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Running on Zero
Running on Zero
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654bfe6 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | export type OrganType = 'liver' | 'heart' | 'kidney' | 'brain' | 'lung';
export interface OrganProfile {
id: OrganType;
name: string;
description: string;
markerGenes: string[];
geneExpressionValues: number[]; // 128-dim GTEx transcriptomic vector
}
export type MedDRAToxicityClass =
| 'hepatotoxicity'
| 'cardiotoxicity'
| 'nephrotoxicity'
| 'neurotoxicity'
| 'pulmotoxicity'
| 'gastrointestinal'
| 'dermatological'
| 'hematological'
| 'metabolic'
| 'systemic_fatigue';
export interface DrugRecord {
id: string;
name: string;
smiles: string;
cid?: number;
fdaApproved: boolean;
indication: string;
adrLabels: Record<MedDRAToxicityClass, number>; // 0 or 1
organScores: Record<OrganType, number>; // Ground truth / benchmark risk score (0.0 to 1.0)
tanimotoBaseline: number; // Tanimoto similarity to SIDER 4.1 reference set
}
export interface EpiADRHyperparameters {
useTissueConditioning: boolean; // True = Cross-Attention GTEx V8, False = Baseline Molecule-Only
crossAttentionHeads: number; // Default 16
learningRate: number; // Default 0.001
epochs: number; // Default 50
batchSize: number; // Default 64
optimizer: 'adam' | 'adamw' | 'sgd';
posWeight: number; // Class imbalance weight (e.g. 2.5)
regularizationL2: number;
dropoutRate: number; // Default 0.2
mcDropoutPasses: number; // N=30 for uncertainty quantification
}
export interface EpochTrainingMetric {
epoch: number;
trainLoss: number;
valLoss: number;
trainAUROC: number;
valAUROC: number;
}
export interface ModelTrainingSummary {
isTrained: boolean;
trainingTimeMs: number;
finalTrainLoss: number;
finalValLoss: number;
finalValAUROC: number;
finalF1Score: number;
epochHistory: EpochTrainingMetric[];
confusionMatrix: {
tp: number;
fp: number;
tn: number;
fn: number;
};
}
export interface AtomicHotspot {
atomIndex: number;
symbol: string;
attentionWeight: number; // 0.0 to 1.0 (XAI Toxicity Hotspot contribution)
subgraphName?: string;
}
export interface ToxicityPredictionResult {
compoundName: string;
smiles: string;
useTissueConditioning: boolean;
// Organ-Specific Zero-Shot Toxicity Scores (0.0 - 1.0)
organScores: Record<OrganType, {
meanRisk: number; // μ
uncertaintySigma: number; // σ from MC Dropout
riskLevel: 'Low' | 'Moderate' | 'High' | 'Severe';
}>;
// MedDRA Clinical Toxicity Classes Risk
meddraScores: Record<MedDRAToxicityClass, number>;
// Tanimoto Structural Applicability Domain
tanimotoSimilarity: number;
applicabilityDomain: 'High Confidence (In-Domain)' | 'Moderate Confidence' | 'Out-of-Domain (Novel Scaffold)';
domainColor: 'green' | 'yellow' | 'red';
// Atomic Hotspots (Explainable AI)
atomicHotspots: AtomicHotspot[];
// Top Driving Toxicophores
toxicophores: string[];
}
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