tape | Tasks Assessing Protein Embeddings , a set | Machine Learning library

 by   songlab-cal Python Version: v0.5 License: BSD-3-Clause

kandi X-RAY | tape Summary

kandi X-RAY | tape Summary

tape is a Python library typically used in Artificial Intelligence, Machine Learning, Deep Learning, Pytorch applications. tape has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install tape' or download it from GitHub, PyPI.

Data, weights, and code for running the TAPE benchmark on a trained protein embedding. We provide a pretraining corpus, five supervised downstream tasks, pretrained language model weights, and benchmarking code. This code has been updated to use pytorch - as such previous pretrained model weights and code will not work. The previous tensorflow TAPE repository is still available at This repository is not an effort to maintain maximum compatibility and reproducability with the original paper, but is instead meant to facilitate ease of use and future development (both for us, and for the community). Although we provide much of the same functionality, we have not tested every aspect of training on all models/downstream tasks, and we have also made some deliberate changes. Therefore, if your goal is to reproduce the results from our paper, please use the original code. Our paper is available at
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            kandi-support Support

              tape has a low active ecosystem.
              It has 547 star(s) with 131 fork(s). There are 22 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 22 open issues and 83 have been closed. On average issues are closed in 36 days. There are 4 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of tape is v0.5

            kandi-Quality Quality

              tape has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              tape is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              tape releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed tape and discovered the below as its top functions. This is intended to give you an instant insight into tape implemented functionality, and help decide if they suit your requirements.
            • Write an lmdb file
            • Encodes the given text
            • Convert a token to an integer
            • Adds special tokens
            • Compute the features from the input sequence
            • Reweights the msa1 hot embedding
            • Compute a 2D feature matrix
            • Extract 1D features from 1D image
            • Converts a list of tensors into a TFRecordDataset
            • Convert a tensor to a numpy array
            • Run training
            • Wait for all sentinels
            • Wait for all sentinels to finish
            • Return a TAPEVisualizer instance
            • Forward forward computation
            • Reverse the given sequence
            • Plots the rects of the two datasets
            • Auto label on axes
            • Calculate the attention matrix
            • Transpose x
            • Perform the forward computation
            • Returns a function that runs the function at start and end times
            • Register a model with the given model
            • Register a model with the given model name
            • Create a task model from a given task name
            • Prune the given heads
            • Return a numpy array
            • Get the version string
            Get all kandi verified functions for this library.

            tape Key Features

            No Key Features are available at this moment for tape.

            tape Examples and Code Snippets

            Using enzyme with Tape and AVA
            npmdot img1Lines of Code : 1dot img1no licencesLicense : No License
            copy iconCopy
            npm i --save-dev enzyme enzyme-adapter-react-16
            
              
            Using enzyme with Tape and AVA
            npmdot img2Lines of Code : 1dot img2no licencesLicense : No License
            copy iconCopy
            npm i --save-dev enzyme enzyme-adapter-react-16
            
              
            Decorator for gradients .
            pythondot img3Lines of Code : 50dot img3License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            def grad_pass_through(f):
              """Creates a grad-pass-through op with the forward behavior provided in f.
            
              Use this function to wrap any op, maintaining its behavior in the forward
              pass, but replacing the original op in the backward graph with an id  
            Call the function .
            pythondot img4Lines of Code : 17dot img4License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            def __call__(self, device, token, args):
                """Calls `self._func` in eager mode, recording the tape if needed."""
                use_tape_cache = (
                    self._support_graph_mode_gradient or tape_lib.could_possibly_record())
            
                if use_tape_cache:
                  wit  
            Initialize the tape .
            pythondot img5Lines of Code : 6dot img5License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            def __init__(self, persistent=False):
                self._c_tape = _tape.Tape(persistent)
                ctx = context_stack.get_default()
                self._tape_context = _tape.TapeContext(
                    ctx, self._c_tape, gradient_registry.get_global_registry())
                self._ctx_manage  

            Community Discussions

            QUESTION

            tf2.0: Gradient Tape returns None gradient in RNN model
            Asked 2022-Mar-27 at 23:56

            In a model with an embedding layer and SimpleRNN layer, I would like to compute the partial derivative dh_t/dh_0 for each step t.

