vladimirkovacevic

Pretrained Molecular Representations - Training GIN prior passing it to InfoGraph

6

In the [Pretrained Molecular Representations](https://torchdrug.ai/docs/tutorials/pretrain.html) tutorial GIN model was passed to InfoGraph: ```model = models.InfoGraph(gin_model, separate_model=False)``` Should GIN be trained first, then passed to InfoGraph?

It is really hard to find which tool in the workflow failed. Can you make this available in bunny output log?

Workflow outputs

2

When running local Bunny executor on workflow (let's say workflow has many tools and outputs) how can I collect all output files?

mhcnuggets scores on TESLA samples

4

I was very curious to test the performance of mhcnuggets 2.3 on the latest dataset with TESLA validated neoantigen candidates published in Cell ([Key Parameters of Tumor Epitope Immunogenicity Revealed...

I'm trying to process a sample with 90 000 observations and it gets killed (deficit of memory) during the execution of _l_search_ function. The machine I'm using has 36 CPUs...

Added Dockerfile that installs all necessary dependencies so the users could easily run the tool.

PoET for peptide binding affinity prediction

2

Would it make sense to utilise PoET for binding affinity prediction (ic50 score) of short peptide sequences (8-16 amino acids)? If yes, do you have any suggestions/comments on how to...

There is incompatibility with OpenAIEmbeddings. If model is used from OpenRouter API instead OpenAI, it outputs embeddings, but embeddings.embed_documents expects response object to have field "data" (langchain_openai/embeddings/base.py, line 585: embeddings.extend(r["embedding"]...

Results from the manuscript

1

I run ToxinPred3.0 on indenpendent test [dataset](https://webs.iiitd.edu.in/raghava/toxinpred3/download.php) reported in the manuscript "ToxinPred 3.0: An improved method for predicting the toxicity of peptides" with 1104 toxic peptides as positive and 1104...

Hi! predict_lst.py and predict_attention.py have models that require embeddings, or, sequence of integers with total size of 300. How to convert list of protein sequences to obtain these embeddings? It...