methylbert

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``` (methylbert_39) python3 test_deconvolute.py Building Vocab Total number of sequences : 612 # of reads in each label: [319. 293.] No detected GPU device. Load the model on CPU The...

hanyangii

About read classificaiton of methylbert

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Hi, I'm trying to apply MethylBERT in my WGBS data, but some problems occurred. I fintuned the methylbert_hg19_4l and used it to distinguish tumor from normal sequence in a test...

guanghaoli

Specification about DMR.csv

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Hi @hanyangii, Could you share more details about the preparation of the DMR.csv? I tried to fine-tune based on a dorado called BAM file, but the fine-tune doesn't seem to...

Yijun-Tian

Issue with Tumor Fraction Prediction Using Pre-trained MethylBERT

3

As described in the [data preparation](https://github.com/hanyangii/methylbert/blob/main/tutorials/01_Data_Preparation.md) tutorial, fine-tuning the MethylBERT model with pure tumor and normal samples is optional. So I used the pre-trained model from https://huggingface.co/hanyangii/methylbert_hg19_12l to directly predict...

LiJingqi7

When running methylbert with `-p hanyangii/methylbert_mm10_4l` option ``` Restore the pretrained model hanyangii/methylbert_mm10_4l Cross entropy loss assigned Some weights of MethylBertEmbeddedDMR were not initialized from the model checkpoint at hanyangii/methylbert_mm10_4l...

hanyangii

Hello! I encountered an issue during pretraining where the forward method doesn't recognize the masked_lm_labels parameter. "/home/mickey/Tools/miniconda3/envs/methylbert/lib/python3.11/site-packages/methylbert/trainer.py", line 287 mask_lm_output = self.model.forward(input_ids = data["input"], masked_lm_labels = data["label"]) Questions: Should the...

sw1125598670

When I executed pip install methylbert, the following error occurred. I would be very grateful if you could help me. (methylbert) C:\Users\Administrator>pip install methylbert Collecting methylbert Using cached methylbert-2.0.2-py3-none-any.whl.metadata (10...

kite-f

Dear @hanyangii , Following your README.md, I used 23 HCC tissue samples and 23 normal tissues to fine-tune the model, and then applied it to 24 HCC plasma samples and...

LiJingqi7