instadeepai/nucleotide-transformer issues and pull requests

#89 - Pre-training data for 1000 Genomes Project

Issue - State: open - Opened by cbirchsy 13 days ago

#88 - A silly question about the label of enhancers mapping to the biological meaning?

Issue - State: closed - Opened by nanu23333 about 1 month ago - 2 comments

#87 - PlantGenomicBenchmark sample size discrepancy

Issue - State: closed - Opened by gonzalobenegas about 1 month ago - 2 comments

#86 - feat: Add SegmentEnformer and SegmentBorzoi example

Issue - State: closed - Opened by yanisadel about 1 month ago

#85 - How can I fine tuning the downstream tasks on my own server?

Issue - State: open - Opened by nanu23333 about 1 month ago - 2 comments

#84 - Request for a numerical version of NT-tasks evaluations

Issue - State: closed - Opened by QiuyiLi 2 months ago - 1 comment

#83 - For genome annotation

Issue - State: open - Opened by starskyzheng 2 months ago - 2 comments

#82 - ClinVAR dataset

Issue - State: open - Opened by WENHUAN22 2 months ago - 1 comment

#81 - pretraining the nucleotide-transformer

Issue - State: open - Opened by mpage21 3 months ago - 2 comments

#80 - The shape of embedding issue

Issue - State: open - Opened by WhiteNan 4 months ago - 2 comments

#79 - Detection Threshold(s) for SegmentNT

Issue - State: closed - Opened by zsewa 4 months ago - 1 comment

#79 - Detection Threshold(s) for SegmentNT

Issue - State: closed - Opened by zsewa 4 months ago - 1 comment

#78 - SegmentNT with a frozen encoder?

Issue - State: open - Opened by Azai-yx 6 months ago

#78 - SegmentNT with a frozen encoder?

Issue - State: open - Opened by Azai-yx 6 months ago

#77 - A little bit different embeddings between jax and pytorch models

Issue - State: closed - Opened by nzhang89 6 months ago - 2 comments

#77 - A little bit different embeddings between jax and pytorch models

Issue - State: closed - Opened by nzhang89 6 months ago - 2 comments

#76 - question about the arguments within the get_pretrained_model() function

Issue - State: open - Opened by hongruhu 7 months ago

#76 - question about the arguments within the get_pretrained_model() function

Issue - State: open - Opened by hongruhu 7 months ago

#75 - 72 load the checkpoints from hf

Pull Request - State: closed - Opened by dallatt 7 months ago

#75 - 72 load the checkpoints from hf

Pull Request - State: closed - Opened by dallatt 7 months ago

#74 - feat: Fix inference notebook

Pull Request - State: closed - Opened by dallatt 7 months ago

#74 - feat: Fix inference notebook

Pull Request - State: closed - Opened by dallatt 7 months ago

#73 - Fix inference notebook

Issue - State: closed - Opened by dallatt 7 months ago

#73 - Fix inference notebook

Issue - State: closed - Opened by dallatt 7 months ago

#72 - Load the checkpoints from HF

Issue - State: closed - Opened by dallatt 7 months ago

#72 - Load the checkpoints from HF

Issue - State: closed - Opened by dallatt 7 months ago

#71 - Update README

Issue - State: closed - Opened by JavierMenRev 7 months ago

#71 - Update README

Issue - State: closed - Opened by JavierMenRev 7 months ago

#70 - Embeddings and hidden states of Agro-NT model (New to this field so please excuse my question if it is really naive/stupid.)

Issue - State: closed - Opened by NikeeShrestha 8 months ago - 3 comments

#70 - Embeddings and hidden states of Agro-NT model (New to this field so please excuse my question if it is really naive/stupid.)

Issue - State: closed - Opened by NikeeShrestha 8 months ago - 3 comments

#69 - Zero Shot Data?

Issue - State: closed - Opened by fma231 8 months ago - 1 comment

#69 - Zero Shot Data?

Issue - State: closed - Opened by fma231 8 months ago - 1 comment

#68 - Can‘t reproduce SegmentNT's MCC score on segmenting 5UTR on test set (chr20 and chr21)

Issue - State: closed - Opened by JasonLinjc 9 months ago - 1 comment

#68 - Can‘t reproduce SegmentNT's MCC score on segmenting 5UTR on test set (chr20 and chr21)

Issue - State: closed - Opened by JasonLinjc 9 months ago - 1 comment

#67 - how to get the segmentation dataset of genomics elements

Issue - State: closed - Opened by lightyisu 9 months ago - 1 comment

#67 - how to get the segmentation dataset of genomics elements

Issue - State: closed - Opened by lightyisu 9 months ago - 1 comment

#66 - error while executing the Google Colab inference_nt notebook

Issue - State: closed - Opened by amitpande74 9 months ago - 2 comments

#66 - error while executing the Google Colab inference_nt notebook

Issue - State: closed - Opened by amitpande74 9 months ago - 2 comments

#65 - The length of input sequence for SegmentNT

Issue - State: closed - Opened by hezt 10 months ago - 1 comment

#65 - The length of input sequence for SegmentNT

Issue - State: closed - Opened by hezt 10 months ago - 1 comment

#64 - where is the intermedia checkpoints

Issue - State: closed - Opened by TerminatorJ 10 months ago - 1 comment

#64 - where is the intermedia checkpoints

Issue - State: closed - Opened by TerminatorJ 10 months ago - 1 comment

#63 - how to deal with the seq position of reference genome?

Issue - State: closed - Opened by zzzseeu 10 months ago - 1 comment

#63 - how to deal with the seq position of reference genome?

Issue - State: closed - Opened by zzzseeu 10 months ago - 1 comment

#62 - Confusion about the max_positions value

Issue - State: closed - Opened by Cheerful0 10 months ago - 1 comment

#62 - Confusion about the max_positions value

Issue - State: closed - Opened by Cheerful0 10 months ago - 1 comment

#61 - feat: Add verbose argument to bypass tqdm freeze

Pull Request - State: closed - Opened by dallatt 10 months ago

#61 - feat: Add verbose argument to bypass tqdm freeze

Pull Request - State: closed - Opened by dallatt 10 months ago

#60 - Enable downloading model without tqdm

Issue - State: closed - Opened by dallatt 10 months ago

#60 - Enable downloading model without tqdm

Issue - State: closed - Opened by dallatt 10 months ago

#59 - Cannot download the pre-training weight

Issue - State: closed - Opened by HelloWorldLTY 10 months ago - 2 comments