sigma | probabilistic model for the sequential dependencies | Machine Learning library

 by   lrgr Python Version: v1.0 License: MIT

kandi X-RAY | sigma Summary

kandi X-RAY | sigma Summary

sigma is a Python library typically used in Artificial Intelligence, Machine Learning, Pytorch applications. sigma has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However sigma build file is not available. You can download it from GitHub.

This repository contains the source code for SigMa (Signature Markov model) and related experiments. SigMa is a probabilistic model of the sequential dependencies among mutation signatures.
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            kandi-support Support

              sigma has a low active ecosystem.
              It has 12 star(s) with 4 fork(s). There are 7 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 1 open issues and 1 have been closed. On average issues are closed in 334 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of sigma is v1.0

            kandi-Quality Quality

              sigma has 0 bugs and 0 code smells.

            kandi-Security Security

              sigma has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              sigma code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              sigma is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              sigma releases are available to install and integrate.
              sigma has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              It has 877 lines of code, 70 functions and 11 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed sigma and discovered the below as its top functions. This is intended to give you an instant insight into sigma implemented functionality, and help decide if they suit your requirements.
            • Load the signatures
            • Get a logger
            • Compute expectation step
            • Compute the logarithm for a given sequence
            • Analyze the MMM
            • Fix NaNs in matrices
            • Calculate the score for each chromosome in a folder
            • Leave one out of the given sequences
            • Return an instance of the model
            • Get a trained model
            • Fit the model
            • Calculate expected weights
            • Returns the log of the emissions
            • Fit the model to the given data
            • Evaluate the expectation step
            • Calculates the probability of each sequence in sequences
            • Compute the viterbi model
            • Return argument parser
            • Get split sequences by a given threshold
            • Extract split sequences from a file
            • Predict the most likely sequences in a sequence
            • Sample a model from a given model
            • Return index of samples in dir_path
            • Predict sequence for a given sequence
            • Returns the log probability of a sequence of sequences
            • Return a JSON representation of the model
            Get all kandi verified functions for this library.

            sigma Key Features

            No Key Features are available at this moment for sigma.

            sigma Examples and Code Snippets

            No Code Snippets are available at this moment for sigma.

            Community Discussions

            QUESTION

            Need to fix Stan code for the generalized pareto distribution to take in real arguments rather than vectors
            Asked 2022-Feb-22 at 22:25

            I am using the functions defined here: Extreme value analysis and user defined probability functions in Stan for modeling the data with a generalized pareto distribution, but my problem is that my model is in a for-loop and expects three real valued arguments, whereas, the gpd functions assume a vector, real, real argument.

            I’m not so sure that my model chunk is so amenable to being vectorized, and so I was thinking I would need to have the gpd functions take in real valued arguments (but maybe I’m wrong).

            I’d appreciate any help with switching the code around to achieve this. Here is my stan code

            ...

            ANSWER

            Answered 2022-Feb-22 at 22:25

            Here is how the log PDF could be adapted. This way, index arrays for subsetting y into censored and non-censored observations can be passed.

            Source https://stackoverflow.com/questions/71163352

            QUESTION

            LaTeX in plot titles using a loop
            Asked 2022-Feb-19 at 18:02

            I just learned how to insert (a limited number of) LaTeX expressions into my plot titles with expression(). How can I generate plots containing LaTeX in their titles using a loop? For example, say I have:

            ...

            ANSWER

            Answered 2022-Feb-19 at 17:04

            We can use bquote instead of expression. This allows partial unquoting, meaning you can substitute the value of i inside the expression by wrapping it like this: .(i)

            Source https://stackoverflow.com/questions/71186976

            QUESTION

            Implementation of the Metropolis-Hasting algorithm for solving gaussian integrals
            Asked 2022-Feb-02 at 20:28

            I am currently having issue with the implementation of the Metropolis-Hastings algorithm.

            I am trying to use the algorithm to calculate integrals of the form

            In using this algorithm, we can obtain a long chain of configurations ( in this case, each configuration is just a single numbers) such that in the tail-end of the chain the probability of having a particular configuration follows (or rather tends to) a gaussian distribution.

            My code seems to be messing up with obtaining the said gaussian distributions. There is a strange dependence on the transition probablity (the probablity of picking a new candidate configuration depending on the previous configuration in the chain). However, if this transition probability is symmetric, there should be no dependence on this function at all (it only affects speed at which phase space [space of potential configurations] is explored and how quickly the chain converges to the desired distribution)!

            In my case I am using a normal distribution transition function (which satisfies the need to be symmetric), with width d. For each d I use I do indeed get a gaussian distribution however the standard deviation, sigma, depends on my choice of d. The resulting gaussian should have a sigma of roughly 0.701 but I find that the value I actually get depends on the parameter d, when it shouldn't.

            I am not sure where the error in this code is, any help would be greatly appreciated!

            ...

            ANSWER

            Answered 2022-Feb-02 at 20:28

            You need to save x even when it doesn't change. Otherwise the center values are under-counted, and more so as d increases, which increases the variance.

            Source https://stackoverflow.com/questions/70958350

            QUESTION

            How to create a progress bar for iterations happening within installed modules
            Asked 2022-Jan-01 at 21:07

            I am aiming to create a progress bar for an iteration happening inside an installed module.

            To create a progress bar for an iteration inside a user-defined function, I pass an tqdm.notebook.tqdm_notebook object as iterable:

            ...

            ANSWER

            Answered 2022-Jan-01 at 21:07

            Of course generally there is no way to directly modify some existing code you didn't write yourself (whether or not it's "installed" is not the issue).