            The structure of my model, including imports and data preprocessing.
            Toxic comment train data available: https://www.kaggle.com/c/jigsaw-multilingual-toxic-comment-classification/data?select=jigsaw-toxic-comment-train.csv
            GloVe 6B 100d embeddings available: https://nlp.stanford.edu/projects/glove/

            ...

            ANSWER

            Answered 2022-Feb-18 at 14:02

            You could maybe try using tf.gradients. Also rather use tf.Variable for h0:

            Source https://stackoverflow.com/questions/71153292

            QUESTION

            Xcode 13.2.1 Preview Not Working but Simulator Works
            Asked 2022-Mar-08 at 09:18

            My Xcode Version 13.2.1 (13C100) got an unknown issue. I did several things like delete Xcode, new install Xcode, restore from backup nothing make any change! Currently, the project can be built and run in the simulator, but not in the preview window! it gives a message:

            Cannot preview in this file - Timed out waiting for connection to DTServiceHub after 15.0 seconds.

            What is the issue here any idea? iMac becomes very slow when I taped the resume button. Please Help!

            ...

            ANSWER

            Answered 2022-Jan-06 at 14:53

            I had a similar problem and was solved when I turned of Automatically refresh canvas

            Source https://stackoverflow.com/questions/70608395

            QUESTION

            String(localized:) has no separate key and value?
            Asked 2022-Mar-05 at 11:32

            New in iOS 15, we are invited to use this String initializer method to make localizable strings in our Swift code:

            ...

            ANSWER

            Answered 2021-Sep-17 at 17:45

            I regard this as a major bug in String(localizable:). If we were using NSLocalizedString, we would have individual key: and value: parameters. String(localizable:) needs that.

            I can think of two workarounds. One is: don't use String(localizable:). Just keep on using NSLocalizedString.

            The other is to localize explicitly for English. Instead of entering the English user-facing text as the localized: parameter, enter a key string. Then, to prevent the keys from appearing in the user interface, export the English localization and "translate" the keys into the desired English user-facing text. Now import the localization to generate the correct English .strings files.

            (If your development language isn't English, substitute the development language into those instructions.)

            Now when you export a different localization, such as French, the element's id value is the key, to which the translator pays no attention, and the is the English, which the translator duly translates.

            To change the English user-facing text later on, edit the English Localizable.strings file — not the code. Nothing will break because the key remains constant.

            Source https://stackoverflow.com/questions/69227554

            QUESTION

            Construct JSON column from R dataframe columns
            Asked 2022-Feb-09 at 21:17

            Here is my dataframe:

            ...

            ANSWER

            Answered 2022-Jan-31 at 18:26

            We may consider to paste/unite the columns and then convert to JSON with toJSON - as the columns have different case, it may be be better to standardize by converting to lower case (tolower - it becomes easier to get the corresponding column value from the _units column). Loop across the columns (length:height), paste (str_c), the corresponding '_units' column values when the value in the column is non-NA (using case_when), then unite those column to a single column, select the columns of interest and convert to JSON (toJSON)

            Source https://stackoverflow.com/questions/70930267

            QUESTION

            Parse JSON column into R dataframe
            Asked 2022-Feb-05 at 15:25

            I have this dataframe:

            ...

            ANSWER

            Answered 2022-Feb-04 at 18:26

            Wrap with list on the output of fromJSON, then use unnest_wider to create separate columns from the named list, join the columns to 'option_2' by coalesceing the 'bubble_height' and 'color'

            Source https://stackoverflow.com/questions/70990935

            QUESTION

            How can I return the value of a key based on a different value in a dictionary
            Asked 2022-Jan-17 at 14:03
            const array = [
              {
                username: "john",
                team: "red",
                score: 5,
                items: ["ball", "book", "pen"]
              },
              {
                username: "becky",
                team: "blue",
                score: 10,
                items: ["tape", "backpack", "pen"]
              },
              {
                username: "susy",
                team: "red",
                score: 55,
                items: ["ball", "eraser", "pen"]
              },
              {
                username: "tyson",
                team: "green",
                score: 1,
                items: ["book", "pen"]
              },
            
            ];
            
            ...

