agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/algorithms/offtarget-module.md

@@ -1,1030 +0,0 @@
-# Off-Target Prediction Module - Detailed Pseudocode
-
-## Overview
-
-The Off-Target Prediction Module identifies and scores potential CRISPR-Cas13 off-target sites using machine learning (gradient boosting) combined with biological feature extraction. The module predicts off-target activity based on mismatch patterns, PAM proximity, chromatin accessibility, and RNA secondary structure.
-
----
-
-## Algorithm 1: Off-Target Site Discovery
-
-**Purpose**: Identify candidate off-target sites using k-mer indexing and fuzzy matching.
-
-```
-ALGORITHM: DiscoverOffTargetSites
-INPUT: gRNA (string of length 20-24), transcriptome (array of RNA sequences),
-       maxMismatches (integer, default = 3)
-OUTPUT: candidateSites (array of OffTargetSite objects)
-
-CONSTANTS:
-    KMER_SIZE = 10
-    SEED_REGION_LENGTH = 12  // Critical seed region at 3' end
-    MAX_CANDIDATES_PER_GRNA = 10000
-
-BEGIN
-    candidateSites ← []
-
-    // Step 1: Extract seed region from gRNA (most critical for binding)
-    seedRegion ← gRNA[length(gRNA) - SEED_REGION_LENGTH : length(gRNA)]
-
-    // Step 2: Build k-mer index for fast candidate lookup
-    kmerIndex ← BuildKmerIndex(transcriptome, KMER_SIZE)
-
-    // Step 3: Find all k-mer matches in seed region
-    seedKmers ← ExtractKmers(seedRegion, KMER_SIZE)
-    potentialMatches ← SET()
-
-    FOR EACH kmer IN seedKmers DO
-        // Allow 1 mismatch in k-mer for fuzzy matching
-        fuzzyMatches ← kmerIndex.GetFuzzyMatches(kmer, maxMismatches = 1)
-        potentialMatches ← potentialMatches UNION fuzzyMatches
-    END FOR
-
-    IF length(potentialMatches) > MAX_CANDIDATES_PER_GRNA THEN
-        LogWarning("Too many candidates ({length(potentialMatches)}), using stricter filtering")
-        // Keep only exact seed matches
-        potentialMatches ← FilterToExactSeedMatches(potentialMatches, seedRegion)
-    END IF
-
-    // Step 4: Verify full gRNA alignment for each candidate
-    FOR EACH match IN potentialMatches DO
-        targetSequence ← ExtractTargetSequence(match.transcriptId, match.position, length(gRNA))
-
-        // Calculate mismatch profile
-        mismatchProfile ← AlignAndCountMismatches(gRNA, targetSequence)
-
-        IF mismatchProfile.totalMismatches <= maxMismatches THEN
-            candidateSites.append({
-                transcriptId: match.transcriptId,
-                position: match.position,
-                targetSequence: targetSequence,
-                mismatchProfile: mismatchProfile,
-                strand: match.strand
-            })
-        END IF
-    END FOR
-
-    LogInfo("Found {length(candidateSites)} candidate off-target sites for gRNA {gRNA}")
-
-    RETURN candidateSites
-END
-
-SUBROUTINE: BuildKmerIndex
-INPUT: transcriptome (array of RNA sequences), kmerSize (integer)
-OUTPUT: kmerIndex (hash table: kmer → array of positions)
-
-BEGIN
-    kmerIndex ← CREATE HASH TABLE
-
-    FOR EACH transcript IN transcriptome DO
-        FOR position ← 0 TO length(transcript.sequence) - kmerSize DO
-            kmer ← transcript.sequence[position : position + kmerSize]
-
-            IF kmer NOT IN kmerIndex THEN
-                kmerIndex[kmer] ← []
-            END IF
-
-            kmerIndex[kmer].append({
-                transcriptId: transcript.id,
-                position: position,
-                strand: '+'
-            })
-        END FOR
-
-        // Also index reverse complement
-        rcSequence ← ReverseComplement(transcript.sequence)
-        FOR position ← 0 TO length(rcSequence) - kmerSize DO
-            kmer ← rcSequence[position : position + kmerSize]
-
-            IF kmer NOT IN kmerIndex THEN
-                kmerIndex[kmer] ← []
