AI System for Molecular ADMET Prediction

Half of drug candidates fail due to ADMET issues—toxicity, undesirable metabolism, poor absorption. Each such molecule consumes millions of dollars in preclinical stages. We develop AI systems that predict ADMET with accuracy sufficient for molecule selection before synthesis. According to Nature Reviews Drug Discovery, about 50% of failures are linked to ADMET.

Why Predicting ADMET Early Is Critical

Late detection of ADMET problems is a major cause of clinical trial failures, so early ADMET prediction is crucial. For instance, hERG channel blockade leads to lethal arrhythmias and drug withdrawal from the market. Our ADMET prediction model, trained on thousands of compounds, identifies such risks in seconds. The prediction accuracy for hERG inhibition exceeds 85% ROC-AUC. A typical ADMET model implementation project saves significant preclinical research costs and reduces the development cycle by 12–18 months. This translates to cost savings of $500,000–$2 million.

Which Models Perform Best for ADMET?

Graph Neural Networks (MPNN, D-MPNN) are the current standard. GNNs surpass fingerprint+ML by 15–20% in ROC-AUC on Therapeutics Data Commons (TDC) benchmarks. For small datasets, XGBoost on ECFP4 fingerprints works well—faster and more interpretable. We combine both approaches in an ensemble.

Multitask learning combines 20+ ADMET tasks in one model. Shared representations improve prediction for properties with limited data. For example, the model trains on solubility, logP, and hERG simultaneously.

from chemprop import args, data, featurizers, models, train

# Chemprop — state-of-the-art for molecular ADMET
arguments = [
    '--data_path', 'admet_train.csv',
    '--dataset_type', 'regression',
    '--target_columns', 'solubility logP hERG_inhibition caco2_permeability',
    '--smiles_columns', 'smiles',
    '--epochs', '50',
    '--batch_size', '64',
    '--ffn_num_layers', '3',
    '--dropout', '0.1',
    '--save_dir', 'admet_model',
]
args.parse_train_args(arguments)
train.cross_validate(...)

Beyond ROC-AUC, we use PR-AUC, F1-score, and calibration coefficient (Expected Calibration Error). For regression tasks, we use RMSE and R².

Improving CYP450 Metabolism Prediction Accuracy

Predicting metabolism by CYP450 enzyme family—one of the hardest ADMET tasks. Isoforms CYP3A4, CYP2D6, CYP2C9 metabolize most drugs. To boost accuracy, we use multitask learning with molecular docking descriptors. This model achieves F1-score 0.88 on the test set, 8% better than single-task alternative.

Prediction Uncertainty Assessment

A model may be unreliable for molecules far from the training distribution. We use Conformal Prediction—a method giving statistically rigorous prediction intervals without distribution assumptions. When outside the applicability domain, the system issues a clear "low confidence prediction" warning. We apply several applicability domain methods: Tanimoto similarity to nearest neighbors, leverage (Williams plot), and distance to k-NN in embedding space.

What's Included (Deliverables)

• Trained model (ONNX or TorchScript format)
• REST API with OpenAPI documentation
• Comprehensive documentation (user guide, API reference)
• API access credentials
• Report with metrics (ROC-AUC, PR-AUC, calibration)
• Analysis of applicability domain and uncertainty
• Team training on model usage
• 3 months of warranty support

How We Work

1. Requirements analysis: define target ADMET properties, collect and clean datasets.
2. Modeling: experiment with architectures, tune hyperparameters (Weights & Biases). We use 5-fold cross-validation and external test sets.
3. Validation: cross-validation, testing on held-out sets, external benchmark verification.
4. Integration: deploy on your infrastructure (SageMaker, Vertex AI) or on-premise.
5. Handover: code, model, documentation, training.

Timelines: from 3 weeks for a single task to 3 months for a full multitask system. Pricing is determined individually—contact us for a commercial proposal.

Our Expertise

5+ years of experience in AI for drug discovery, over 50 completed projects in molecular modeling. We guarantee quality and on-time delivery. We use a modern stack: PyTorch, Hugging Face Transformers, Chemprop, RDKit, Weights & Biases. Request a free analysis of your data—we will check its suitability for ADMET modeling and propose an optimal architecture. Get a consultation right now by sending a request through the form on our website.

