25 skills found
joshspeagle / DynestyDynamic Nested Sampling package for computing Bayesian posteriors and evidences
jenniferlu717 / BrackenBracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Joshuaalbert / JaxnsProbabilistic Programming and Nested sampling in JAX
quantopian / BayesalphaBayesian models to compute performance and uncertainty of returns and alpha.
Aryia-Behroziuan / NeuronsAn ANN is a model based on a collection of connected units or nodes called "artificial neurons", which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit information, a "signal", from one artificial neuron to another. An artificial neuron that receives a signal can process it and then signal additional artificial neurons connected to it. In common ANN implementations, the signal at a connection between artificial neurons is a real number, and the output of each artificial neuron is computed by some non-linear function of the sum of its inputs. The connections between artificial neurons are called "edges". Artificial neurons and edges typically have a weight that adjusts as learning proceeds. The weight increases or decreases the strength of the signal at a connection. Artificial neurons may have a threshold such that the signal is only sent if the aggregate signal crosses that threshold. Typically, artificial neurons are aggregated into layers. Different layers may perform different kinds of transformations on their inputs. Signals travel from the first layer (the input layer) to the last layer (the output layer), possibly after traversing the layers multiple times. The original goal of the ANN approach was to solve problems in the same way that a human brain would. However, over time, attention moved to performing specific tasks, leading to deviations from biology. Artificial neural networks have been used on a variety of tasks, including computer vision, speech recognition, machine translation, social network filtering, playing board and video games and medical diagnosis. Deep learning consists of multiple hidden layers in an artificial neural network. This approach tries to model the way the human brain processes light and sound into vision and hearing. Some successful applications of deep learning are computer vision and speech recognition.[68] Decision trees Main article: Decision tree learning Decision tree learning uses a decision tree as a predictive model to go from observations about an item (represented in the branches) to conclusions about the item's target value (represented in the leaves). It is one of the predictive modeling approaches used in statistics, data mining, and machine learning. Tree models where the target variable can take a discrete set of values are called classification trees; in these tree structures, leaves represent class labels and branches represent conjunctions of features that lead to those class labels. Decision trees where the target variable can take continuous values (typically real numbers) are called regression trees. In decision analysis, a decision tree can be used to visually and explicitly represent decisions and decision making. In data mining, a decision tree describes data, but the resulting classification tree can be an input for decision making. Support vector machines Main article: Support vector machines Support vector machines (SVMs), also known as support vector networks, are a set of related supervised learning methods used for classification and regression. Given a set of training examples, each marked as belonging to one of two categories, an SVM training algorithm builds a model that predicts whether a new example falls into one category or the other.[69] An SVM training algorithm is a non-probabilistic, binary, linear classifier, although methods such as Platt scaling exist to use SVM in a probabilistic classification setting. In addition to performing linear classification, SVMs can efficiently perform a non-linear classification using what is called the kernel trick, implicitly mapping their inputs into high-dimensional feature spaces. Illustration of linear regression on a data set. Regression analysis Main article: Regression analysis Regression analysis encompasses a large variety of statistical methods to estimate the relationship between input variables and their associated features. Its most common form is linear regression, where a single line is drawn to best fit the given data according to a mathematical criterion such as ordinary least squares. The latter is often extended by regularization (mathematics) methods to mitigate overfitting and bias, as in ridge regression. When dealing with non-linear problems, go-to models include polynomial regression (for example, used for trendline fitting in Microsoft Excel[70]), logistic regression (often used in statistical classification) or even kernel regression, which introduces non-linearity by taking advantage of the kernel trick to implicitly map input variables to higher-dimensional space. Bayesian networks Main article: Bayesian network A simple Bayesian network. Rain influences whether the sprinkler is activated, and both rain and the sprinkler influence whether the grass is wet. A Bayesian network, belief network, or directed acyclic graphical model is a probabilistic graphical model that represents a set of random variables and their conditional independence with a directed acyclic graph (DAG). For example, a Bayesian network could represent the probabilistic relationships between diseases and symptoms. Given symptoms, the network can be used to compute the probabilities of the presence of various diseases. Efficient algorithms exist that perform inference and learning. Bayesian networks that model sequences of variables, like speech signals or protein sequences, are called dynamic Bayesian networks. Generalizations of Bayesian networks that can represent and solve decision problems under uncertainty are called influence diagrams. Genetic algorithms Main article: Genetic algorithm A genetic algorithm (GA) is a search algorithm and heuristic technique that mimics the process of natural selection, using methods such as mutation and crossover to generate new genotypes in the hope of finding good solutions to a given problem. In machine learning, genetic algorithms were used in the 1980s and 1990s.