adam | genomics analysis platform with specialized file formats
kandi X-RAY | adam Summary
kandi X-RAY | adam Summary
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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Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of adam
adam Key Features
adam Examples and Code Snippets
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
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,
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
Trending Discussions on adam
QUESTION
ANSWER
Answered 2021-Mar-18 at 15:40You need to define a different surrogate posterior. In Tensorflow's Bayesian linear regression example https://colab.research.google.com/github/tensorflow/probability/blob/master/tensorflow_probability/examples/jupyter_notebooks/Probabilistic_Layers_Regression.ipynb#scrollTo=VwzbWw3_CQ2z
you have the posterior mean field as such
QUESTION
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 17:27As 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.
QUESTION
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 15:41I'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.
QUESTION
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 20:41When 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.
QUESTION
Say I have an MLP that looks like:
...ANSWER
Answered 2021-Jun-15 at 02:43In 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
QUESTION
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 18:41This 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?
QUESTION
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 19:07for 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:
QUESTION
I have multiple dictionaries in one variable results. How to return only 1st dictionary value from that?
...ANSWER
Answered 2021-Jun-14 at 14:20If you have a list or a tuple of dictionaries, you can use indexing:
QUESTION
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 14:52TL;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:
QUESTION
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 13:45You have very less data, just 2 columns, 80 rows and 2 target variables. All you can do is:
- Add more data.
- Normalize your data and then feed it to the neural network.
- 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.
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