            ANSWER

            Answered 2022-Jan-17 at 14:03

            Since the result of filter method is an array, you can map over your filtered array and extract just username property, like this:

            Source https://stackoverflow.com/questions/70742536

            QUESTION

            How can I actually grab the data out of a running stream/websocket within a function?
            Asked 2022-Jan-11 at 11:53

            I am quite confused how to handle websockets/streams data within a function in Python.

            I have a Python script that triggers a ws/stream which runs 24/7:

            ...

            ANSWER

            Answered 2022-Jan-11 at 11:53

            First, you can directly access the dictionary fields as members of the Quote objects - i.e. you can just do q.ask_price to get the price from the received Quotes.

            In your quote_callback function you get every Quote object as an argument. So, if you always only want to access the last received Quote object which has symbol = "HB", you could define a global dictionary named e.g. quotes which will contain one key == symbol and value == last Quote with that symbol per symbol type.

            Now, in get_quote you can use a simple dictionary lookup for the desired key in the quotes dictionary. In the end, you need to repeatedly call get_quote until a quote object with the desired symbol value is received. The whole code could look like this:

            Source https://stackoverflow.com/questions/70612635

            QUESTION

            How to definitely solve the scanf input stream problem
            Asked 2022-Jan-07 at 13:57

            Suppose I want to run the following C snippet:

            ...

            ANSWER

            Answered 2022-Jan-07 at 13:57

            but what is the purpose of scanf then?

            An excellent question.

            Is it simply an useless broken function that should never be used?

            It is almost useless. It is, arguably, quite broken. It should almost never be used.

            Why is it in the libraries to begin with then?

            My personal belief is that it was an experiment. It tries to be the opposite of printf. But that turned out not to be such a good idea in practice, and the function never got used very much, and pretty much fell out of favor, except for one particular use case...

            This seems really absurd, especially considering all beginners are taught to use scanf...

            You're absolutely right. It is really quite absurd.

            There's a reason all beginners are taught to use scanf. During week 1 of your first C programming class, you might write the little program

            Source https://stackoverflow.com/questions/70620657

            QUESTION

            Use of tf.GradientTape() exhausts all the gpu memory, without it it doesn't matter
            Asked 2022-Jan-07 at 11:47

            I'm working on Convolution Tasnet, model size I made is about 5.05 million variables.

            I want to train this using custom training loops, and the problem is,

            ...

            ANSWER

            Answered 2022-Jan-07 at 11:08

            Gradient tape triggers automatic differentiation which requires tracking gradients on all your weights and activations. Autodiff requires multiple more memory. This is normal. You'll have to manually tune your batch size until you find one that works, then tune your LR. Usually, the tune just means guess & check or grid search. (I am working on a product to do all of that for you but I'm not here to plug it).

            Source https://stackoverflow.com/questions/70615673

            QUESTION

            Tensorflow `tf.function` fails if function is called with two identical arguments
            Asked 2021-Dec-27 at 21:22

            In my TF model, my call functions calls an external energy function which is dependent on a function where single parameter is passed twice (see simplified version below):

            ...

            ANSWER

            Answered 2021-Dec-21 at 10:58

            Interesting question! I think the error originates from retracing, which causes the tf.function to evaluate the python snippets in energy more than once. See this issue. Also, this could be related to a bug.

            A couple observations:

            1. Removing the tf.function decorator from calc_sw3 works and is consistent with the docs:

            [...] tf.function applies to a function and all other functions it calls.

            So if you apply tf.function explicitly to calc_sw3 again, you may trigger a retracing, but then you may wonder why calc_sw3_noerr works? That is, it must have something to do with the variable gamma.

            2. Adding input signatures to the tf.function above the energy function, while leaving the rest of the code the way it is, also works:

            Source https://stackoverflow.com/questions/70426458

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

            Vulnerabilities

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