            If you think it's really of general use or interest you could propose a patch to allow this function to take, e.g., a callback function to call on each loop. It might be useful if it's a slow function in general (I did notice some things in the implementation that could be changed to speed it up, but that's another matter).

            You could of course find a number of clever hacks to make it work in this one specific case, though it would be fragile considering that it's a hack designed specifically to the implementation details of this function. I found a few possibilities for this.

            The simplest seems to be this stupid trick:

            Make an ndarray subclass (I called it tqdm_array) which when iterated in Python returns an iterator over a tqdm progress bar which wraps the array itself:

            Source https://stackoverflow.com/questions/70542600

            QUESTION

            What is necessary for a function to be able to take stacked NumPy arguments?
            Asked 2021-Dec-09 at 17:33

            While plotting with a meshgrid defined like this:

            ...

            ANSWER

            Answered 2021-Dec-09 at 17:33

            Look at the array shapes:

            Source https://stackoverflow.com/questions/70293921

            QUESTION

            How do I make x and y axes thicker with Plots (Julia)?
            Asked 2021-Nov-28 at 20:42

            How can I make the lines for the x- and y-axes thicker in Julia Plots? Is there a simple way to achieve this?

            MWE:

            ...

            ANSWER

            Answered 2021-Nov-28 at 20:42

            Currently, there does not seem to be an attribute for axes thickness in Plots.jl.

            As a workaround, you may use the attribute thickness_scaling, which will scale the thickness of everything: lines, grid lines, axes lines, etc. Since you only want to change the thickness of axes, you need to scale down the others. Here is your example code doing that using pyplot backend.

            Source https://stackoverflow.com/questions/70133581

            QUESTION

            Needing advice on MCMC estimation in R
            Asked 2021-Nov-11 at 10:55

            Suppose the random variable X ∼ N(μ,σ2) distribution

            and I am given the observations x =(0.7669, 1.6709, 0.8944, 1.0321, 0.0793, 0.1033, 1.2709, 0.7798, 0.6483, 0.3256)

            Given prior distribution μ ∼ N(0, (100)^2) and σ2 ∼ Inverse − Gamma(5/2, 10/2).

            I am trying to give a MCMC estimation of the parameter.

            Here is my sample code, I am trying to use Random Walk MCMC to do the estimation, but it seems that it does not converge:

            ...

            ANSWER

            Answered 2021-Nov-11 at 10:55

            There are a few problems with the code.

            1. You calculate the log-likelihood, but ignore the log-prior. So effectively you're using a uniform prior, not the one you specified.

            2. The initial calculation of the log likelihood has parentheses in the wrong place:

            Source https://stackoverflow.com/questions/69924551

            QUESTION

            Gradient exploding problem in a graph neural network
            Asked 2021-Oct-29 at 16:33

            I have a gradient exploding problem which I couldn't solve after trying for several days. I implemented a custom message passing graph neural network in TensorFlow which is used to predict a continuous value from graph data. Each graph is associated with one target value. Each node of a graph is represented by a node attribute vector, and the edges between nodes are represented by an edge attribute vector.

            Within a message passing layer, node attributes are updated in a certain way (e.g., by aggregating other node/edge attributes), and these updated node attributes are returned.

            Now, I managed to figure out where the gradient problem occurs in my code. I have the below snippet.

            ...

            ANSWER

            Answered 2021-Oct-29 at 16:33

            Looks great, as you have already followed most of the solutions to resolve gradient exploding problem. Below is the list of all solutions you can try

            Solutions to avoid Gradient Exploding problem

            1. Appropriate Weight initialization: utilise appropriate weight Initialization based on the activation function used.

              Initialization Activation Function He ReLU & variants LeCun SELU Glorot Softmax, Logistic, None, Tanh
            2. Redesigning your Neural network: use fewer layers in neural network and/or use smaller batch size

            3. Choosing Non Saturation activation function: choose the right activation function with reduced learning rates

              • ReLU
              • Leaky ReLU
              • randomized leaky ReLU (RReLU)
              • parametric leaky ReLU (PReLU)
              • exponential linear unit (ELU)
            4. Batch Normalisation: Ideally using batch normalisation before/after each layer, based on what works best for your dataset.

            Source https://stackoverflow.com/questions/69427103

            QUESTION

            Why does Agda require pattern matching here
            Asked 2021-Oct-20 at 14:08

            I have the following:

            ...

            ANSWER

            Answered 2021-Oct-20 at 14:08

            Agda compiles all definitions by pattern matching to a case tree, as described in the user manual page on function definitions. In your case, the case tree looks as follows:

            Source https://stackoverflow.com/questions/69646979

            QUESTION

            Using input from different module to subset data in shiny
            Asked 2021-Sep-16 at 08:26

            I am still quite new to coding but wanted to learn about modules. I am trying to build an app that will display data based on a selected date range. I tried to do this with different modules for selecting the dates and other modules to handle data and eventually create plots. The goal is to reuse some of these modules in different parts of the app. I seem to have become stuck following the article here. I realise that the article describes the callModule method of using modules.

            Here is a sample of the app and modules:

            ...

            ANSWER

            Answered 2021-Sep-16 at 08:26

            You were almost there, here's the complete example for reproducibility (fixing some issues with your example):

            Source https://stackoverflow.com/questions/69168879

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install sigma

            You can download it from GitHub.
            You can use sigma like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            Please report bugs and feature requests in the Issues tab of this GitHub repository. For further questions, please email Max Leiserson and Itay Sason directly.
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