adam | genomics analysis platform with specialized file formats

 by   bigdatagenomics Scala Version: adam-parent-spark3_2.12-1.0 License: Apache-2.0

kandi X-RAY | adam Summary

kandi X-RAY | adam Summary

adam is a Scala library typically used in Big Data, Spark, Hadoop applications. adam has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. You can download it from GitHub.

ADAM is a library and command line tool that enables the use of [Apache Spark] to parallelize genomic data analysis across cluster/cloud computing environments. ADAM uses a set of schemas to describe genomic sequences, reads, variants/genotypes, and features, and can be used with data in legacy genomic file formats such as SAM/BAM/CRAM, BED/GFF3/GTF, and VCF, as well as data stored in the columnar [Apache Parquet] format. On a single node, ADAM provides competitive performance to optimized multi-threaded tools, while enabling scale out to clusters with more than a thousand cores. ADAM’s APIs can be used from Scala, Java, Python, R, and SQL.
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            kandi-support Support

              adam has a medium active ecosystem.
              It has 943 star(s) with 306 fork(s). There are 100 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 31 open issues and 1159 have been closed. On average issues are closed in 255 days. There are 3 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of adam is adam-parent-spark3_2.12-1.0

            kandi-Quality Quality

              adam has no bugs reported.

            kandi-Security Security

              adam has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              adam is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              adam releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            adam Key Features

            No Key Features are available at this moment for adam.

            adam Examples and Code Snippets

            Initialize Adam optimizer .
            pythondot img1Lines of Code : 43dot img1License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            def __init__(self,
                           learning_rate=0.001,
                           beta_1=0.9,
                           beta_2=0.999,
                           epsilon=1e-7,
                           amsgrad=False,
                           name='Adam',
                           **kwargs):
                """Construct a new Ada  
            Calculate the Adam algorithm .
            pythondot img2Lines of Code : 25dot img2no licencesLicense : No License
            copy iconCopy
            def adam(cost, params, lr0=1e-5, beta1=0.9, beta2=0.999, eps=1e-8):
              # cast
              lr0 = np.float32(lr0)
              beta1 = np.float32(beta1)
              beta2 = np.float32(beta2)
              eps = np.float32(eps)
              one = np.float32(1)
              zero = np.float32(0)
            
              grads = T.grad(cost,   
            Initialize Adam .
            pythondot img3Lines of Code : 20dot img3License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            def __init__(self,
                           lr=0.001,
                           beta_1=0.9,
                           beta_2=0.999,
                           epsilon=None,
                           decay=0.,
                           amsgrad=False,
                           **kwargs):
                super(Adam, self).__init__(**kwargs)  

            Community Discussions

            QUESTION

            Not able to get reasonable results from DenseVariational
            Asked 2021-Jun-15 at 16:05

            I am trying a regression problem with the following dataset (sinusoidal curve) of size 500

            First, I tried with 2 dense layer with 10 units each

            ...

            ANSWER

            Answered 2021-Mar-18 at 15:40

            QUESTION

            Model.evaluate returns 0 loss when using custom model
            Asked 2021-Jun-15 at 15:52

            I am trying to use my own train step in with Keras by creating a class that inherits from Model. It seems that the training works correctly but the evaluate function always returns 0 on the loss even if I send to it the train data, which have a big loss value during the training. I can't share my code but was able to reproduce using the example form the Keras api in https://keras.io/guides/customizing_what_happens_in_fit/ I changed the Dense layer to have 2 units instead of one, and made its activation to sigmoid.

            The code:

            ...

            ANSWER

            Answered 2021-Jun-12 at 17:27

            As you manually use the loss and metrics function in the train_step (not in the .compile) for the training set, you should also do the same for the validation set or by defining the test_step in the custom model in order to get the loss score and metrics score. Add the following function to your custom model.

            Source https://stackoverflow.com/questions/67951244

            QUESTION

            Node.js can't read else if or else part
            Asked 2021-Jun-15 at 15:41

            I wrote a discord bot. "o" is first letter of play. "atla" is skip. When I wrote -o MUSIC_NAME, music is adding queue and starting to play. And when I write again, just adding queue. Everything is okay still here. When I wrote -atla. It's also working perfectly. But when I allow to changing auto music itself, it's changing music automatically. But problem is here. The end of the last music not working else if (list.length === 0) block in endHandler function. How can I fix that? Thanks for your attention.

            ...

            ANSWER

            Answered 2021-Jun-15 at 15:41

            I'm not familiar with Discord bots but I don't think your endHandler will ever run the else if part the way it is because your code is always creating a new dispatcher when it plays the next song, but never sets up a finish handler for it.

            Source https://stackoverflow.com/questions/67988144

            QUESTION

            Rspec: How to verify if a record has been deleted?
            Asked 2021-Jun-15 at 15:40

            I have created a simple Rspec test to verfiy if a model created has been deleted. However, the test fails because the model still exists. Can anyone provide any assistance on how to determine if the record was actually deleted?

            ...