Industry AI Solutions: Healthcare, Finance, Retail, Manufacturing

We encounter the same pain points: a general text model doesn’t distinguish medical nomenclature, and a standard object detector confuses “weld seam scratch” with “casing scratch.” Each time these are different defects with different consequences. To avoid this, we build industry-specific solutions on top of general methods, but with deep domain knowledge — from regulatory requirements to data specifics. Over 5 years, we have completed 80+ projects in fintech, healthcare, retail, and manufacturing, and none were without adaptation to a specific business case.

Healthcare: Regulatory Maze and Data Governance

Medical AI differs not in technical algorithms but in a compliance-first approach. Depending on the country of application, the model may be a Class II or III medical device requiring clinical trials (FDA, CE MDR, GOST R). We ensure compliance with these standards at the architecture stage — fixing them post-factum is 10× more expensive.

Medical imaging. Detection on X‑rays, CT, MRI is a mature area. Models on ResNet, EfficientNet, SegFormer achieve AUC 0.94–0.97 on standard tasks (pneumonia on CXR, polyps on colonoscopy). Key issue is generalization: a model trained on data from one scanner manufacturer degrades on another due to differences in preprocessing and artifacts. Solution: domain adaptation via MONAI (Medical Open Network for AI) from NVIDIA, which includes DICOM loading, 3D augmentation, and confidence calibration. TotalSegmentator — for automatic segmentation of 117 structures on CT, production‑ready, Apache 2.0 license.

Clinical NLP. Extracting structured information from clinical records: diagnoses (ICD‑10/11), prescriptions, dates, indicators. medspaCy, scispaCy, MedCAT — specialized NLP libraries with ontologies (SNOMED‑CT, UMLS). Fine‑tuning BioBERT or ClinicalBERT on our data yields F1 0.85–0.92 on NER tasks versus F1 0.65–0.72 for general BERT. We verified this on a project with a regional oncology center — cancer stage extraction accuracy increased by 23%.

Clinical decision support. LLM assistants for clinical decision support are a regulatory gray area. We use an RAG system on top of clinical guidelines (UpToDate, local protocols) with explicit citation for each statement. The model does not diagnose but helps find relevant protocols. Stack: LlamaIndex + pgvector + pubmedbert-base-embeddings + Llama Guard for safety. Data in DICOM/HL7 FHIR, on‑premise deployment mandatory.

Finance: How to Ensure Interpretability of a Scoring Model under Basel IV?

The financial sector is one of the most mature in applying ML, but regulation is maximal. Every model affecting credit decisions falls under Basel IV, EU AI Act, GDPR Article 22. We deliver AI solutions for fintech that satisfy these requirements — in a project for a top‑10 bank we deployed a scoring model where each record required SHAP explanations.

Credit scoring. Gradient boosting (LightGBM, XGBoost) dominates. Neural networks yield +0.5–2% AUC but lose interpretability. Standard: LightGBM + SHAP to explain each decision. Fairness checking is mandatory: Fairlearn or aif360 for auditing disparate impact on protected attributes (age, gender). The default class is 1–5% — with an imbalance of 1:30, a model with 97% accuracy may have recall 0.2. Solution: focal loss, class_weight='balanced', SMOTE + careful validation. In one fintech scoring project, the model reduced credit losses by $2.1 million annually.

Algorithmic trading and risk management. LSTM and Transformer for price forecasting are popular but unstable in production due to non‑stationarity of financial series. A more robust approach: ML for signal generation (classification: up/down over horizon N) with traditional portfolio optimization on top. Backtesting via Zipline‑Reloaded, vectorbt, QuantLib. Proper backtesting is critical — look‑ahead bias kills results. We guarantee a clean experiment: all data at signal time is available in real time.

AML (Anti‑Money Laundering). Graph Neural Networks for analyzing transaction networks is an actively developing area. PyG, DGL for GNN. Task: detect suspicious patterns in transaction graphs (layering, structuring). Recall is more critical than precision — better 10 false alarms than miss one money laundering. In a project for a large payment service, we increased recall by 18% without increasing false positive rate.

