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Model: yerevann/chemlactica-125m Source: Original Platform
2026-09-06 17:50:17 +08:00
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+*.7z filter=lfs diff=lfs merge=lfs -text
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--- a/README.md
+++ b/README.md
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+---
+license: cc-by-nc-4.0
+language:
+- en
+library_name: transformers
+pipeline_tag: text-generation
+base_model: facebook/galactica-125m
+tags:
+- chemistry
+- molecular-generation
+- molecular-property-prediction
+- arxiv:2407.18897
+---
+
+# Chemlactica-125M
+
+Chemlactica-125M is a 125M-parameter causal language model for molecular generation, property conditioning, property prediction, and optimization. It continues pretraining from [Galactica-125M](https://huggingface.co/facebook/galactica-125m) on [PubChemForLM](https://huggingface.co/datasets/yerevann/PubChemForLM): 40 billion tokens describing more than 110 million PubChem molecules, computed properties, and molecular similarities.
+
+## Model details
+
+- Architecture: `OPTForCausalLM`; 12 layers, hidden size 768, 12 attention heads
+- Context length: 2,048 tokens
+- Training objective: causal language modeling
+- Training-data cutoff: January 26, 2023
+- Molecular preprocessing: RDKit-canonicalized SMILES; numeric properties rounded to two decimals
+
+## Prompt format
+
+Chemlactica prompts begin with `</s>`. Generate a molecule by ending a structured property prefix with `[START_SMILES]`:
+
+```text
+</s>[SAS]2.25[/SAS][SIMILAR]CC(=O)OC1=CC=CC=C1C(=O)O 0.62[/SIMILAR][START_SMILES]
+```
+
+The similarity field is `reference SMILES`, a space, then the target ECFP Tanimoto similarity. To predict a property, provide the molecule and open the desired property tag:
+
+```text
+</s>[START_SMILES]CC(=O)OC1=CC=CC=C1C(=O)O[END_SMILES][SAS]
+```
+
+Common trained tags include `[SAS]`, `[QED]`, `[WEIGHT]`, `[TPSA]`, `[CLOGP]`, `[FORMULA]`, `[RINGCOUNT]`, and `[SIMILAR]`. Use only tags present in the training format; arbitrary natural-language instructions or oracle names are unsupported.
+
+## Usage
+
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+
+model_id = "yerevann/chemlactica-125m"
+tokenizer = AutoTokenizer.from_pretrained(model_id)
+model = AutoModelForCausalLM.from_pretrained(
+    model_id, device_map="auto", torch_dtype="auto"
+)
+
+prompt = "</s>[QED]0.80[/QED][START_SMILES]"
+inputs = tokenizer(prompt, return_tensors="pt").to(model.device)
+outputs = model.generate(
+    **inputs, max_new_tokens=128, do_sample=True, temperature=0.8, top_p=0.95
+)
+print(tokenizer.decode(outputs[0], skip_special_tokens=False))
+```
+
+For optimization, use the [Mol-E implementation and canonical PMO prompt registry](https://github.com/YerevaNN/ChemLactica/tree/main/chemlactica/mol_opt). In the five-seed PMO-10K reproduction, this checkpoint obtains summed Top-10 AUC scores of 16.944598 (task-agnostic) and 20.429421 (task-informed) across 23 tasks.
+
+## Intended use and limitations
+
+This checkpoint is intended for research on small-molecule language modeling and optimization. Generated strings may be invalid, duplicated, chemically implausible, difficult to synthesize, unsafe, or outside the requested property range. Reported properties are predictions or optimization-oracle outputs, not experimental measurements. PubChem-derived data may contain errors or biases, and the model has no knowledge of changes after the cutoff date. Do not use it for clinical decisions or as a substitute for experimental and expert review.
+
+## Resources and license
+
+- Paper: [Small Molecule Optimization with Large Language Models](https://arxiv.org/abs/2407.18897)
+- Code: [YerevaNN/ChemLactica](https://github.com/YerevaNN/ChemLactica)
+- Data: [yerevann/PubChemForLM](https://huggingface.co/datasets/yerevann/PubChemForLM)
+- Family: [Chemlactica-1.3B](https://huggingface.co/yerevann/chemlactica-1.3b), [Chemma-2B](https://huggingface.co/yerevann/chemma-2b)
+
+The checkpoint is released under [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). Users must also comply with applicable terms of the base model and source data.
