---
base_model: microsoft/mpnet-base
datasets:
- SwastikN/sxc_med_llm_chemical_gen
language:
- en
library_name: sentence-transformers
license: apache-2.0
metrics:
- cosine_accuracy
- dot_accuracy
- manhattan_accuracy
- euclidean_accuracy
- max_accuracy
pipeline_tag: sentence-similarity
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:117502
- loss:MultipleNegativesRankingLoss
widget:
- source_sentence: Help me make the molecule CC(=O)OC[C@H](OC(C)=O)C(=O)N1CCCC[C@H]1C1CCN(C(=O)c2cc3ccccc3n2C)CC1
with the same hydrogen bond donors. The output molecule should be similar to the
input molecule. Please inform me of the number of hydrogen bond donor(s) of the
optimized molecule.
sentences:
- Your requirements guided the optimization, resulting in the molecule "CC(=O)OC(CCl)C(Cc1cccs1)[C@H](OC(C)=O)C(=O)N1CCCC[C@H]1C1CCN(C(=O)c2cc3ccccc3n2C)CC1"
with an approximate hydrogen bond donor(s) of 0.
- Given a molecule expressed in SMILES string, help me optimize it according to
my requirements.
- Help me adapt a molecular structure denoted in SMILES string based on my preferences.
- source_sentence: How can we modify the molecule CCC(CC)=C(CC)c1ccccc1OC(=O)OC(N=[N+]=[N-])c1ccccc1
to decrease its blood-brain barrier penetration (BBBP) value while keeping it
similar to the input molecule? Please inform me of the BBBP value of the optimized
molecule.
sentences:
- Describe a technology used for measuring people's emotional responses.
- I've successfully optimized the molecule according to your needs, resulting in
"CCOC(=O)c1ccccc1OC(=O)OC(N=[N+]=[N-])c1ccccc1" with an approximate BBBP value
of 0.71.
- Given a molecule expressed in SMILES string, help me optimize it according to
my requirements.
- source_sentence: How can we modify the molecule C/C(=C/C(=O)N1CC[C@H](CC(CCCCCC(CO)C(=O)O)NC(=O)OC(C)(C)C)[C@H]1c1cccnc1)C(=O)O
to increase its blood-brain barrier penetration (BBBP) value while keeping it
similar to the input molecule?
sentences:
- Given a molecule expressed in SMILES string, help me optimize it according to
my requirements.
- Aid me in refining a molecular structure written in SMILES notation based on my
criteria.
- Taking your requirements into account, I've optimized the molecule to "C/C(=C/C(=O)N1CC[C@H](CNC(=O)[C@H](CO)NC(=O)OC(C)(C)C)[C@H]1c1cccnc1)C(=O)O".
- source_sentence: Support me in transforming the molecule [SMILES] by incorporating
the same hydrogen bond acceptors and maintaining its resemblance to the original
molecule.
sentences:
- Taking your requirements into account, I've optimized the molecule to "CCOc1cccc(C2c3c(oc4ccc(C)cc4c3=O)C(=O)N2CCN(CC)CC)c1".
- Help me adapt a molecular structure denoted in SMILES string based on my preferences.
- Help me adapt a molecular structure denoted in SMILES string based on my preferences.
- source_sentence: With a molecule represented by the SMILES string CNNNCC(=O)N[C@H](C)C[C@@H](C)NCc1ccc2c(c1)CCC2,
propose adjustments that can increase its logP value while keeping the output
molecule structurally related to the input molecule.
sentences:
- Aid me in refining a molecular structure written in SMILES notation based on my
criteria.
- Given a molecule expressed in SMILES string, help me optimize it according to
my requirements.