Retail and e‑commerce: Recommendation Systems and Demand Forecasting

Recommendation systems. Current architectural standard: two‑tower model for retrieval + ranking with cross‑features. TensorFlow Recommenders or Merlin from NVIDIA for GPU‑accelerated feature processing. For small catalogs (<100k items), LightFM is sufficient. A common mistake is training on implicit feedback without accounting for position bias. Solution: IPW (Inverse Propensity Weighting) or randomized logging on a portion of traffic. Development time for a basic recommendation system is 4–8 weeks, including A/B test.

Demand forecasting and inventory optimization. Hierarchical forecasting: SKU → category → store → region. HierarchicalForecast from Nixtla automatically reconciles forecasts across levels. TFT or N‑HiTS for base forecast, gradient boosting for adjustment on exogenous factors (promotions, weather, events). One retail project led to a 15% reduction in stock‑outs due to precise promotion calibration.

Visual search and size compatibility. CLIP embeddings for image search — deploy in 2–3 weeks: clip‑ViT‑B‑32 or clip‑ViT‑L‑14, Faiss or Qdrant index, REST API. For size recommendation — specific models on return data and reviews with fit indication.

Manufacturing: Quality Inspection and Predictive Maintenance

Quality control and defect detection. CV models for product inspection are one of the most mature industry tasks. YOLOv10 for defect detection, SegFormer for segmentation. Specifics: class imbalance (defects are rare), high recall requirement (missing a defect is worse than false alarm). Typical dataset: 500–2000 defect images + 500–1000 normal. Few‑shot learning via DINO or SAM 2 works with 50–100 annotated examples. We gained experience on an electronics production line — recall 0.95 at FPR 0.03. A predictive maintenance deployment saved a manufacturing client $500,000 per year in unplanned downtime.

Predictive maintenance. Vibration sensors, current sensors, thermocouples → feature extraction → anomaly or mode classification. Models: LSTM‑AE for unsupervised, LightGBM for supervised (if failure history is available). Integration with SCADA/OPC‑UA via opcua-asyncio or MQTT. Key metric: False Negative Rate — a missed pre‑failure is more costly than a false alarm. Threshold tuned to business cost of each error type. Timeline: 3 to 6 months to production.

Digital twin and simulation. Surrogate models — ML models replacing expensive physical simulation. If a CFD simulation takes 6 hours and a surrogate (trained on 10,000 simulations) takes 0.01 seconds, that's 2,000,000× speedup for optimization. SALib for sensitivity analysis, botorch for Bayesian optimization on top of surrogate.

General Principles of Industry AI

Regardless of industry, there are patterns that work everywhere. Data matters more than architecture. In healthcare, 1000 quality labeled images are better than 100,000 poor ones. In manufacturing, 200 real defect examples are more valuable than 10,000 synthetic ones. Compliance‑first design — regulatory requirements are easier to embed into architecture from the start than to add later. Logging, explainability, versioning from day one. Domain expert on the team — an ML engineer without domain knowledge does slowly and error‑prone what an ML engineer plus a doctor/financier/technologist does quickly and correctly.

We guarantee certification to customer requirements (ISO 13485, SOC 2, GDPR) and provide full model documentation (model card, datasheet, compliance report). Our experience: 10,000+ engineering hours and 80+ projects.

Work Process for an Industry AI Solution

1. Domain immersion (2–3 days) — interviews with experts, studying regulatory requirements, auditing available data.
2. MVP design (1–2 weeks) — stack and architecture selection, feasibility assessment.
3. Development and validation (from 4 weeks to 6 months depending on industry) — model training, testing, compliance.
4. Integration and deployment (1–4 weeks) — on‑premise / cloud / edge, documentation, staff training.
5. Support and monitoring — model drift, retraining, SLA.

Estimated timelines:

Cost is calculated individually for each project. Get a consultation — we will evaluate your dataset, regulatory map, and business goals.

Why Choose Our Industry AI Solutions?

• 80+ completed projects in fintech, healthcare, retail, and manufacturing.
• 5 years on the market — proven experience with compliance and deployment.
• Quality guarantee: we ensure target metrics (AUC, recall, latency p99) and provide full documentation.
• Licensed technologies: PyTorch, MONAI, LightGBM, Qdrant — we use open‑source with commercially safe licenses.
• Flexibility: we work as a contractor or as an extension of your team.

Contact us for a free data audit and consultation. Request a proposal with a detailed work plan. We will discuss your task and prepare a commercial proposal.