anonimoustt

Hi I am new to AmpliGraph Embedding. I want to know, will AmpliGraph Embedding accurately generate embedding of a protein sequence? I was exploring the ScoringBasedEmbeddingModel used in Ampligraph Embedding...

KeyLLM error: AttributeError: 'str' object has no attribute 'completions'

9

I was trying to run the following code from your GitHub but got the following error: import openai from keybert.llm import OpenAI from keybert import KeyLLM from sentence_transformers import SentenceTransformer...

Module Not Foud

3

Hi, I am getting following error while executing the following code: from dotmotif import Motif from dotmotif.executors.NeuPrintExecutor import NeuPrintExecutor ModuleNotFoundError Traceback (most recent call last) [](https://localhost:8080/#) in () 1 from...

is it possible to get the importance score of the protein sequence?

8

I was just wondering is it possible to get the importance score of the protein sequence using EvoProtGrad model? For instance, in https://huggingface.co/datasets/waylandy/phosformer_curated data there are kinase enzymes. Now I...

Weight of Sequence

1

Hi, Is it possible to get the weight of a protein sequence using EvoProtGrad?

**Background and Context** Integrating two or more embedding models **Description** Hi, is it possible to ingrate two different embedding models? Let us say model1 = ScoringBasedEmbeddingModel(k=5, eta=1, scoring_type='TransE'), and model...

I was trying following code and found an error from transformers import AutoModelForSequenceClassification, AutoTokenizer from transformers_interpret import ZeroShotClassificationExplainer tokenizer = AutoTokenizer.from_pretrained('facebook/bart-large-mnli') model = AutoModelForSequenceClassification.from_pretrained('facebook/bart-large-mnli') zero_shot_explainer = ZeroShotClassificationExplainer(model, tokenizer) word_attributions =...

Hi, I was trying TransE embedding of Grape, and I am curious how to get embedding of each node or relation as a vector. For example, Protein 1 enables Protein...

Question: Is it possible get the embedding of the relations and entities separately using Ontoprotein ?

6

Hi, I am just curious is it possible to get the embedding of proteins and relations in https://www.zjukg.org/project/ProteinKG25/ separately using huggingface ontoprotein model ( https://huggingface.co/zjunlp/OntoProtein)? Let us say, Protein_1 Enables...

Re-train or fine tuning ESM-3 model

2

Hi, Is it possible to fine-tune or re-train the ESM-3 model with the protein sequence and structure or pdb file, and then apply the fine-tuned model to generate sequence or...