--- a/config.json
+++ b/config.json
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+{
+  "_name_or_path": "yerevann/chemlactica-125m",
+  "_remove_final_layer_norm": false,
+  "activation_dropout": 0.0,
+  "activation_function": "gelu",
+  "architectures": [
+    "OPTForCausalLM"
+  ],
+  "attention_dropout": 0.1,
+  "bos_token_id": 0,
+  "do_layer_norm_before": true,
+  "dropout": 0.1,
+  "enable_bias": true,
+  "eos_token_id": 2,
+  "ffn_dim": 3072,
+  "hidden_size": 768,
+  "init_std": 0.02,
+  "layer_norm_elementwise_affine": true,
+  "layerdrop": 0.0,
+  "learned_embeddings": true,
+  "max_position_embeddings": 2048,
+  "model_type": "opt",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 1,
+  "scale_embeddings": false,
+  "torch_dtype": "float32",
+  "transformers_version": "4.39.0",
+  "use_cache": true,
+  "vocab_size": 50072,
+  "word_embed_proj_dim": 768
+}
--- a/generation_config.json
+++ b/generation_config.json
@@ -0,0 +1,7 @@
+{
+  "_from_model_config": true,
+  "bos_token_id": 0,
+  "eos_token_id": 2,
+  "pad_token_id": 1,
+  "transformers_version": "4.39.0"
+}
--- a/model.safetensors
+++ b/model.safetensors
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+version https://git-lfs.github.com/spec/v1
+oid sha256:2f01ca8c842e447fb81987d01e6f56c0fb567300c2a6981137d8bc924cdd8a40
+size 500365200
--- a/special_tokens_map.json
+++ b/special_tokens_map.json
@@ -0,0 +1,91 @@
+{
+  "additional_special_tokens": [
+    "[SYNONYM]",
+    "[RELATED]",
+    "[SIMILAR]",
+    "[PROPERTY]",
+    "[SAS]",
+    "[WEIGHT]",
+    "[TPSA]",
+    "[CLOGP]",
+    "[QED]",
+    "[NUMHDONORS]",
+    "[NUMHACCEPTORS]",
+    "[NUMHETEROATOMS]",
+    "[NUMROTATABLEBONDS]",
+    "[NOCOUNT]",
+    "[NHOHCOUNT]",
+    "[RINGCOUNT]",
+    "[HEAVYATOMCOUNT]",
+    "[FRACTIONCSP3]",
+    "[NUMAROMATICRINGS]",
+    "[NUMSATURATEDRINGS]",
+    "[NUMAROMATICHETEROCYCLES]",
+    "[NUMAROMATICCARBOCYCLES]",
+    "[NUMSATURATEDHETEROCYCLES]",
+    "[NUMSATURATEDCARBOCYCLES]",
+    "[NUMALIPHATICRINGS]",
+    "[NUMALIPHATICHETEROCYCLES]",
+    "[NUMALIPHATICCARBOCYCLES]",
+    "[IUPAC]",
+    "[VAR_NAME]",
+    "[VAR_DESC]",
+    "[VAR_VAL]",
+    "[ASSAY_NAME]",
+    "[ASSAY_DESC]",
+    "[/SYNONYM]",
+    "[/RELATED]",
+    "[/SIMILAR]",
+    "[/PROPERTY]",
+    "[/SAS]",
+    "[/WEIGHT]",
+    "[/TPSA]",
+    "[/CLOGP]",
+    "[/QED]",
+    "[/NUMHDONORS]",
+    "[/NUMHACCEPTORS]",
+    "[/NUMHETEROATOMS]",
+    "[/NUMROTATABLEBONDS]",
+    "[/NOCOUNT]",
+    "[/NHOHCOUNT]",
+    "[/RINGCOUNT]",
+    "[/HEAVYATOMCOUNT]",
+    "[/FRACTIONCSP3]",
+    "[/NUMAROMATICRINGS]",
+    "[/NUMSATURATEDRINGS]",
+    "[/NUMAROMATICHETEROCYCLES]",
+    "[/NUMAROMATICCARBOCYCLES]",
+    "[/NUMSATURATEDHETEROCYCLES]",
+    "[/NUMSATURATEDCARBOCYCLES]",
+    "[/NUMALIPHATICRINGS]",
+    "[/NUMALIPHATICHETEROCYCLES]",
+    "[/NUMALIPHATICCARBOCYCLES]",
+    "[/IUPAC]",
+    "[/VAR_NAME]",
+    "[/VAR_DESC]",
+    "[/VAR_VAL]",
+    "[/ASSAY_NAME]",
+    "[/ASSAY_DESC]"
+  ],
+  "bos_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
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+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "<pad>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}
--- a/tokenizer.json
+++ b/tokenizer.json
--- a/tokenizer_config.json
+++ b/tokenizer_config.json
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+{
+  "added_tokens_decoder": {
+    "0": {
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
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+    },
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+      "rstrip": false,
+      "single_word": false,
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+      "lstrip": false,
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+      "special": true
+    },
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "4": {
+      "content": "[START_REF]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "5": {
