110 skills found · Page 1 of 4
manodeep / Corrfunc⚡️⚡️⚡️Blazing fast correlation functions on the CPU.
Aastha2104 / Parkinson Disease PredictionIntroduction Parkinson’s Disease is the second most prevalent neurodegenerative disorder after Alzheimer’s, affecting more than 10 million people worldwide. Parkinson’s is characterized primarily by the deterioration of motor and cognitive ability. There is no single test which can be administered for diagnosis. Instead, doctors must perform a careful clinical analysis of the patient’s medical history. Unfortunately, this method of diagnosis is highly inaccurate. A study from the National Institute of Neurological Disorders finds that early diagnosis (having symptoms for 5 years or less) is only 53% accurate. This is not much better than random guessing, but an early diagnosis is critical to effective treatment. Because of these difficulties, I investigate a machine learning approach to accurately diagnose Parkinson’s, using a dataset of various speech features (a non-invasive yet characteristic tool) from the University of Oxford. Why speech features? Speech is very predictive and characteristic of Parkinson’s disease; almost every Parkinson’s patient experiences severe vocal degradation (inability to produce sustained phonations, tremor, hoarseness), so it makes sense to use voice to diagnose the disease. Voice analysis gives the added benefit of being non-invasive, inexpensive, and very easy to extract clinically. Background Parkinson's Disease Parkinson’s is a progressive neurodegenerative condition resulting from the death of the dopamine containing cells of the substantia nigra (which plays an important role in movement). Symptoms include: “frozen” facial features, bradykinesia (slowness of movement), akinesia (impairment of voluntary movement), tremor, and voice impairment. Typically, by the time the disease is diagnosed, 60% of nigrostriatal neurons have degenerated, and 80% of striatal dopamine have been depleted. Performance Metrics TP = true positive, FP = false positive, TN = true negative, FN = false negative Accuracy: (TP+TN)/(P+N) Matthews Correlation Coefficient: 1=perfect, 0=random, -1=completely inaccurate Algorithms Employed Logistic Regression (LR): Uses the sigmoid logistic equation with weights (coefficient values) and biases (constants) to model the probability of a certain class for binary classification. An output of 1 represents one class, and an output of 0 represents the other. Training the model will learn the optimal weights and biases. Linear Discriminant Analysis (LDA): Assumes that the data is Gaussian and each feature has the same variance. LDA estimates the mean and variance for each class from the training data, and then uses properties of statistics (Bayes theorem , Gaussian distribution, etc) to compute the probability of a particular instance belonging to a given class. The class with the largest probability is the prediction. k Nearest Neighbors (KNN): Makes predictions about the validation set using the entire training set. KNN makes a prediction about a new instance by searching through the entire set to find the k “closest” instances. “Closeness” is determined using a proximity measurement (Euclidean) across all features. The class that the majority of the k closest instances belong to is the class that the model predicts the new instance to be. Decision Tree (DT): Represented by a binary tree, where each root node represents an input variable and a split point, and each leaf node contains an output used to make a prediction. Neural Network (NN): Models the way the human brain makes decisions. Each neuron takes in 1+ inputs, and then uses an activation function to process the input with weights and biases to produce an output. Neurons can be arranged into layers, and multiple layers can form a network to model complex decisions. Training the network involves using the training instances to optimize the weights and biases. Naive Bayes (NB): Simplifies the calculation of probabilities by assuming that all features are independent of one another (a strong but effective assumption). Employs Bayes Theorem to calculate the probabilities that the instance to be predicted is in each class, then finds the class with the highest probability. Gradient Boost (GB): Generally used when seeking a model with very high predictive performance. Used to reduce bias and variance (“error”) by combining multiple “weak learners” (not very good models) to create a “strong learner” (high performance model). Involves 3 elements: a loss function (error function) to be optimized, a weak learner (decision tree) to make predictions, and an additive model to add trees to minimize the loss function. Gradient descent is used to minimize error after adding each tree (one by one). Engineering Goal Produce a machine learning model to diagnose Parkinson’s disease given various features of a patient’s speech with at least 90% accuracy and/or a Matthews Correlation Coefficient of at least 0.9. Compare various algorithms and parameters to determine the best model for predicting Parkinson’s. Dataset Description Source: the University of Oxford 195 instances (147 subjects with Parkinson’s, 48 without Parkinson’s) 22 features (elements that are possibly characteristic of Parkinson’s, such as frequency, pitch, amplitude / period of the sound wave) 1 label (1 for Parkinson’s, 0 for no Parkinson’s) Project Pipeline pipeline Summary of Procedure Split the Oxford Parkinson’s Dataset into two parts: one for