- In line with your criteria, I've optimized the molecule and present it as "C[C@H](C[C@@H](C)NC(=O)COC(C)(C)C)NCc1ccc2c(c1)CCC2".
model-index:
- name: MPNet base trained on AllNLI triplets
results:
- task:
type: triplet
name: Triplet
dataset:
name: all nli dev
type: all-nli-dev
metrics:
- type: cosine_accuracy
value: 0.6562222222222223
name: Cosine Accuracy
- type: dot_accuracy
value: 0.5342222222222223
name: Dot Accuracy
- type: manhattan_accuracy
value: 0.7075555555555556
name: Manhattan Accuracy
- type: euclidean_accuracy
value: 0.6584444444444445
name: Euclidean Accuracy
- type: max_accuracy
value: 0.7075555555555556
name: Max Accuracy
- type: cosine_accuracy
value: 0.9804444444444445
name: Cosine Accuracy
- type: dot_accuracy
value: 0.01888888888888889
name: Dot Accuracy
- type: manhattan_accuracy
value: 0.9811111111111112
name: Manhattan Accuracy
- type: euclidean_accuracy
value: 0.9802222222222222
name: Euclidean Accuracy
- type: max_accuracy
value: 0.9811111111111112
name: Max Accuracy
---
# MPNet base trained on AllNLI triplets
This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [microsoft/mpnet-base](https://huggingface.co./microsoft/mpnet-base) on the [sxc_med_llm_chemical_gen](https://huggingface.co./datasets/SwastikN/sxc_med_llm_chemical_gen) dataset. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.
## Model Details
### Model Description
- **Model Type:** Sentence Transformer
- **Base model:** [microsoft/mpnet-base](https://huggingface.co./microsoft/mpnet-base)
- **Maximum Sequence Length:** 512 tokens
- **Output Dimensionality:** 768 tokens
- **Similarity Function:** Cosine Similarity
- **Training Dataset:**
- [sxc_med_llm_chemical_gen](https://huggingface.co./datasets/SwastikN/sxc_med_llm_chemical_gen)
- **Language:** en
- **License:** apache-2.0
### Model Sources
- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
- **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co./models?library=sentence-transformers)
### Full Model Architecture
```
SentenceTransformer(
(0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: MPNetModel
(1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)
```
## Usage
### Direct Usage (Sentence Transformers)
First install the Sentence Transformers library:
```bash
pip install -U sentence-transformers
```
Then you can load this model and run inference.
```python
from sentence_transformers import SentenceTransformer
# Download from the 🤗 Hub
model = SentenceTransformer("Saideepthi55/sentencetransformer-ft")
# Run inference
sentences = [
'With a molecule represented by the SMILES string CNNNCC(=O)N[C@H](C)C[C@@H](C)NCc1ccc2c(c1)CCC2, propose adjustments that can increase its logP value while keeping the output molecule structurally related to the input molecule.',
'Given a molecule expressed in SMILES string, help me optimize it according to my requirements.',
'In line with your criteria, I\'ve optimized the molecule and present it as "C[C@H](C[C@@H](C)NC(=O)COC(C)(C)C)NCc1ccc2c(c1)CCC2".',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]
# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]
```
## Evaluation
### Metrics
#### Triplet
* Dataset: `all-nli-dev`
* Evaluated with [TripletEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.TripletEvaluator)
| Metric | Value |
|:-------------------|:-----------|
| cosine_accuracy | 0.6562 |
| dot_accuracy | 0.5342 |
| manhattan_accuracy | 0.7076 |
| euclidean_accuracy | 0.6584 |
| **max_accuracy** | **0.7076** |
#### Triplet
* Dataset: `all-nli-dev`
* Evaluated with [TripletEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.TripletEvaluator)
| Metric | Value |
|:-------------------|:-----------|
| cosine_accuracy | 0.9804 |
| dot_accuracy | 0.0189 |
| manhattan_accuracy | 0.9811 |
| euclidean_accuracy | 0.9802 |
| **max_accuracy** | **0.9811** |
## Training Details
### Training Dataset
#### sxc_med_llm_chemical_gen
* Dataset: [sxc_med_llm_chemical_gen](https://huggingface.co./datasets/SwastikN/sxc_med_llm_chemical_gen) at [ae28874](https://huggingface.co./datasets/SwastikN/sxc_med_llm_chemical_gen/tree/ae28874de7084969f9aa310b357ac699dbbafa23)
* Size: 117,502 training samples
* Columns: input
, instruction
, and output
* Approximate statistics based on the first 1000 samples:
| | input | instruction | output |
|:--------|:-----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------|
| type | string | string | string |
| details |
| List the countries of the Middle East
| Egypt, Israel, Iran, Iraq, Jordan, Kuwait, Lebanon, Qatar, Saudi Arabia, Syria, Turkey, The United Arab Emirates, Oman, and Yemen.
