaya Jia's programs and executables
• Jieping Ye's research codes release
• John Paisley's research code release
• Jon Wellner's work on statistics
• Jose M. Bioucas Dias' research codes release
• Julien Mairal's research code release
• Jun Li's research codes release
• Junzhou Huang's research codes release
• Justin Haldar's research code release
• Kai Yu'sreproducible research codes release
• Kaihua Zhang's research code release
• Keigo Hirakara's research codes release
• Kilian Q. Weinberger 's research code release
• Kevin Murphy's Bayes Net Toolbox for Matlab
• Kyoung Mu Lee 's software release
• Laurens van der Maaten's software collection
• LaurentPerrinet's SparseHebbianlearning source codes
• Lawrence Carin's research code release
• LCAV's reproducible research at EPFL
• LEAR's learning and recognition in vision
• Lei Zhang's MATLAB codes releases
• Leo Grady's matlab codes on hisreproducible research
• Leslie Ying's research codes release
• Lina Karam's research software release
• Mahdi Soltanolkotabi 's research code release
• MalcolmA. MacIver's AnimalLab
• Marco Zuliani'sreproducible research codes release
• Mariana S. C. Almeida 'sreproducible research code release
• Mark A. Davenport's research code release
• Mark Schmidt's reseach on learning on probabilistic graphical models
• MATTHIAS J. EHRHARDT's research code release
• Matthew Zeiler'sreproducible research code release
• MD Anderson Cancer Center: Bioinformatics
• Michael Elad'ssource code collection on his research
• Michael J. Brown's research codes release
• Michal Cernansky's research code release
• Michael Lustig's research code release
• Miguel Á. Carreira-Perpiñán 's research software release
• Mikel Rodriguez's source codes release
• Minmin Chen'sreproducible research code release
• Ming-ming Chen'sreproducible research code release
• Ming-Hsuan Yang'sreproducible research works
• Mingyuan Zhou's research codes release
• Naiyan Wang's research codes release
• Neil Lawrence's reproducible research in machine learning
• Ofir Pele's research codes release
• Onur Guleryuz's research codes release
• Owen Carmichael's software release
• Pascal Getreuer's software release
• Patrik O Hoyer's source code collection on hisreproducible research
• Paven Turaga's research code release
• Pedro Domingos' research codes release
• PF Felzenszwalb 's research codes release
• Penn State LPAC research code release
• Peter Getreuer'sreproducible research code release
• Peter Kovesi's matlab functions for CV and image processing
• Peyman Milanfar'sresearch code release
• Philipp Krahenbuhl's research codes release
• Qi Wei's research code release
• Qingxiong Yang's research codes release
• Quoc V. Le's research codes release
• Rene Vidal's Visionlabreproducible research code release
• Raj Gupta'sreproducible research code release
• Radu Timofte's research code release
• Raquel Urtasun 's research codes release
• Rick Chartland's release on hisreproducible research
• Robert Nowak's source code release
• Ruslan Salakhutdinov's research codes release
• Scott Acton's research software releases
• Shai Bagon's Matlab Code
• Shaoting Zhang'sreproducible research code release
• Simoncelli's LCVreproducible research codes release
• Sinisa Todorovic'sreproducible research codes release
• Song-chun Zhu's source codes on image segmentation and active basis
• Stanley Chan's research codes release
• Takumi Kobayashi's research code release
• Thomas Brox's research codes release
• Tony Xu Han'sreproducible research code release
• UCF vision lab source code collection
• UIUC's salient patch feature collection
• USC's iLab Neuromorphic Vision C++ Toolkit
• UWO vision labreproducible research code release
• Vanderbilt's StatReport
• Vladimir Kolmogorov's research codes release
• Wavelab (at Univ. of Salzburg) software release
• WILLOW's research code release
• Wotao Yin's research code release
• Xavier Bresson's source codes accompanying his papers on image processing
• Xiaodi Hou's research codes release
• Xiaofei He's dimensionality reduction source code collection
• Xiaofeng Ren's research codes release
• Xiaogang Wang's research codes release
• Xiaolin Wu's research codes release
• Xiaoming Huo's software release
• Xiaoou Tang's MM Lab research code release
• Xiaowei Zhou's research code release
• Xubo Song's matlab codes on herreproducible research
• Yair Weiss' research codes release
• Yi Ma's source code collection on hisreproducible research
• Yi Wang's research codes release
• York vision research center's software release
• Yu-wing Tai'sreproducible research code releases
• Yuanjie Zheng's source codes release
• Yue M Lu's source codes on hisreproducible research
• Yue Wang at VT-CBIL's research code release
• Zhilin Zhang's research codes release
• Zhoulin Jiang's research code release
• Zhuowen Tu's research code releases

Google Scholar is great but if most papers in computational sciences could be accessed along with their source codes (not just the citation number), the world for scientific researchers will be even better. It is easy to find papers these days but when can finding the source codes of a paper become easy too? I think Don Knuth's old-day advices onLiterate Programmingare still relevant to the current state of reproducible research. I believe that the time is ripe for significantly promoting experimentally reproducible research (just like mathemathetical theories - mentally reproducible research), and that we can best achieve this by considering research codes to be works of literature (so they can be easily picked up by other researchers).Only when the reproducibility of research in computational science becomes a default instead of a luxury, can we look further by standing on each other's shoulders.
 
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