training, one for validation (evaluate how well the model performs) Train each of the following algorithms with the training set: Logistic Regression, Linear Discriminant Analysis, k Nearest Neighbors, Decision Tree, Neural Network, Naive Bayes, Gradient Boost Evaluate results using the validation set Repeat for the following training set to validation set splits: 80% training / 20% validation, 75% / 25%, and 70% / 30% Repeat for a rescaled version of the dataset (scale all the numbers in the dataset to a range from 0 to 1: this helps to reduce the effect of outliers) Conduct 5 trials and average the results Data a_o a_r m_o m_r Data Analysis In general, the models tended to perform the best (both in terms of accuracy and Matthews Correlation Coefficient) on the rescaled dataset with a 75-25 train-test split. The two highest performing algorithms, k Nearest Neighbors and the Neural Network, both achieved an accuracy of 98%. The NN achieved a MCC of 0.96, while KNN achieved a MCC of 0.94. These figures outperform most existing literature and significantly outperform current methods of diagnosis. Conclusion and Significance These robust results suggest that a machine learning approach can indeed be implemented to significantly improve diagnosis methods of Parkinson’s disease. Given the necessity of early diagnosis for effective treatment, my machine learning models provide a very promising alternative to the current, rather ineffective method of diagnosis. Current methods of early diagnosis are only 53% accurate, while my machine learning model produces 98% accuracy. This 45% increase is critical because an accurate, early diagnosis is needed to effectively treat the disease. Typically, by the time the disease is diagnosed, 60% of nigrostriatal neurons have degenerated, and 80% of striatal dopamine have been depleted. With an earlier diagnosis, much of this degradation could have been slowed or treated. My results are very significant because Parkinson’s affects over 10 million people worldwide who could benefit greatly from an early, accurate diagnosis. Not only is my machine learning approach more accurate in terms of diagnostic accuracy, it is also more scalable, less expensive, and therefore more accessible to people who might not have access to established medical facilities and professionals. The diagnosis is also much simpler, requiring only a 10-15 second voice recording and producing an immediate diagnosis. Future Research Given more time and resources, I would investigate the following: Create a mobile application which would allow the user to record his/her voice, extract the necessary vocal features, and feed it into my machine learning model to diagnose Parkinson’s. Use larger datasets in conjunction with the University of Oxford dataset. Tune and improve my models even further to achieve even better results. Investigate different structures and types of neural networks. Construct a novel algorithm specifically suited for the prediction of Parkinson’s. Generalize my findings and algorithms for all types of dementia disorders, such as Alzheimer’s. References Bind, Shubham. "A Survey of Machine Learning Based Approaches for Parkinson Disease Prediction." International Journal of Computer Science and Information Technologies 6 (2015): n. pag. International Journal of Computer Science and Information Technologies. 2015. Web. 8 Mar. 2017. Brooks, Megan. "Diagnosing Parkinson's Disease Still Challenging." Medscape Medical News. National Institute of Neurological Disorders, 31 July 2014. Web. 20 Mar. 2017. Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection', Little MA, McSharry PE, Roberts SJ, Costello DAE, Moroz IM. BioMedical Engineering OnLine 2007, 6:23 (26 June 2007) Hashmi, Sumaiya F. "A Machine Learning Approach to Diagnosis of Parkinson’s Disease."Claremont Colleges Scholarship. Claremont College, 2013. Web. 10 Mar. 2017. Karplus, Abraham. "Machine Learning Algorithms for Cancer Diagnosis." Machine Learning Algorithms for Cancer Diagnosis (n.d.): n. pag. Mar. 2012. Web. 20 Mar. 2017. Little, Max. "Parkinsons Data Set." UCI Machine Learning Repository. University of Oxford, 26 June 2008. Web. 20 Feb. 2017. Ozcift, Akin, and Arif Gulten. "Classifier Ensemble Construction with Rotation Forest to Improve Medical Diagnosis Performance of Machine Learning Algorithms." Computer Methods and Programs in Biomedicine 104.3 (2011): 443-51. Semantic Scholar. 2011. Web. 15 Mar. 2017. "Parkinson’s Disease Dementia." UCI MIND. N.p., 19 Oct. 2015. Web. 17 Feb. 2017. Salvatore, C., A. Cerasa, I. Castiglioni, F. Gallivanone, A. Augimeri, M. Lopez, G. Arabia, M. Morelli, M.c. Gilardi, and A. Quattrone. "Machine Learning on Brain MRI Data for Differential Diagnosis of Parkinson's Disease and Progressive Supranuclear Palsy."Journal of Neuroscience Methods 222 (2014): 230-37. 2014. Web. 18 Mar. 2017. Shahbakhi, Mohammad, Danial Taheri Far, and Ehsan Tahami. "Speech Analysis for Diagnosis of Parkinson’s Disease Using Genetic Algorithm and Support Vector Machine."Journal of Biomedical Science and Engineering 07.04 (2014): 147-56. Scientific Research. July 2014. Web. 2 Mar. 2017. "Speech and Communication." Speech and Communication. Parkinson's Disease Foundation, n.d. Web. 22 Mar. 2017. Sriram, Tarigoppula V. S., M. Venkateswara Rao, G. V. Satya Narayana, and D. S. V. G. K. Kaladhar. "Diagnosis of Parkinson Disease Using Machine Learning and Data Mining Systems from Voice Dataset." SpringerLink. Springer, Cham, 01 Jan. 1970. Web. 17 Mar. 2017.
