tape | Tasks Assessing Protein Embeddings , a set | Machine Learning library
kandi X-RAY | tape Summary
kandi X-RAY | tape Summary
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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Top functions reviewed by kandi - BETA
- 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
tape Key Features
tape Examples and Code Snippets
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
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
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
Trending Discussions on tape
QUESTION
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 14:02You could maybe try using tf.gradients
. Also rather use tf.Variable
for h0
:
QUESTION
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 14:53QUESTION
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 17:45I 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.
QUESTION
Here is my dataframe:
...ANSWER
Answered 2022-Jan-31 at 18:26We 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
)
QUESTION
I have this dataframe:
...ANSWER
Answered 2022-Feb-04 at 18:26Wrap 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 coalesce
ing the 'bubble_height' and 'color'
QUESTION
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 14:03Since the result of filter
method is an array, you can map over your filtered array and extract just username
property, like this:
QUESTION
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 11:53First, 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 Quote
s.
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:
QUESTION
Suppose I want to run the following C snippet:
...ANSWER
Answered 2022-Jan-07 at 13:57but 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
QUESTION
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 11:08Gradient 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).
QUESTION
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 10:58Interesting 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:
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