larngroup / tag-dta Goto Github PK
View Code? Open in Web Editor NEWTAG-DTA: Binding Region-Guided Strategy to Predict Drug-Target Affinity Using Transformers
TAG-DTA: Binding Region-Guided Strategy to Predict Drug-Target Affinity Using Transformers
Hi there! Im getting an out of memory error when running the evalation code 'python main.py --inference_option Evaluation'. I tried it on an A10 20GB and A100 80GB but getting the same error either way.
2024-01-09 15:35:39.453000: W external/local_tsl/tsl/framework/bfc_allocator.cc:497] ******************************************************************************__________________
2024-01-09 15:35:39.453020: W tensorflow/core/framework/op_kernel.cc:1827] RESOURCE_EXHAUSTED: failed to allocate memory
Traceback (most recent call last):
File "/miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/TAG-DTA/TAG-DTA/source/main.py", line 694, in
run_eval_model(FLAGS)
File "/miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/TAG-DTA/TAG-DTA/source/main.py", line 664, in run_eval_model
aff_preds = model([affinity_data_val[0], affinity_data_val[1]], training=False)[1]
File "miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler
raise e.with_traceback(filtered_tb) from None
File "/miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/TAG-DTA/TAG-DTA/source/transformer_encoder.py", line 174, in call
x, attn_enc_w = layer(x, mask)
File "/miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/TAG-DTA/TAG-DTA/source/transformer_encoder.py", line 83, in call
attn_out, attn_w = self.mha_layer([x, x, x], mask=mask)
File "/miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/TAG-DTA/TAG-DTA/source/mha_layer.py", line 154, in call
attention_output, attention_weights = self.attention([query, key, value], mask=mask)
File "/miniconda3/envs/TAG-DTA_mantis/lib/python3.9/site-packages/TAG-DTA/TAG-DTA/source/mha_layer.py", line 62, in call
scaled_attention_scores += (mask * -1e9)
tensorflow.python.framework.errors_impl.ResourceExhaustedError: Exception encountered when calling layer 'scaled_dot_product_attention' (type scaled_dot_product_attention).
{{function_node _wrapped__AddV2_device/job:localhost/replica:0/task:0/device:GPU:0}} failed to allocate memory [Op:AddV2] name:
Call arguments received by layer 'scaled_dot_product_attention' (type scaled_dot_product_attention):
• inputs=['tf.Tensor(shape=(4867, 4, 576, 64), dtype=float32)', 'tf.Tensor(shape=(4867, 4, 576, 64), dtype=float32)', 'tf.Tensor(shape=(4867, 4, 576, 64), dtype=float32)']
• mask=tf.Tensor(shape=(4867, 1, 1, 576), dtype=float32)
Hello, I have been able to reproduce results from model training and validation. I am curious if there is a way to predict binding pocket and bindining affinity for a specific protein using all of the drugs in the dataset.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.