End of training

README.md

@@ -1,4 +1,5 @@
 ---
+library_name: transformers
 base_model: JuIm/ProGemma2
 tags:
 - generated_from_trainer
@@ -12,32 +13,40 @@ should probably proofread and complete it, then remove this comment. -->
 
 # ProGemma2
 
-This is a custom configuration of Google’s Gemma 2 LLM that is being pre-trained on amino acid sequences of 512 AA or less in length. Periodic updates are made to this page as training reaches new checkpoints.
+This model is a fine-tuned version of [JuIm/ProGemma2](https://huggingface.co/JuIm/ProGemma2) on an unknown dataset.
 
-The purpose of this model was to investigate the differences between ProGemma and ProtGPT (GPT-2 architecture) as it pertains to sequence generation. Training loss is ~2.2. Perplexity scores as well as AlphaFold 3’s ptm, pLDDT, and iptm scores are generally in line with ProtGPT’s scores for sequence lengths < 250, although the testing phase is still very early. I have yet to do testing for sequence lengths > 250. More robust testing is also required for lengths < 250 AA. In my very preliminary testing, HHblit e-values of ~0.1 are achieved with relatively easily.
+## Model description
 
-Controlled generation is not a capability of this model, and therefore serves as a method to significantly improve generation as, in principal, a sequence that performs a given function or resides in a particular cellular location can be generated.
+More information needed
 
-In sequence generation, a top_k of 950 appears to work well as it prevents repetition. This is also seen in ProtGPT.
+## Intended uses & limitations
 
-Below is code using the Transformers library to generate sequences using ProGemma.
+More information needed
 
-from transformers import pipeline, AutoTokenizer, AutoModelForCausalLM
+## Training and evaluation data
 
-model = AutoModelForCausalLM.from_pretrained("JuIm/ProGemma2")
+More information needed
 
-tokenizer = AutoTokenizer.from_pretrained("JuIm/Amino-Acid-Sequence-Tokenizer")
+## Training procedure
 
-progemma = pipeline("text-generation", model=model, tokenizer=tokenizer)
+### Training hyperparameters
 
-sequence = progemma("", top_k=950, max_length=100, num_return_sequences=1, do_sample=True, repetition_penalty=1.2, eos_token_id=21, pad_token_id=22, bos_token_id=20)
+The following hyperparameters were used during training:
+- learning_rate: 0.001
+- train_batch_size: 2
+- eval_batch_size: 8
+- seed: 42
+- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
+- lr_scheduler_type: linear
+- lr_scheduler_warmup_ratio: 0.4
+- training_steps: 3500
+
+### Training results
 
-s = sequence[0]['generated_text']
 
-print(s)
 
 ### Framework versions
 
-- Transformers 4.42.4
+- Transformers 4.44.2
 - Pytorch 2.4.0+cu121
 - Tokenizers 0.19.1

config.json

@@ -26,7 +26,7 @@
   "rope_theta": 10000.0,
   "sliding_window": 256,
   "torch_dtype": "float32",
-  "transformers_version": "4.42.4",
+  "transformers_version": "4.44.2",
   "use_cache": true,
   "vocab_size": 24
 }

generation_config.json

@@ -4,5 +4,5 @@
   "cache_implementation": "hybrid",
   "eos_token_id": 21,
   "pad_token_id": 22,
-  "transformers_version": "4.42.4"
+  "transformers_version": "4.44.2"
 }

model.safetensors

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runs/Sep05_14-29-10_d40fbdb96b4d/events.out.tfevents.1725546554.d40fbdb96b4d.1521.0

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training_args.bin

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