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### Code for "Community production modulates coral reef pH and the sensitivity of ecosystem calcification to ocean acidification"

Thomas DeCarlo
Script for calculating coral reef community metabolism on Dongsha Atoll (see associated paper). Metabolic rate uncertainties are estimated using Monte Carlo iterations.

### 3D Convolutional Neural Networks for Speaker Recognition

Amirsina Torfi, Nasser M. Nasrabadi & Jeremy Dawson
This code is aimed to provide the implementation for Speaker Verification (SR) by using 3D convolutional neural networks following the SR protocol.

### Exploring Causal Relationships in Visual Object Tracking

Karel Lebeda, Simon Hadfield & Richard Bowden
This folder contains source code for causality detection in visual object tracking and for causal predictions, which may be used to help a tracker. It is based on our ICCV2015 paper Exploring Causal Relationships in Visual Object Tracking, our subsequent journal paper, which is currently under review, and parts of my thesis. If you use this code in an academic work, please cite the ICCV paper (unless the follow-up journal has been already published): Lebeda,...

### Geomagnetic Field Based Indoor Landmark Classification Using Deep Learning

Bimal Bhattarai, Rohan Kumar Yadav, Hui-Seon Gang & Jae-Young Pyun
The unstable nature of RF signals and the need for external infrastructure inside buildings have limited the use of positioning techniques, such as Wi-Fi and Bluetooth fingerprinting. Compared to these techniques, the geomagnetic field exhibits a stable signal strength in the time domain.

### UniWalk: Unidirectional Random Walk Based Scalable SimRank Computation over Large Graph

Junshuai Song, Xiongcai Luo, Jun Gao, Chang Zhou, Hu Wei & Jeffrey Xu Yu
UniWalk is designed to enable the fast top-k SimRank computation over large undirected graphs. The original UniWalk is a Monte Carlo based method. It directly locates the top-k similar vertices for any single source vertex u via approximately R sampling paths originating from u only. Related work has been published in ICDE 2017 ("UniWalk: Unidirectional Random Walk Based Scalable SimRank Computation over Large Graph"). Here, in order to overcome the "rectification issue" in the original...

### FMRIPrep: a robust preprocessing pipeline for functional MRI

Oscar Esteban, Christopher J. Markiewicz, Ross W Blair., Craig A. Moodie, A. Ilkay Isik, Asier Erramuzpe, James D. Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S. Ghosh, Jessey Wright, Joke Durnez, Russell A. Poldrack & Krzysztof J. Gorgolewski
Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize data before statistical analysis. Generally, researchers create ad hoc preprocessing workflows for each new dataset, building upon a large inventory of tools available for each step. The complexity of these workflows has snowballed with rapid advances in MR data acquisition and image processing techniques. We introduce fMRIPrep, an analysis-agnostic tool that addresses the challenge of robust and reproducible preprocessing for task-based and resting...

### Java code for Quantum Processor Emulator

Andrea Bianchini
This App is a Quantum Processor Emulator entirely developed in Java. You can program emulator by entering in input file quantum_input.txt simple instructions, one for each line. Quantum computers will use two fundamental properties of the quantum world: superposition and entanglement. So, what is superposition? Qubits can be in the “|0⟩” state (called a zero-ket), the “|1⟩” state (called the one-ket), or a linear combination of the two (superposition). The half-angle bracket notation |⟩ is...

### Enhanced Just Noticeable Difference Model for Images with Pattern Complexity

Jinjian Wu, Leida Li, Weisheng Dong, Guangming Shi, Weisi Lin & C.-C. Jay Kuo
Pattern-complexity-JND-code include a main algorithom and a func_JND_modeling_pattern_complexity function algorithom. The main algorithm demo_pattern_complexity_based_JND_modelig is an implementation of the algorithm for creating the Pattern Complexity based Just Noticeable Difference Modeling.