tjhwangxiong / TCGAplotA number of functions were generated to perform pan-cancer DEG analysis, correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Methods for visualization were provided in order to easily perform integrative pan-cancer multi-omics analysis.
rmjarvis / TreeCorrCode for efficiently computing 2-point and 3-point correlation functions. For documentation, go to
EZ4BYG / Signal ToolsSignal Processing toolbox, including DFT, IDFT, Wavelet, τp transform, HHT. Besides, this repository aslo has other useful functions, such as 1D/2D Convolution, Cross-Correlation, Filtering and Denosing.
SaifAati / Geospatial COSICorr3DTools and libraries for processing satellite images (push-broom, frame and push-frame), including rigorous sensor model (RSM) refinement, rational function model (RFM) refinement, orthorectification, sub-pixel image correlation, and 3D surface displacement extraction.
franciscovillaescusa / Pylians3Libraries to analyze numerical simulations (python3)
bideeen / Building A Trading Strategy With Pythontrading strategy is a fixed plan to go long or short in markets, there are two common trading strategies: the momentum strategy and the reversion strategy. Firstly, the momentum strategy is also called divergence or trend trading. When you follow this strategy, you do so because you believe the movement of a quantity will continue in its current direction. Stated differently, you believe that stocks have momentum or upward or downward trends, that you can detect and exploit. Some examples of this strategy are the moving average crossover, the dual moving average crossover, and turtle trading: The moving average crossover is when the price of an asset moves from one side of a moving average to the other. This crossover represents a change in momentum and can be used as a point of making the decision to enter or exit the market. You’ll see an example of this strategy, which is the “hello world” of quantitative trading later on in this tutorial. The dual moving average crossover occurs when a short-term average crosses a long-term average. This signal is used to identify that momentum is shifting in the direction of the short-term average. A buy signal is generated when the short-term average crosses the long-term average and rises above it, while a sell signal is triggered by a short-term average crossing long-term average and falling below it. Turtle trading is a popular trend following strategy that was initially taught by Richard Dennis. The basic strategy is to buy futures on a 20-day high and sell on a 20-day low. Secondly, the reversion strategy, which is also known as convergence or cycle trading. This strategy departs from the belief that the movement of a quantity will eventually reverse. This might seem a little bit abstract, but will not be so anymore when you take the example. Take a look at the mean reversion strategy, where you actually believe that stocks return to their mean and that you can exploit when it deviates from that mean. That already sounds a whole lot more practical, right? Another example of this strategy, besides the mean reversion strategy, is the pairs trading mean-reversion, which is similar to the mean reversion strategy. Whereas the mean reversion strategy basically stated that stocks return to their mean, the pairs trading strategy extends this and states that if two stocks can be identified that have a relatively high correlation, the change in the difference in price between the two stocks can be used to signal trading events if one of the two moves out of correlation with the other. That means that if the correlation between two stocks has decreased, the stock with the higher price can be considered to be in a short position. It should be sold because the higher-priced stock will return to the mean. The lower-priced stock, on the other hand, will be in a long position because the price will rise as the correlation will return to normal. Besides these two most frequent strategies, there are also other ones that you might come across once in a while, such as the forecasting strategy, which attempts to predict the direction or value of a stock, in this case, in subsequent future time periods based on certain historical factors. There’s also the High-Frequency Trading (HFT) strategy, which exploits the sub-millisecond market microstructure. That’s all music for the future for now; Let’s focus on developing your first trading strategy for now! A Simple Trading Strategy As you read above, you’ll start with the “hello world” of quantitative trading: the moving average crossover. The strategy that you’ll be developing is simple: you create two separate Simple Moving Averages (SMA) of a time series with differing lookback periods, let’s say, 40 days and 100 days. If the short moving average exceeds the long moving average then you go long, if the long moving average exceeds the short moving average then you exit. Remember that when you go long, you think that the stock price will go up and will sell at a higher price in the future (= buy signal); When you go short, you sell your stock, expecting that you can buy it back at a lower price and realize a profit (= sell signal). This simple strategy might seem quite complex when you’re just starting out, but let’s take this step by step: First define your two different lookback periods: a short window and a long window. You set up two variables and assign one integer per variable. Make sure that the integer that you assign to the short window is shorter than the integer that you assign