644 Works

Exploratory subgroup analysis of the SEAQUAMAT trial using Random Forests: a generic template for the ML analysis of RCT data with binary outcomes

James Andrew Watson & Chris Holmes
This computational notebook (written in R) runs an exploratory subgroup analysis on the SEAQUAMAT trial data. This implements and illustrates the concepts of Holmes & Watson (2018) for exploratory subgroup analysis using Machine Learning protocols with valid control of the type I error. SEAQUAMAT was a multi-centre randomised controlled trial comparing mortality between intravenous quinine and intravenous artesunate in adults with severe malaria in South East Asia. The code is as generic in order to...

Code for: Self-esteem, relationship threat, and dependency regulation: Independent replication of Murray, Rose, Bellavia, Holmes, and Kusche (2002) Study 3

Lorne Campbell, Rhonda N. Balzarini, Taylor Kohut, Kiersten Dobson, Christian M. Hahn, Sarah E. Moroz & Sarah C.E. Stanton
Across three studies, Murray, Rose, Bellavia, Holmes, and Kusche (2002) found that low self-esteem individuals responded in a negative manner compared to those high in self-esteem in the face of relationship threat, perceiving their partners and relationships less positively. This was the first empirical support for the hypothesized dynamics of a dependency regulation perspective, and has had a significant impact on the field of relationship science. In the present research, we sought to reproduce the...

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...

MATLAB Code to Correct for CdTe Escape Peaks

Md Foiez Ahmed & Selcuk Yasar
This is a MATLAB script to correct for distortion observed in x-ray spectra measured using Cadmium Telluride (CdTe) detector due to so call escape events. To use this code, one needs to have access to the measured spectra and the CdTe detector efficiency files along with escape probabilities at Cd or Te x-ray fluorescence peaks (can be obtained using Monte Carlo codes, as are given here: for four Cd/Te peaks calculated using Geant4).

Cognition Open Data (COD) Reproducibility Report: DFDwT

Tom Hardwicke
This is one of 35 analytic reproducibility reports arising from the Cognition Open Data (COD) project. DFDwT is the ID code used to refer to this specific report. The COD project involved attempting to reproduce a subset of key target outcomes reported in 35 articles published in the journal Cognition by repeating the original analyses upon the original data. For more details, please visit the Open Science Framework project: https://osf.io/wn8fd/.

MMSE-based analytical estimator for uncertain power system with limited number of measurements

Hasnae Bilil & Hamid Gharavi
We propose a new state estimation method referred to as `mean squared estimator' (MSE) to deal with the uncertain nature of the power system parameters. The estimator aims at achieving minimum mean squared error (MMSE) and benefits from the prior study of SPF, which involves the probability density functions (PDF's) of the system parameters. The main advantage of this estimator is based on its ability to instantaneously incorporate the dynamics of the power system. Moreover,...

MAPS: Optimized GPU and Multi-GPU Programming Framework

Tal Ben-Nun, Ely Levy, Amnon Barak & Eri Rubin
MAPS (Memory Access Pattern Specification) is an open-source, header-only C++ CUDA template library for automatic multi-GPU programming and optimization of GPU kernels, implementing the Memory-Oriented Programming model. The framework leverages memory access patterns to provide near-optimal performance on various architectures. Using MAPS: - Automatically produces optimized GPU code - Separates complex indexing and shared memory optimizations from the algorithm - Transparently manages multi-GPU memory segmentation and inter-GPU communication - Provides familiar STL-based interfaces (containers and...

An LMI Approach to Stability Analysis of Coupled Parabolic Systems

Masashi Wakaiki
This module is for stability analysis of coupled parabolic partial differential equations. The analysis is based on linear matrix inequalities.

The Choquet Integral Neuron (PyTorch)

Muhammad Aminul Islam, Derek T. Anderson, Anthony J. Pinar, Timothy C. Havens, Grant Scott & James M. Keller
Information fusion is an essential part of numerous engineering systems and biological functions, e.g., human cognition. Fusion occurs at many levels, ranging from the low-level combination of signals to the high-level aggregation of heterogeneous decision-making processes. While the last decade has witnessed an explosion of research in deep learning, fusion in neural networks has not observed the same revolution. Specifically, most neural fusion approaches are ad hoc, are not understood, are distributed versus localized, and/or...

SIFTpack: a compact representation for efficient SIFT matching

Alexandra Gilinsky & Lihi Zelnik-Manor
Computing distances between large sets of SIFT descriptors is a basic step in numerous algorithms in computer vision. When the number of descriptors is large, as is often the case, computing these distances can be extremely time consuming. We propose the SIFTpack: a compact way of storing SIFT descriptors, which enables significantly faster calculations between sets of SIFTs than the current solutions. SIFTpack can be used to represent SIFTs densely extracted from a single image...

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

Ruibang Luo
16GT is a variant caller utilizing a 16-genotype probabilistic model to unify SNP and indel calling in a single algorithm. 16GT is easy to use. The default parameters will fit most of the use cases with human genome. For the detailed parameters for each module, please run the module to get an info.

NoSE: NoSQL Schema Evaluator

Michael J. Mior, Kenneth Salem, Ashraf Aboulnaga & Rui Liu
This algorithm comprises the core of NoSE: a schema design tool for NoSQL databases. More information is available at https://michael.mior.ca/projects/nose/.