### A Modularized Efficient Framework for Non-Markov Time Series Estimation

Gabriel Schamberg, Demba Ba & Todd P. Coleman
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"...

### An Attribute-based Availability Model for Large Scale IaaS Clouds with CARMA

Hongwu LYU, Jane Hillston, Paul Piho & Huiqiang Wang
This program models a cloud system by CARMA. * There are 3 kind of tasks arrival including burst tasks, constant tasks and periodic tasks. * And the PMs of clouds are divided into the normal resources and the slack resources, * where the normal resources consist of HOT/WARM/COLD, and the slack resources contains RESERVED/OPPORTUNISTIC. * Moreover,in the process of scheduling, the strategy of choosing a PM includes best fit, worst fit, best stochastic fit and...

### Enhancing Fundamental Energy Limits of Field-Coupled Nanocomputing Circuits

Jeferson F. Chaves, Marco A. Ribeiro, Frank S. Torres & Omar P. Vilela Neto
Energy dissipation of future integrated systems, consisting of a myriad of devices, is a challenge that cannot be solved solely by emerging technologies and process improvements. Even though approaches like Field-Coupled Nanocomputing allow computations near the fundamental energy limits, there is a demand for strategies that enable the recycling of bits' energy to avoid thermalization of information. In this direction, we propose a new kind of partially reversible systems by exploiting fan-outs in logic networks....

### Semantic Cognition Pupil

Jason Geller, Daniel Mirman & Jon-Frederick Landrigan
Semantic knowledge includes taxonomic and thematic relationships, which may comprise complementary semantic sub-systems, or a single semantic system with differing control processes. The latter view is most clearly supported by a recent report (Thompson et al., 2017) suggesting that low-strength thematic relationships (i.e., relations based on participation in the same event or scenarios) require more effort or cognitive control than low-strength taxonomic relationships (i.e., relations based on similar internal features). We tested this hypothesis in...

### r-value

Ruth Heller, Marina Bogomolov & Yoav Benjamini
The use of big data is becoming a central way of discovering knowledge in modern science. Large amounts of potential findings are screened to discover the few real ones. To verify these discoveries a follow-up study is often conducted, wherein only the promising discoveries are followed up. Such follow-up studies are common in genomics, in proteomics, and in other areas where high-throughput methods are used. We show how to decide whether promising findings from the...

### Multiscale Anomaly Detection Using Diffusion Maps

Gal Mishne & Israel Cohen
We propose a multiscale approach to anomaly detection in images, combining spectral dimensionality reduction and a nearest-neighbor-based anomaly score. We use diffusion maps to embed the data in a low dimensional representation, which separates the anomaly from the background. The diffusion distance between points is then used to estimate the local density of each pixel in the new embedding. The diffusion map is constructed based on a subset of samples from the image and then...

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

Dogac Basaran, Ali Taylan Cemgil & Emin Anarim
This project provides the implementation of the algorithm proposed in the article "Multiresolution alignment for multiple unsynchronized audio sequences using sequential Monte Carlo samplers" (https://doi.org/10.1016/j.dsp.2017.10.024). 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 https://github.com/ElsevierSoftwareX/SOFTX-D-17-00088. The difference between Code Ocean and GitHub is that the...

### Partially Blind Handovers for mmWave New Radio Aided by Sub-6 GHz LTE Signaling

Faris B. Mismar
The reproducible code for the paper 'Partially Blind Handovers for mmWave New Radio Aided by Sub-6 GHz LTE Signaling'. For a base station that supports cellular communications in sub-6 GHz LTE and millimeter (mmWave) bands, we propose a supervised machine learning algorithm to improve the success rate in the handover between the two radio frequencies using sub-6 GHz and mmWave prior channel measurements within a temporal window. The main contributions of our paper are: 1)...

