update with major refactor

README.md

@@ -4,7 +4,7 @@
 from huggingface_hub import snapshot_download
 from pathlib import Path
 
-model_name = "genbio-ai/dnafm-7b-nt-promoter-all-ckpt"
+model_name = "genbio-ai/aido_dna_7b-nt-promoter-all-ckpt"
 genbio_models_path = Path.home().joinpath('genbio_models', model_name)
 genbio_models_path.mkdir(parents=True, exist_ok=True)
 snapshot_download(repo_id=model_name, local_dir=genbio_models_path)
@@ -12,12 +12,12 @@ snapshot_download(repo_id=model_name, local_dir=genbio_models_path)
 ### Load model for inference
 ```python
 import torch
-from genbio_finetune.tasks import SequenceClassification
+from modelgenerator.tasks import SequenceClassification
 
 ckpt_path = genbio_models_path.joinpath('model.ckpt')
 model = SequenceClassification.load_from_checkpoint(ckpt_path, strict_loading=False).eval()
 
-collated_batch = model.collate({"sequences": ["ACGT", "AGCT"]})
+collated_batch = model.transform({"sequences": ["ACGT", "AGCT"]})
 logits = model(collated_batch)
 print(logits)
 print(torch.argmax(logits, dim=-1))

config.yaml

@@ -141,10 +141,10 @@ trainer:
   reload_dataloaders_every_n_epochs: 0
   default_root_dir: logs
 model:
-  class_path: genbio_finetune.tasks.SequenceClassification
+  class_path: modelgenerator.tasks.SequenceClassification
   init_args:
     backbone:
-      class_path: genbio_finetune.models.dnafm
+      class_path: modelgenerator.backbones.aido_dna_7b
       init_args:
         from_scratch: false
         use_peft: true
@@ -155,7 +155,7 @@ model:
         config_overwrites: null
         model_init_args: null
         max_length: 302
-    adapter: genbio_finetune.models.LinearCLSAdapter
+    adapter: modelgenerator.adapters.LinearCLSAdapter
     n_classes: 2
     optimizer:
       class_path: torch.optim.AdamW
@@ -173,14 +173,14 @@ model:
         differentiable: false
         fused: null
     lr_scheduler:
-      class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
+      class_path: modelgenerator.lr_schedulers.CosineWithWarmup
       init_args:
         warmup_ratio: 0.1
     use_legacy_adapter: false
     strict_loading: true
     reset_optimizer_states: false
 data:
-  class_path: genbio_finetune.data.NTClassification
+  class_path: modelgenerator.data.NTClassification
   init_args:
     hf_name: InstaDeepAI/nucleotide_transformer_downstream_tasks
     task: promoter_all