Heman Gharibnejad, Barry I. Schneider, Mark Leadingham & Henry J. Schmale
This is a FORTRAN code for a 1 dimensional atom model interaction with a laser pulse following the description given in the journal paper: J. Javanainen, J. H. Eberly, and Qichang Su, “Numerical simulations of multiphoton ionization and above-threshold electron spectra,” Phys. Rev. A, vol. 38, no. 7, pp. 3430--3446, 1988.

Schema Perception

Christopher Baldassano, Uri Hasson & Kenneth A Norman
This capsule demonstrates the analyses described in "Representation of real-world event schemas during narrative perception" by Baldassano, Hasson, and Norman. We analyzed fMRI data from 44 human subjects presented with sixteen three-minute stories, consisting of four schematic events drawn from two different scripts (eating at a restaurant or going through the airport). Aside from this shared script structure, the stories varied widely in terms of their characters and storylines, and were presented in two highly...

Channel Training for Analog FDD Repeaters: Optimal Estimators and Cramér-Rao Bounds

Stefan Wesemann & Thomas Marzetta
For frequency division duplex channels, a simple pilot loop-back procedure has been proposed that allows the estimation of the UL & DL channels at an antenna array without relying on any digital signal processing at the terminal side. For this scheme, we derive the maximum likelihood (ML) estimators for the UL & DL channel subspaces, formulate the corresponding Cramér-Rao bounds and show the asymptotic efficiency of both (SVD-based) estimators by means of Monte Carlo simulations....

Universal Formulation of PDE Stability Analysis via SOS

Matthew M. Peet
An implementation of the stability analysis test for a universal class of PDEs in a single spatial variable on a bounded domain.

Distributionally Robust and Multi-Objective Nonnegative Matrix Factorization

Nicolas Gillis, Le Thi Khanh Hien, Valentin Leplat & Vincent Tan
This Matlab code allows you to solve the NMF problem where the objective function is a weighted sum of several β-divergences measuring the error between the input matrix X and the factorization WH, where W≥0 and H ≥0. It also allows you to solve the distributionally robust NMF (DR-NMF) problem where the goal is to minimize the maximum value among the β-divergences. See the paper N. Gillis, L. T. K. Hien, V. Leplat, V. Y....

CULP: Classification Using Link Prediction

Seyed Amin Fadaee & Maryam Amir Haeri
This is the implementation of the CULP classification algorithm from the paper Classification Using Link Prediction. Abstract: Link prediction in a graph is the problem of detecting the missing links that would be formed in the near future. Using a graph representation of the data, we can convert the problem of classification to the problem of link prediction which aims at finding the missing links between the unlabeled data (unlabeled nodes) and their classes. To...

Identifying Gene Expression Programs of Cell-type Identity and Cellular Activity with Single-Cell RNA-Seq

Dylan Kotliar, Adrian Veres, M. Aurel Nagy, Shervin Tabrizi, Eran Hodis, Douglas A. Melton & Pardis C. Sabeti
This capsule is meant to accompany a manuscript "Identifying Gene Expression Programs of Cell-type Identity and Cellular Activity with Single-Cell RNA-Seq." It includes all of the analysis and libraries to recapitulate the figures and computations in this manuscript. Identifying gene expression programs underlying both cell-type identity and cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although single-cell RNA-Seq (scRNA-Seq) can quantify transcripts in individual...

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.

TVA-based simulation of temporal order judgments (TOJs)

Jan Tünnermann
Just a simple simulation of the TVA-based TOJ model, which we have used in several publications. The script will simulate Whole Report (of two stimuli) and Temporal-Order Judgment data at fine grained levels. Different levels can be set in the code. All other parameters can be set in the interface.

Multi-Scale Patch-Based Image Restoration - Denoising

Vardan Papyan & Michael Elad
Many image restoration algorithms in recent years are based on patch-processing. The core idea is to ecompose the target image into fully overlapping patches, restore each of them separately, and then merge the results by a plain averaging. This concept has been demonstrated to be highly effective, leading often times to state-of-the-art results in denoising, inpainting, deblurring, segmentation, and other applications. While the above is indeed effective, this approach has one major flaw: the prior...

Expected Improvement Matrix-Based Infill Criteria for Expensive Multiobjective Optimization (Matlab code)

Dawei Zhan, Yuansheng Cheng & Jun Liu
The existing multiobjective expected improvement (EI) criteria are often computationally expensive because they are calculated using multivariate piecewise integrations, the number of which increases exponentially with the number of objectives. In order to solve this problem, this paper proposes a new approach to develop cheap-to-evaluate multiobjective EI criteria based on the proposed EI matrix (EIM). The elements in the EIM are the single-objective EIs that the studying point has beyond each Pareto front approximation point...

DEIP - Discontinuous Element Insertion Program

Timothy Truster
DEIP is a MATLAB/OCTAVE toolbox for inserting zero-thickness elements into a continuous finite element mesh in two and three dimensions. These elements are used for intrinsic cohesive zone modeling and for the Discontinuous Galerkin method. The algorithm is topology based and is suitable for complex, unstructured meshes. The code has capabilities for the following element types: - Two-dimensional meshes: 3, 4, 6, and 9-node elements - Three-dimensional meshes: 4, 5, 6, 8, 10, 14, 18,...

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