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Dear Author,
Thank you for developing such a perfect model like C.Origami. It's a great work, but I have encountered some difficulties.
First, I have DNA sequence information from other species,…
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I'd like to consult about a camera pose conversion issue while conducting experiments on the dna dataset. I've rewritten the dna dataset into colmap format for training, but the results are poor. Here…
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Hello developers,
Very cool tool and great paper.
I was wondering if this tool could be adapted for non-human samples (e.x. cattle)? Or was it specifically developed or trained with hg19 in mi…
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- [ ] Datasets
- [ ] AlphaFold 3 PDB dataset
- [x] PDB mmCIF filtering script (`scripts/filter_pdb_mmcifs.py`)
- [x] Fix periodic residue count-chemical component coun…
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(modelenv) lsl@asus:~$ bonito train --epochs 1 --lr 5e-4 --pretrained dna_r10.4.1_e8.2_400bps_hac@v5.0.0 --directory /data/training/ctc-data /data/training/fine-tuned-model
[loading model]
[using pr…
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I am currently working on training a model to detect DNA modifications in **all contexts (all positions)** using Remora. During the data preparation step, I encountered an issue where the `--motif` ar…
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I want to know what is the training and testing dataset for ipdSummry model to detect DNA methylation.
In this paper "Direct detection of DNA methylation during single-molecule, real-time sequencin…
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Hi,
i'm wondering if it is neccessary to reverse all input DNA sequence to positive strand when using sei. Biologically speaking both strand should have the same peak but i'm not sure whether this is…
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**Use-cases/examples of this new feature**
Model training on data from DNA-encoded library screening.
**Desired solution/workflow**
Implement the custom loss described in this paper: https://pubs…
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When calling :
hidden_states = model(inputs)[0] # [1, sequence_length, 768]
we receive traceback:
in :1 │
│ …