+      "content": "[END_REF]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "6": {
+      "content": "[IMAGE]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "7": {
+      "content": "<fragments>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
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+      "special": true
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+      "content": "<work>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
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+    },
+    "10": {
+      "content": "</work>",
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+      "lstrip": false,
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+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "content": "[END_SUB]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "content": "[START_DNA]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "16": {
+      "content": "[END_DNA]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "17": {
+      "content": "[START_AMINO]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "18": {
+      "content": "[END_AMINO]",
+      "lstrip": false,
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+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
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+      "content": "[START_SMILES]",
+      "lstrip": false,
+      "normalized": false,
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+    },
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+      "content": "[END_SMILES]",
+      "lstrip": false,
+      "normalized": false,
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+      "special": true
+    },
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+      "special": true
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+      "special": true
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+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
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+      "special": true
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+      "content": "[CLOGP]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "content": "[QED]",
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+      "normalized": false,
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+    },
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+    },
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+    "[NUMROTATABLEBONDS]",
+    "[NOCOUNT]",
+    "[NHOHCOUNT]",
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+    "[FRACTIONCSP3]",
+    "[NUMAROMATICRINGS]",
+    "[NUMSATURATEDRINGS]",
+    "[NUMAROMATICHETEROCYCLES]",
+    "[NUMAROMATICCARBOCYCLES]",
+    "[NUMSATURATEDHETEROCYCLES]",
+    "[NUMSATURATEDCARBOCYCLES]",
+    "[NUMALIPHATICRINGS]",
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+    "[NUMALIPHATICCARBOCYCLES]",
+    "[IUPAC]",
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+    "[/SAS]",
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+    "[/TPSA]",
+    "[/CLOGP]",
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+    "[/NUMHDONORS]",
+    "[/NUMHACCEPTORS]",
+    "[/NUMHETEROATOMS]",
+    "[/NUMROTATABLEBONDS]",
+    "[/NOCOUNT]",
+    "[/NHOHCOUNT]",
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+    "[/HEAVYATOMCOUNT]",
+    "[/FRACTIONCSP3]",
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+    "[/NUMSATURATEDRINGS]",
+    "[/NUMAROMATICHETEROCYCLES]",
+    "[/NUMAROMATICCARBOCYCLES]",
+    "[/NUMSATURATEDHETEROCYCLES]",
+    "[/NUMSATURATEDCARBOCYCLES]",
+    "[/NUMALIPHATICRINGS]",
+    "[/NUMALIPHATICHETEROCYCLES]",
+    "[/NUMALIPHATICCARBOCYCLES]",
+    "[/IUPAC]",
+    "[/VAR_NAME]",
+    "[/VAR_DESC]",
+    "[/VAR_VAL]",
+    "[/ASSAY_NAME]",
+    "[/ASSAY_DESC]"
+  ],
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+  "eos_token": "</s>",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "<pad>",
+  "tokenizer_class": "PreTrainedTokenizerFast"
+}