Natural product classification prediction

natural-product-classification-prediction

Summary

This skill deploys a pre-trained deep-learning classifier to predict natural-product chemical classes from SMILES molecular strings via a containerized REST API. It is used when you need to rapidly annotate chemical structures with their likely biosynthetic or functional class.

When to use

You have molecular structures encoded as SMILES strings and need to classify them into natural-product chemical classes. This skill is appropriate when you want to batch-query a pre-trained model via HTTP, optionally retrieving cached results to improve latency for repeated queries on the same structures.

When NOT to use

• Input is not a valid SMILES string or contains syntax errors that the parser cannot handle.
• You require real-time model retraining or fine-tuning; this skill uses frozen pre-trained models only.
• Your workflow demands sub-millisecond latency; containerized inference introduces network and serialization overhead.

Inputs

• SMILES string(s) representing molecular structures
• Optional cached flag (boolean) for retrieval of prior predictions

Outputs

• Natural-product chemical classification label(s)
• Prediction confidence or probability score(s)

How to apply

First, download and verify the pre-trained NP Classifier models by running the provided shell script (get_models.sh) and confirming model layer names match the expected schema (input layers 'input_2048' and 'input_4096', output layer 'output'). Convert Keras models to HDF5 TensorFlow 2.3.0 format using Python with TensorFlow. Set up a Docker network (nginx-net) for service communication, then build and deploy the API server via docker-compose (make server-compose). Query the /classify endpoint by passing SMILES strings as the smiles parameter; optionally add a cached flag to retrieve prior classification results instead of re-running inference. Verify predictions by checking the model metadata endpoint (/model/metadata) and spot-checking outputs against known structures.

Related tools

• Docker (Container runtime for isolated, reproducible API server deployment)
• docker-compose (Orchestration tool to define and run multi-container services (nginx, TensorFlow Serving, classifier API))
• TensorFlow 2.3.0 (Framework used to convert Keras models into HDF5 format for TensorFlow Serving)
• Keras (Source model architecture format; models are trained and exported as Keras then converted to TF2 HDF5)
• TensorFlow Serving (Model serving system that handles predictions routed through the /classify endpoint)
• NP Classifier Repository (Source of pre-trained models, deployment configuration, and API endpoint logic) — https://github.com/mwang87/NP-Classifier

Examples

curl 'http://localhost:8080/classify?smiles=CC(=O)Oc1ccccc1C(=O)O&cached=true'

Evaluation signals

• Model metadata endpoint (/model/metadata) returns correctly named input layers ('input_2048', 'input_4096') and output layer ('output').
• Test SMILES strings consistently return valid classification labels from the model's known class vocabulary.
• Repeated queries with cached flag parameter return identical results in faster wall-clock time than non-cached queries.
• API responds with HTTP 200 and JSON-formatted predictions; invalid SMILES strings produce clear error messages.
• Spot-check a sample of predictions against domain knowledge or reference datasets to verify classification accuracy is within expected bounds.

Limitations

• Model predictions are limited to chemical classes present in the training data; out-of-distribution structures may receive low-confidence or incorrect annotations.
• The skill requires TensorFlow 2.3.0 specifically for model conversion; later or earlier versions may introduce incompatibilities.
• Privacy trade-off: the system logs which structures were classified (for caching) but not which users queried them; query patterns may still be reconstructible.
• Caching assumes SMILES strings are canonicalized; non-canonical representations of the same molecule will be treated as distinct queries and not cached together.

Evidence

• [readme] NP Classifier models are verified and deployed via Docker with pre-trained layer naming conventions: "Input layers' names should be "input_2048" and "input_4096". Output layer's name should be "output""
• [readme] SMILES strings are passed as query parameters to the /classify endpoint for classification: "Classify programmatically /classify?smiles=<>"
• [readme] Optional cached parameter improves performance for repeated structure queries: "You can also provide cached flag to the params to get the cached version so make it faster"
• [readme] Keras models must be converted to HDF5 TensorFlow 2.3.0 format before deployment: "Make sure you have python installed and tensorflow version 2.3.0 installed to convert the keras models into HDF5 TF2 models"
• [readme] Local deployment via Docker and docker-compose is the standard deployment pattern: "We typically will deploy this locally. To bring everything up, you need docker and docker-compose."
• [readme] TensorFlow Serving routes predictions through a metadata and classification endpoint: "We pass through tensorflow serving at this url: /model/metadata"