to the long window variable! Next, make an empty signals DataFrame, but do make sure to copy the index of your aapl data so that you can start calculating the daily buy or sell signal for your aapl data. Create a column in your empty signals DataFrame that is named signal and initialize it by setting the value for all rows in this column to 0.0. After the preparatory work, it’s time to create the set of short and long simple moving averages over the respective long and short time windows. Make use of the rolling() function to start your rolling window calculations: within the function, specify the window and the min_period, and set the center argument. In practice, this will result in a rolling() function to which you have passed either short_window or long_window, 1 as the minimum number of observations in the window that are required to have a value, and False, so that the labels are not set at the center of the window. Next, don’t forget to also chain the mean() function so that you calculate the rolling mean. After you have calculated the mean average of the short and long windows, you should create a signal when the short moving average crosses the long moving average, but only for the period greater than the shortest moving average window. In Python, this will result in a condition: signals['short_mavg'][short_window:] > signals['long_mavg'][short_window:]. Note that you add the [short_window:] to comply with the condition “only for the period greater than the shortest moving average window”. When the condition is true, the initialized value 0.0 in the signal column will be overwritten with 1.0. A “signal” is created! If the condition is false, the original value of 0.0 will be kept and no signal is generated. You use the NumPy where() function to set up this condition. Much the same like you read just now, the variable to which you assign this result is signals['signal'][short_window], because you only want to create signals for the period greater than the shortest moving average window! Lastly, you take the difference of the signals in order to generate actual trading orders. In other words, in this column of your signals DataFrame, you’ll be able to distinguish between long and short positions, whether you’re buying or selling stock.
sjczheng / EpiDISHThis package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.
usnistgov / PyPRISMA framework for conducting polymer reference interaction site model (PRISM) calculations
wavefunction91 / GauXCGauXC is a modern, modular C++ library for the evaluation of quantities related to the exchange-correlation (XC) energy (e.g. potential, etc) in the Gaussian basis set discretization of Kohn-Sham density function theory (KS-DFT) on heterogenous architectures.
yitaohu88 / Empirical Method In FinanceWinter 2020 Course description: Econometric and statistical techniques commonly used in quantitative finance. Use of estimation application software in exercises to estimate volatility, correlations, stability, regressions, and statistical inference using financial time series. Topic 1: Time series properties of stock market returns and prices Class intro: Forecasting and Finance The random walk hypothesis Stationarity Time-varying volatility and General Least Squares Robust standard errors and OLS Topic 2: Time-dependence and predictability ARMA models The likelihood function, exact and conditional likelihood estimation Predictive regressions, autocorrelation robust standard errors The Campbell-Shiller decomposition Present value restrictions Multivariate analysis: Vector Autoregression (VAR) models, the Kalman Filter Topic 3: Heteroscedasticity Time-varying volatility in the data Realized Variance ARCH and GARCH models, application to Value-at-Risk Topic 4: Time series properties of the cross-section of stock returns Single- and multifactor models Economic factors: Models and data exploration Statistical factors: Principal Components Analysis Fama-MacBeth regressions and characteristics-based factors
pierrebaudot / Infotopopycomputes most of information functions (joint entropy, conditional, mutual information, total correlation information distance) and deep information networks
cosmodesi / Pycorr2-pt correlation function estimation
igmhub / Piccaset of tools for continuum fitting, correlation function calculation, cosmological fits...
dMaggot / LibxcorrCross Correlation function for C using FFTW
DheerajKumar97 / Automated ML Application For EDA Streamlit Deployment HerokuThis project is designed as Automated Application for performing Exploratory Data Analysis for given Dataset to generate insights using Python, Streamlit. For executing all the operations customized function has been created and with support of these functions every step will be executed. EDA like basic information about data, Tabulation Analysis, Distribution Analysis, Correlation Analysis and it has been extended to perform Advance Statistical Analysis with some Basic Feature Engineering has been Automated. This Project has been Deployed with Streamlit in Heroku Cloud Platform
cheng-zhao / FCFCFast Correlation Function Calculator
IPS-LMU / Wrasspwrassp is a wrapper for R around Michel Scheffers's libassp (Advanced Speech Signal Processor). The libassp library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner. The wrassp package is used by the EMU Speech Database Management System (EMU-SDMS) to perform signal processing routines.
iSarmad / DispNetCorr1D PytorchThis repository only provides the 1D correlation function/ layer needed for DispNetCorr1D in Pytorch.