[71][72] Conversely, machine learning techniques have been used to improve the performance of genetic and evolutionary algorithms.[73] Training models Usually, machine learning models require a lot of data in order for them to perform well. Usually, when training a machine learning model, one needs to collect a large, representative sample of data from a training set. Data from the training set can be as varied as a corpus of text, a collection of images, and data collected from individual users of a service. Overfitting is something to watch out for when training a machine learning model. Federated learning Main article: Federated learning Federated learning is an adapted form of distributed artificial intelligence to training machine learning models that decentralizes the training process, allowing for users' privacy to be maintained by not needing to send their data to a centralized server. This also increases efficiency by decentralizing the training process to many devices. For example, Gboard uses federated machine learning to train search query prediction models on users' mobile phones without having to send individual searches back to Google.[74] Applications There are many applications for machine learning, including: Agriculture Anatomy Adaptive websites Affective computing Banking Bioinformatics Brain–machine interfaces Cheminformatics Citizen science Computer networks Computer vision Credit-card fraud detection Data quality DNA sequence classification Economics Financial market analysis[75] General game playing Handwriting recognition Information retrieval Insurance Internet fraud detection Linguistics Machine learning control Machine perception Machine translation Marketing Medical diagnosis Natural language processing Natural language understanding Online advertising Optimization Recommender systems Robot locomotion Search engines Sentiment analysis Sequence mining Software engineering Speech recognition Structural health monitoring Syntactic pattern recognition Telecommunication Theorem proving Time series forecasting User behavior analytics In 2006, the media-services provider Netflix held the first "Netflix Prize" competition to find a program to better predict user preferences and improve the accuracy of its existing Cinematch movie recommendation algorithm by at least 10%. A joint team made up of researchers from AT&T Labs-Research in collaboration with the teams Big Chaos and Pragmatic Theory built an ensemble model to win the Grand Prize in 2009 for $1 million.[76] Shortly after the prize was awarded, Netflix realized that viewers' ratings were not the best indicators of their viewing patterns ("everything is a recommendation") and they changed their recommendation engine accordingly.[77] In 2010 The Wall Street Journal wrote about the firm Rebellion Research and their use of machine learning to predict the financial crisis.[78] In 2012, co-founder of Sun Microsystems, Vinod Khosla, predicted that 80% of medical doctors' jobs would be lost in the next two decades to automated machine learning medical diagnostic software.[79] In 2014, it was reported that a machine learning algorithm had been applied in the field of art history to study fine art paintings and that it may have revealed previously unrecognized influences among artists.[80] In 2019 Springer Nature published the first research book created using machine learning.[81] Limitations Although machine learning has been transformative in some fields, machine-learning programs often fail to deliver expected results.[82][83][84] Reasons for this are numerous: lack of (suitable) data, lack of access to the data, data bias, privacy problems, badly chosen tasks and algorithms, wrong tools and people, lack of resources, and evaluation problems.[85] In 2018, a self-driving car from Uber failed to detect a pedestrian, who was killed after a collision.[86] Attempts to use machine learning in healthcare with the IBM Watson system failed to deliver even after years of time and billions of dollars invested.[87][88] Bias Main article: Algorithmic bias Machine learning approaches in particular can suffer from different data biases. A machine learning system trained on current customers only may not be able to predict the needs of new customer groups that are not represented in the training data. When trained on man-made data, machine learning is likely to pick up the same constitutional and unconscious biases already present in society.[89] Language models learned from data have been shown to contain human-like biases.[90][91] Machine learning systems used for criminal risk assessment have been found to be biased against black people.