### fiber Fabry-Perot with Gaussian beam propagation MATLAB Code

Kaixuan Zhang, Yves-Alain Peter & Martin Rochette
chalcogenide fiber Fabry-Perot filter with Gaussian beam propagation. Abstract: We demonstrate the first mid-infrared compatible all-fiber Fabry-Perot filter. It consists of chalcogenide fibers terminated with high-reflective coatings made of germanium and calcium fluoride. In addition to the transmission compatibility with mid-infrared wavelength, the filter has both tunability and free spectral range >350 nm as well as a finesse of 27. To demonstrate the application of the filter, a thulium-doped fiber laser is built and shows...

### Phase Congruency Parameter Optimization

Seyed Mohammad Mahdi Alavi & Yunyan Zhang
Inspired by the work of Oppenheim and Lim (IEEE Proceedings, vol. 69, pp. 529–541, 1981) who demonstrated that the phase of the image contains more information than its magnitude, I have been developing novel tools for the optimal detection of image features based on the concept of phase congruency (PC). PC principle states that image features are mainly perceived at the points where the Fourier components of the image are maximally in phase. Many papers...

### SPARTA: Sparse Phase Retrieval via Truncated Amplitude Flow

Gang Wang, Liang Zhang, Georgios B. Giannakis, Mehmet Akcakaya & Jie Chen
This is the matlab implementation of the SPARTA algorithm proposed in the manuscript "Sparse Phase Retrieval via Truncated Amplitude Flow" by G. Wang (UMN), L. Zhang (UMN), G. B. Giannakis (UMN), M. Akcakaya (UMN), and J. Chen (BIT).

### 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...

Weiwei Dai, Ivan Selesnick, John-Ross Rizzo, Janet Rucker & Todd Hudson
A parametric model for saccadic eye movement The saccade model corresponds to the 'main sequence' formula $V_p = \eta(1 - e^{-A/c})$ where $V_p$ is the peak saccadic velocity and $A$ is the saccadic amplitude and $\eta$ and $c$ are parameters of positive value.

### Who were the voters behind the Schulz effect? A long-term analysis of individual voter trajectories in the run-up to the 2017 German federal election (Wuttke/Schoen)

Alexander Wuttke & Harald Schoen
In early 2017, after the nomination of Martin Schulz as candidate for chancellor the SPD experienced a rapid surge in public support as measured in public opinion polls. For a short period the SPD seemed capable of becoming the largest party in the 2017 German federal election. Yet, the upward trend proved short-lived and the SPD ended up with the worst election result since 1949. Using data from a multi-wave panel survey, this analysis demonstrated...

### 6mer seed toxicity in tumor suppressive microRNAs: eCDF plots for toxic/nontoxic seed matches in essential and non-essential genes

Elizabeth T Bartom & Quan Q Gao
This capsule takes a set of seeds and sets of genic sequences, and checks whether different parts of genes and different sets of genes have different seed profiles for toxic and non-toxic seeds.

### Discovering Conditional Functional Dependencies

Joeri Rammelaere & Floris Geerts
The code capsule contains algorithms for the discovery of approximate conditional functional dependencies, based on support and confidence thresholds. The implementations of the algorithms are based on the existing (C)Tane and Eclat algorithms. This source code accompanies the paper "Revisiting Conditional Functional Dependency Discovery: Splitting the “C” from the “FD”.". * Abstract * Many techniques for cleaning dirty data are based on enforcing some set of integrity constraints. Conditional functional dependencies (CFDs) are a combination...

### Interactive demonstration of plateau-generating mechanisms in temporal order judgments (TOJs)

Jan Tünnermann
This capsule provides an interactive demonstration of plateau-generating mechanisms in temporal order judgments (TOJs) to accompany our publication "Stuck on a Plateau? A Model-Based Approach to Fundamental Issues in Visual Temporal-Order Judgments". The TVA-reset model assumes a processing reset when the second stimulus is presented in brief succession after the first stimulus (assumed to equal TVA's t0 parameter). The alternative range of indecision model was proposed by García-Pérez & Alcalá-Quintana.

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