|
| Support me in refining the molecule CCC(C)=C(CC)c1ccc(Nc2nc3nonc3nc2N2CCC(Oc3ccc(Cl)cc3)CC2)cc1 to have a more drug-like nature, ensuring it remains close to the input molecule. Please inform me of the QED value of the optimized molecule.
| Help me adapt a molecular structure denoted in SMILES string based on my preferences.
| I've optimized the molecule according to your requirements, yielding the structure "COC(=O)c1ccc(Nc2nc3nonc3nc2N2CCC(Oc3ccc(Cl)cc3)CC2)cc1" and an estimated QED value of 0.4.
|
|
| Create a social media strategy to attract followers on Twitter.
| The social media strategy for Twitter should involve Tweeting on a regular basis, with content that is engaging and relevant to the target audience. This can include retweetable quotes, links to videos and articles, sharing photos/images, polls, and so on. It is also beneficial for the information to include hashtags relevant to the content and any relevant topics of the industry.
It is also important to leverage Twitter influencers and accounts, as well as engaging with potential followers regularly and DM them when necessary. Additionally, running campaigns, contests and giveaways to gain more followers should also be part of the strategy. Finally, hashtag research should be conducted to increase the reach of the tweets.
|
* Loss: [MultipleNegativesRankingLoss
](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
```json
{
"scale": 20.0,
"similarity_fct": "cos_sim"
}
```
### Evaluation Dataset
#### sxc_med_llm_chemical_gen
* Dataset: [sxc_med_llm_chemical_gen](https://huggingface.co./datasets/SwastikN/sxc_med_llm_chemical_gen) at [ae28874](https://huggingface.co./datasets/SwastikN/sxc_med_llm_chemical_gen/tree/ae28874de7084969f9aa310b357ac699dbbafa23)
* Size: 4,500 evaluation samples
* Columns: input
, instruction
, and output
* Approximate statistics based on the first 1000 samples:
| | input | instruction | output |
|:--------|:-----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------|
| type | string | string | string |
| details | With a molecule represented by the SMILES string COc1ccc(CN(C(=O)Nc2ccc([C@H](C#N)c3ccccc3)c(Cl)c2)C2CC2)cc1, propose adjustments that can decrease its blood-brain barrier permeability (BBBP) value by at least 0.1 compared to the pre-optimized value while keeping the output molecule structurally related to the input molecule. Please inform me of the BBBP value of the optimized molecule.
| Help me adapt a molecular structure denoted in SMILES string based on my preferences.
| I've optimized the molecule according to your requirements, yielding the structure "CC(C)c1cccc(Oc2ccc(CN(C(=O)Nc3ccc([C@H](C#N)c4ccccc4)c(Cl)c3)C3CC3)cc2)c1" and an estimated BBBP value of 0.34.
|
| Which modifications can be applied to the molecule Cc1nn(-c2cc3cc(F)ccc3s2)c2ncc(C(=O)N3CCCC3c3nnc4n3CCCCC4)cc12 to increase its water solubility value while ensuring it remains similar to the original molecule?
| Aid me in refining a molecular structure written in SMILES notation based on my criteria.
| I've optimized the molecule according to your requirements, resulting in the following structure: "Cc1nn(C)c2ncc(C(=O)N3CCCC3c3nnc4n3CCCCC4)cc12".
|
|
| Describe the benefits of having a mentor.
| Having a mentor can provide tremendous benefits, including guidance, advice, support and connection to a network of contacts. Mentors can offer valuable feedback, help to create goals and strategies, and provide the accountability necessary to carry out the desired goals. They can also provide a fresh perspective which can help to create new ideas and solutions.
|
* Loss: [MultipleNegativesRankingLoss
](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
```json
{
"scale": 20.0,
"similarity_fct": "cos_sim"
}
```
### Training Hyperparameters
#### Non-Default Hyperparameters
- `eval_strategy`: steps
- `learning_rate`: 2e-05
- `num_train_epochs`: 1
- `warmup_ratio`: 0.1
- `fp16`: True
#### All Hyperparameters