[92][93] In 2015, Google photos would often tag black people as gorillas,[94] and in 2018 this still was not well resolved, but Google reportedly was still using the workaround to remove all gorillas from the training data, and thus was not able to recognize real gorillas at all.[95] Similar issues with recognizing non-white people have been found in many other systems.[96] In 2016, Microsoft tested a chatbot that learned from Twitter, and it quickly picked up racist and sexist language.[97] Because of such challenges, the effective use of machine learning may take longer to be adopted in other domains.[98] Concern for fairness in machine learning, that is, reducing bias in machine learning and propelling its use for human good is increasingly expressed by artificial intelligence scientists, including Fei-Fei Li, who reminds engineers that "There’s nothing artificial about AI...It’s inspired by people, it’s created by people, and—most importantly—it impacts people. It is a powerful tool we are only just beginning to understand, and that is a profound responsibility.”[99] Model assessments Classification of machine learning models can be validated by accuracy estimation techniques like the holdout method, which splits the data in a training and test set (conventionally 2/3 training set and 1/3 test set designation) and evaluates the performance of the training model on the test set. In comparison, the K-fold-cross-validation method randomly partitions the data into K subsets and then K experiments are performed each respectively considering 1 subset for evaluation and the remaining K-1 subsets for training the model. In addition to the holdout and cross-validation methods, bootstrap, which samples n instances with replacement from the dataset, can be used to assess model accuracy.[100] In addition to overall accuracy, investigators frequently report sensitivity and specificity meaning True Positive Rate (TPR) and True Negative Rate (TNR) respectively. Similarly, investigators sometimes report the false positive rate (FPR) as well as the false negative rate (FNR). However, these rates are ratios that fail to reveal their numerators and denominators. The total operating characteristic (TOC) is an effective method to express a model's diagnostic ability. TOC shows the numerators and denominators of the previously mentioned rates, thus TOC provides more information than the commonly used receiver operating characteristic (ROC) and ROC's associated area under the curve (AUC).[101] Ethics Machine learning poses a host of ethical questions. Systems which are trained on datasets collected with biases may exhibit these biases upon use (algorithmic bias), thus digitizing cultural prejudices.[102] For example, using job hiring data from a firm with racist hiring policies may lead to a machine learning system duplicating the bias by scoring job applicants against similarity to previous successful applicants.[103][104] Responsible collection of data and documentation of algorithmic rules used by a system thus is a critical part of machine learning. Because human languages contain biases, machines trained on language corpora will necessarily also learn these biases.[105][106] Other forms of ethical challenges, not related to personal biases, are more seen in health care. There are concerns among health care professionals that these systems might not be designed in the public's interest but as income-generating machines. This is especially true in the United States where there is a long-standing ethical dilemma of improving health care, but also increasing profits. For example, the algorithms could be designed to provide patients with unnecessary tests or medication in which the algorithm's proprietary owners hold stakes. There is huge potential for machine learning in health care to provide professionals a great tool to diagnose, medicate, and even plan recovery paths for patients, but this will not happen until the personal biases mentioned previously, and these "greed" biases are addressed.[107] Hardware Since the 2010s, advances in both machine learning algorithms and computer hardware have led to more efficient methods for training deep neural networks (a particular narrow subdomain of machine learning) that contain many layers of non-linear hidden units.[108] By 2019, graphic processing units (GPUs), often with AI-specific enhancements, had displaced CPUs as the dominant method of training large-scale commercial cloud AI.[109] OpenAI estimated the hardware compute used in the largest deep learning projects from AlexNet (2012) to AlphaZero (2017), and found a 300,000-fold increase in the amount of compute required, with a doubling-time trendline of 3.4 months.[110][111] Software Software suites containing a variety of machine learning algorithms include the following: Free and open-source so
guoliu / OptimizerMCMC, Differential Evolution Markov Chain, Ensemble Kalman filter, Approximate Bayesian Computing-Population Monte Carlo, and modeling averaging methods in Matlab.
pearsonkyle / Nbody AIA python 3 package for generating N-body simulations, computing transit timing variations (TTV) and retrieving orbit parameters from TTV measurements within a Bayesian framework using machine learning
Zheng-Meng / Reservoir Computing And Hyperparameter OptimizationReservoir computing for short-and long-term prediction of chaotic systems, with tasks Lorenz and Mackey-Glass systems. Bayesian optimization (hyperparameter optimization algorithm) is used to tune the hyperparameters and improve the performance.
