Upload file

README.md

@@ -0,0 +1,55 @@
+---
+tags:
+- dna
+- human_genome
+---
+
+# WARNING
+
+This readme should be changed according to current model. Num steps: 1925000
+
+# GENA-LM
+
+GENA-LM is a transformer masked language model trained on human DNA sequence.
+
+Differences between GENA-LM and DNABERT:
+- BPE tokenization instead of k-mers;
+- input sequence size is about 3000 nucleotides (512 BPE tokens) compared to 510 nucleotides of DNABERT
+- pre-training on T2T vs. GRCh38.p13 human genome assembly.
+
+Source code and data: https://github.com/AIRI-Institute/GENA_LM
+
+## Examples
+### How to load the model to fine-tune it on classification task
+```python
+from src.gena_lm.modeling_bert import BertForSequenceClassification
+from transformers import AutoTokenizer
+
+tokenizer = AutoTokenizer.from_pretrained('AIRI-Institute/gena-lm-bert-base')
+model = BertForSequenceClassification.from_pretrained('AIRI-Institute/gena-lm-bert-base')
+```
+
+## Model description
+GENA-LM model is trained in a masked language model (MLM) fashion, following the methods proposed in the BigBird paper by masking 85% of tokens. Model config for `gena-lm-bert-base` is similar to the bert-base:
+
+- 512 Maximum sequence length
+- 12 Layers, 12 Attention heads
+- 768 Hidden size
+- 32k Vocabulary size
+
+We pre-trained `gena-lm-bert-base` using the latest T2T human genome assembly (https://www.ncbi.nlm.nih.gov/assembly/GCA_009914755.3/). Pre-training was performed for 500,000 iterations with the same parameters as in BigBird, except sequence length was equal to 512 tokens and we used pre-layer normalization in Transformer.
+
+## Downstream tasks
+Currently, gena-lm-bert-base model has been finetuned  and tested on promoter prediction task.  Its' performance is comparable to previous SOTA results. We plan to fine-tune and make available models for other downstream tasks in the near future.
+
+### Fine-tuning GENA-LM on our data and scoring
+After fine-tuning gena-lm-bert-base on promoter prediction dataset, following results were achieved: 
+
+| model                    | seq_len (bp) | F1    |
+|--------------------------|--------------|-------|
+| DeePromoter              | 300          | 95.60 |
+| GENA-LM bert-base (ours) | 2000         | 95.72 |
+| BigBird                  | 16000        | 99.90 |
+
+We can conclude that our model achieves comparable performance to the previously published results for promoter prediction task.
+

config.json

@@ -0,0 +1,28 @@
+{
+  "architectures": [
+    "BertForMaskedLM"
+  ],
+  "auto_map": {
+    "AutoModel": "modeling_bert.BertForMaskedLM"
+  },
+  "attention_probs_dropout_prob": 0.1,
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 3,
+  "pre_layer_norm": true,
+  "last_layer_norm": false,
+  "position_embedding_type": "absolute",
+  "transformers_version": "4.6.0.dev0",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 32000
+}

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2f2400ba33d01df2bd58be5f8556f5b09bb69b70edb6f82eec31dc2247d90c1c
+size 541124033

special_tokens_map.json

@@ -0,0 +1 @@
+{"unk_token": "[UNK]", "sep_token": "[SEP]", "pad_token": "[PAD]", "cls_token": "[CLS]", "mask_token": "[MASK]"}

tokenizer_config.json

@@ -0,0 +1 @@
+{"tokenizer_class": "PreTrainedTokenizerFast"}