            ANSWER

            Answered 2021-Feb-08 at 20:41

            When you delete a record from a database, an object still persists in memory. That's why expect(person).to be_empty() fails.

            RSpec has the change matcher. ActiveRecord has the persisted? method. It returns false if a record is not persisted in a database.

            Source https://stackoverflow.com/questions/66108221

            QUESTION

            How to add several binary classifiers at the end of a MLP with Keras?
            Asked 2021-Jun-15 at 02:43

            Say I have an MLP that looks like:

            ...

            ANSWER

            Answered 2021-Jun-15 at 02:43

            In your problem you are trying to use Sequential API to create the Model. There are Limitations to Sequential API, you can just create a layer by layer model. It can't handle multiple inputs/outputs. It can't be used for Branching also.

            Below is the text from Keras official website: https://keras.io/guides/functional_api/

            The functional API makes it easy to manipulate multiple inputs and outputs. This cannot be handled with the Sequential API.

            Also this stack link will be useful for you: Keras' Sequential vs Functional API for Multi-Task Learning Neural Network

            Now you can create a Model using Functional API or Model Sub Classing.

            In case of functional API Your Model will be

            Assuming Output_1 is classification with 17 classes Output_2 is calssification with 2 classes and Output_3 is regression

            Source https://stackoverflow.com/questions/67977986

            QUESTION

            Move 2nd level sub-array to the top of the 1st level multidimentional array based on value of the sub-array
            Asked 2021-Jun-14 at 21:35

            I'm looping through a multidimensional array and am left with some values.

            This is the complete PHP code.

            ...

            ANSWER

            Answered 2021-Jun-09 at 18:41

            This will reorder $array2 (into a new variable $final). First it assembles a simple array $people of the names, then it reassembles $array2 by prioritizing based on the $people array. Was this what you wanted to accomplish?

            Source https://stackoverflow.com/questions/67909656

            QUESTION

            Tensorflow ValueError: Dimensions must be equal: LSTM+MDN
            Asked 2021-Jun-14 at 19:07

            I am trying to make a next-word prediction model with LSTM + Mixture Density Network Based on this implementation(https://www.katnoria.com/mdn/).

            Input: 300-dimensional word vectors*window size(5) and 21-dimensional array(c) representing topic distribution of the document, used to train hidden initial states.

            Output: mixing coefficient*num_gaussians, variance*num_gaussians, mean*num_gaussians*300(vector size)

            x.shape, y.shape, c.shape with an experimental 161 obserbations gives me such:

            (TensorShape([161, 5, 300]), TensorShape([161, 300]), TensorShape([161, 21]))

            ...

            ANSWER

            Answered 2021-Jun-14 at 19:07

            for MDN model , the likelihood for each sample has to be calculated with all the Gaussians pdf , to do that I think you have to reshape your matrices ( y_true and mu) and take advantage of the broadcasting operation by adding 1 as the last dimension . e.g:

            Source https://stackoverflow.com/questions/67965364

            QUESTION

            I have multiple dictionaries in one variable results. How to return only 1st dictionary value from that?
            Asked 2021-Jun-14 at 17:27

            I have multiple dictionaries in one variable results. How to return only 1st dictionary value from that?

            ...

            ANSWER

            Answered 2021-Jun-14 at 14:20

            If you have a list or a tuple of dictionaries, you can use indexing:

            Source https://stackoverflow.com/questions/67971908

            QUESTION

            SHAP DeepExplainer with TensorFlow 2.4+ error
            Asked 2021-Jun-14 at 14:52

            I'm trying to compute shap values using DeepExplainer, but I get the following error:

            keras is no longer supported, please use tf.keras instead

            Even though i'm using tf.keras?

            ...

            ANSWER

            Answered 2021-Jun-14 at 14:52

            TL;DR

            • Add tf.compat.v1.disable_v2_behavior() at the top for TF 2.4+
            • calculate shap values on numpy array, not on df

            Full reproducible example:

            Source https://stackoverflow.com/questions/66814523

            QUESTION

            Why I am retrieving high value loss for neural network regression
            Asked 2021-Jun-14 at 13:45

            I have data in the following format consisting of 80 instances. I need to predict two-parameter latency and accuracy

            ...

            ANSWER

            Answered 2021-Jun-14 at 13:45

            You have very less data, just 2 columns, 80 rows and 2 target variables. All you can do is:

            1. Add more data.
            2. Normalize your data and then feed it to the neural network.
            3. If neural network not giving good accuracy, try Random Forest or XGBoost.

            I also want to add one thing that is your neural network architecture is wrong. Dense layer with 2 outputs and a softmax activation isn't going to give you good result here. You have to use TensorFlow's Funtional API and make 1 input 2 output neural network architecture.

            Source https://stackoverflow.com/questions/67970580

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

            Vulnerabilities

            No vulnerabilities reported

            Install adam

            You can download it from GitHub.

            Support

            ADAM’s documentation is available at http://adam.readthedocs.io. ADAM’s core API documentation is available at http://javadoc.io/doc/org.bdgenomics.adam/adam-core-spark3_2.12.
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