fonnesbeck / Bayes Pydata London 2024Probabilistic Programming and Bayesian Computing with PyMC
vkgnandhu177 / Bayesian Regression And Bitcoin# Bayesian-Regression-to-Predict-Bitcoin-Price-Variations Predicting the price variations of bitcoin, a virtual cryptographic currency. These predictions could be used as the foundation of a bitcoin trading strategy. To make these predictions, we will have to familiarize ourself with a machine learning technique, Bayesian Regression, and implement this technique in Python. # Datasets We have the datasets in the data folder. The original raw data can be found here: http://api.bitcoincharts.com/v1/csv/. The datasets from this site have three attributes: (1) time in epoch, (2) price in USD per bitcoin, and (3) bitcoin amount in a transaction (buy/sell). However, only the first two attributes are relevant to this project. To make the data to have evenly space records, we took all the records within a 20 second window and replaced it by a single record as the average of all the transaction prices in that window. Not every 20 second window had a record; therefore those missing entries were filled using the prices of the previous 20 observations and assuming a Gaussian distribution. The raw data that has been cleaned is given in the file dataset.csv Finally, as discussed in the paper, the data was divided into a total of 9 different datasets. The whole dataset is partitioned into three equally sized (50 price variations in each) subsets: train1, train2, and test. The train sets are used for training a linear model, while the test set is for evaluation of the model. There are three csv files associated with each subset of data: *_90.csv, *_180.csv, and *_360.csv. In _90.csv, for example, each line represents a vector of length 90 where the elements are 30 minute worth of bitcoin price variations (since we have 20 second intervals) and a price variation in the 91st column. Similarly, the *_180.csv represents 60 minutes of prices and *_360.csv represents 120 minutes of prices. # Project Requirements We are expected to implement the Bayesian Regression model to predict the future price variation of bitcoin as described in the reference paper. The main parts to focus on are Equation 6 and the Predicting Price Change section. # Logic in bitcoin.py 1. Compute the price variations (Δp1, Δp2, and Δp3) for train2 using train1 as input to the Bayesian Regression equation (Equations 6). Make sure to use the similarity metric (Equation 9) in place of the Euclidean distance in Bayesian Regression (Equation 6). 2. Compute the linear regression parameters (w0, w1, w2, w3) by finding the best linear fit (Equation 8). Here you will need to use the ols function of statsmodels.formula.api. Your model should be fit using Δp1, Δp2, and Δp3 as the covariates. Note: the bitcoin order book data was not available, so you do not have to worry about the rw4 term. 3. Use the linear regression model computed in Step 2 and Bayesian Regression estimates, to predict the price variations for the test dataset. Bayesian Regression estimates for test dataset are computed in the same way as they are computed for train2 dataset – using train1 as an input. 4. Once the price variations are predicted, compute the mean squared error (MSE) for the test dataset (the test dataset has 50 vectors => 50 predictions).
bio-phys / BioEMGPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the characterization of structural models with respect to individual electron microscopy images.
ebprado / MOTR BARTR scripts and data sets that can be used to reproduce the results presented in the paper "Bayesian additive regression trees with model trees". Statistics and Computing 31, 20 (2021).
ababalolgatech / Bayesian Seismic InversionThe class computes the Bayesian Seismic Inversion results . Some modules are missing due to its proprietary natures, updates with an executable file is coming soon.
malikfahad / Particle FilterParticle filters or Sequential Monte Carlo (SMC) methods are a set of genetic, Monte Carlo algorithms used to solve filtering problems arising in signal processing and Bayesian statistical inference. The filtering problem consists of estimating the internal states in dynamical systems when partial observations are made, and random perturbations are present in the sensors as well as in the dynamical system. The objective is to compute the posterior distributions of the states of some Markov process, given some noisy and partial observations. Particle filters implement the prediction-updating transitions of the filtering equation directly by using a genetic type mutation-selection particle algorithm. The samples from the distribution are represented by a set of particles; each particle has a likelihood weight assigned to it that represents the probability of that particle being sampled from the probability density function.
fonnesbeck / Pymc Sdss 2024SDSS 2024 Course: Probabilistic Programming and Bayesian Computing with PyMC
Lucaweihs / SBICComputing the Singular Bayesian Information Criterion
bayesball / JSM2019R code for JSM short course on Bayesian Computing and Multilevel Models
ncrump / HPCSome high performance computing in C and Fortran 90 using OpenMP and MPI. Includes starter examples, parallel Poisson solver, parallel particle mesh simulation, parallel 2d random walk, parallel Bayesian Metropolis Monte Carlo sampler.
niyajaison / Bayesian NetworkComputes the probability of any combination of events given any other combination of events in a Bayesian network
OliPerkins1987 / LULCSDThe rhapsody (R applied system dynamics) package contains a set of classes or containers for building system dynamics modelling in R. It provides tools to build system dynamics models using input templates, as well as capacity for batch-running, scenario building and parameter selection with approximate Bayesian computing.
