Neural network architecture design

neural-network-architecture-design

Summary

Design and instantiate a CNN architecture for automated LCMS false positive peak classification, tuned with specific hyperparameters to balance training convergence and validation generalization. This skill is essential when building a fresh neural network model for MS1 peak filtering tasks where domain-specific parameters (matrix size, margin, scan count thresholds) and optimizer settings directly impact classification performance.

When to use

You have raw mzML files and feature tables (CSV from mzMine or XCMS) for LCMS data, have generated training/validation/test batches with known class imbalance, and need to train a CNN model from scratch to achieve AUC ROC > 0.9 for distinguishing true from false positive MS1 peaks. Use this skill when full model training is preferred over transfer learning (i.e., you have ≥500 peaks per class available).

When NOT to use

• Input dataset has fewer than 500 labeled peaks in the smallest class — transfer learning is recommended instead.
• Feature table is not in CSV format or was not generated by mzMine/XCMS — data import must be handled separately first.
• You have a pre-trained model suitable for your task and only need to tune final layers — use transfer learning workflow instead.

Inputs

• Raw mzML files (LC-MS data)
• Feature table in CSV format (mzMine or XCMS output)
• Training/validation/test batches (80:10:10 split) from Neural Network Handler
• Keras/TensorFlow training logs

Outputs

• Trained CNN model (Keras/TensorFlow object)
• Training and validation accuracy curves
• ROC curve and AUC ROC score
• True vs. false positive classification DataFrame

How to apply

Initialize a Neural Network Handler with domain-specific parameters: matrice_size=120 (image patch dimensions), margin=1 (pixel padding around detected peaks), and min_scan_num=5 (minimum spectral points per peak). Call create_batches(validation_split=0.1, normalise_class=False) to generate 80:10:10 training/test/validation splits. Create a fresh CNN model via create_model(lr=0.00001, optimizer='Adam') — the learning rate of 1e-5 is critical to prevent gradient instability on normalized batch inputs. Train via train_model(1000) starting with 1000 epochs, monitoring returned Keras/TensorFlow logs for training and validation accuracy convergence. If no plateau is observed after initial training, resume training by calling train_model() again with additional epochs. Halt training when validation accuracy plateaus or training accuracy reaches ~100% while validation lags significantly (indicating overfitting). Compute final ROC-AUC using get_true_vs_false_positive_df() paired with scikit-learn's auc() function on False Positive Rate vs. True Positive Rate.

Related tools

• NeatMS (Provides Neural Network Handler class, batch creation, model initialization (create_model), training orchestration (train_model), and evaluation utilities (get_true_vs_false_positive_df) for LCMS peak classification) — https://github.com/bihealth/NeatMS
• TensorFlow (Backend computational engine for CNN model construction and training; manages gradient computation and optimization)
• Keras (High-level API layer for defining CNN architecture, optimizer selection (Adam), and learning rate specification)
• scikit-learn (Computes ROC curve and AUC metric from true vs. predicted classification labels)
• NumPy (Numerical array operations for batch data manipulation and feature preprocessing)
• pandas (Loads and manipulates feature tables (CSV) and classification results DataFrames)

Examples

from neatms import NeatMSExperiment, NeuralNetworkHandler
handler = NeuralNetworkHandler()
handler.create_batches(validation_split=0.1, normalise_class=False)
model = handler.create_model(lr=0.00001, optimizer='Adam')
handler.train_model(1000)
df = handler.get_true_vs_false_positive_df()
from sklearn.metrics import auc
auc_score = auc(df['fpr'], df['tpr'])

Evaluation signals

• Training and validation accuracy curves are parallel and both plateau by final epoch (no gap > 5–10% indicates no overfitting).
• Final AUC ROC score is ≥ 0.9 on the held-out test set, computed via scikit-learn.metrics.auc(fpr, tpr).
• Validation accuracy is within 2–5% of training accuracy at convergence; training accuracy does not reach ~100% while validation stagnates.
• get_true_vs_false_positive_df() DataFrame contains predictions for all test samples with no NaN values in predicted class column.
• Model weights file is saved and can be reloaded; training can be resumed via train_model() without reinitializing parameters.

Limitations

• NeatMS does not provide automatic early stopping callbacks; manual monitoring and halting of training is required to avoid overfitting.
• Requires ≥500 labeled peaks per class for reliable full model training; smaller datasets will underperform and likely overfit.
• The fixed matrice_size=120 and margin=1 parameters assume consistent peak shape and isotope pattern width in input mzML files; non-standard peak geometries may require retuning.
• No changelog is available; version compatibility between NeatMS, TensorFlow, and Keras must be verified independently.
• The learning rate of 0.00001 is optimized for the provided example dataset; other LCMS instruments or preprocessing pipelines may require empirical re-tuning.

Evidence

• [other] Create a Neural Network Handler with default parameters (matrice_size=120, margin=1, min_scan_num=5): "Create a Neural Network Handler with default parameters (matrice_size=120, margin=1, min_scan_num=5) and call create_batches(validation_split=0.1, normalise_class=False) to generate training, test,"
• [other] Initialize a fresh CNN model using create_model(lr=0.00001, optimizer='Adam') with default hyperparameters and train via train_model(1000): "Initialize a fresh CNN model using create_model(lr=0.00001, optimizer='Adam') with default hyperparameters and train via train_model(1000) for an initial epoch count."
• [other] Monitor training and validation accuracy on the returned Keras/TensorFlow logs; if no plateau is observed, resume training by calling train_model() again: "Monitor training and validation accuracy on the returned Keras/TensorFlow logs; if no plateau is observed, resume training by calling train_model() again with additional epochs."
• [other] Inspect training and validation accuracy curves to confirm no overfitting (training accuracy ≈ validation accuracy); if training reaches ~100% while validation lags significantly, halt training.: "Inspect training and validation accuracy curves to confirm no overfitting (training accuracy ≈ validation accuracy); if training reaches ~100% while validation lags significantly, halt training."
• [intro] NeatMS relies on neural network based classification to enable automated filtering of false positive MS1 peaks reported by commonly used LCMS data processing pipelines.: "NeatMS relies on neural network based classification to enable automated filtering of false positive MS1 peaks reported by commonly used LCMS data processing pipelines."
• [other] Compute ROC curve and AUC using get_true_vs_false_positive_df() data with scikit-learn's auc() function on False Positive Rate vs. True Positive Rate.: "Compute ROC curve and AUC using get_true_vs_false_positive_df() data with scikit-learn's auc() function on False Positive Rate vs. True Positive Rate."
• [methods] When choosing this option, we recommend that you have at the very least 500 peaks for each class (or 500 peaks in the smallest class).: "When choosing this option, we recommend that you have at the very least 500 peaks for each class (or 500 peaks in the smallest class)."
• [methods] NeatMS does not currently provides callback functions to automatically stop the training. Calling the training method will simply resume the training.: "NeatMS does not currently provides callback functions to automatically stop the training. Calling the training method will simply resume the training."