-            END IF
-
-            kmerIndex[kmer].append({
-                transcriptId: transcript.id,
-                position: length(transcript.sequence) - position,
-                strand: '-'
-            })
-        END FOR
-    END FOR
-
-    LogInfo("Built k-mer index with {length(kmerIndex)} unique k-mers")
-
-    RETURN kmerIndex
-END
-
-SUBROUTINE: AlignAndCountMismatches
-INPUT: gRNA (string), target (string)
-OUTPUT: mismatchProfile (object)
-
-BEGIN
-    IF length(gRNA) != length(target) THEN
-        RETURN error("Length mismatch between gRNA and target")
-    END IF
-
-    totalMismatches ← 0
-    seedMismatches ← 0
-    mismatchPositions ← []
-
-    seedStart ← length(gRNA) - 12  // Last 12 bases are seed region
-
-    FOR i ← 0 TO length(gRNA) - 1 DO
-        IF gRNA[i] != target[i] THEN
-            totalMismatches ← totalMismatches + 1
-            mismatchPositions.append(i)
-
-            IF i >= seedStart THEN
-                seedMismatches ← seedMismatches + 1
-            END IF
-        END IF
-    END FOR
-
-    RETURN {
-        totalMismatches: totalMismatches,
-        seedMismatches: seedMismatches,
-        mismatchPositions: mismatchPositions,
-        alignment: CreateAlignmentString(gRNA, target)
-    }
-END
-```
-
-**Complexity Analysis**:
-- **Time**: O(T × L) for index building, O(K × log T) for k-mer lookup per gRNA
-  - T = transcriptome size
-  - L = average transcript length
-  - K = number of k-mers in gRNA
-- **Space**: O(T × L / K) for k-mer index
-- **Typical Performance**: 100-1000 ms per gRNA for human transcriptome
-
----
-
-## Algorithm 2: Feature Extraction
-
-**Purpose**: Extract biological features for machine learning prediction.
-
-```
-ALGORITHM: ExtractOffTargetFeatures
-INPUT: gRNA (string), candidateSite (OffTargetSite),
-       alignedReads (BAM file), chromatinData (BigWig file)
-OUTPUT: featureVector (array of floats)
-
-BEGIN
-    features ← []
-
-    // === Sequence-based features ===
-
-    // 1. Mismatch distribution features
-    mismatchProfile ← candidateSite.mismatchProfile
-    features.append(mismatchProfile.totalMismatches)
-    features.append(mismatchProfile.seedMismatches)
-    features.append(mismatchProfile.totalMismatches - mismatchProfile.seedMismatches)  // Non-seed mismatches
-
-    // 2. Position-weighted mismatch score
-    // Mismatches closer to PAM (3' end) are more important
-    positionWeightedScore ← 0
-    FOR EACH mismatchPos IN mismatchProfile.mismatchPositions DO
-        // Weight increases from 0.5 at 5' end to 2.0 at 3' end
-        weight ← 0.5 + 1.5 × (mismatchPos / length(gRNA))
-        positionWeightedScore ← positionWeightedScore + weight
-    END FOR
-    features.append(positionWeightedScore)
-
-    // 3. GC content features
-    gRNAGC ← CalculateGCContent(gRNA)
-    targetGC ← CalculateGCContent(candidateSite.targetSequence)
-    features.append(gRNAGC)
-    features.append(targetGC)
-    features.append(ABS(gRNAGC - targetGC))  // GC content difference
-
-    // 4. Homopolymer runs (AAAA, TTTT, etc. affect binding)
-    gRNAMaxHomopolymer ← FindMaxHomopolymerLength(gRNA)
-    targetMaxHomopolymer ← FindMaxHomopolymerLength(candidateSite.targetSequence)
-    features.append(gRNAMaxHomopolymer)
-    features.append(targetMaxHomopolymer)
-
-    // === Structure-based features ===
-
-    // 5. RNA secondary structure energy
-    gRNAStructure ← PredictRNAStructure(gRNA)
-    targetStructure ← PredictRNAStructure(candidateSite.targetSequence)
-    features.append(gRNAStructure.freeEnergy)
-    features.append(targetStructure.freeEnergy)
-    features.append(ABS(gRNAStructure.freeEnergy - targetStructure.freeEnergy))
-
-    // 6. Structure accessibility (unpaired probability)
-    gRNAAccessibility ← CalculateAccessibility(gRNAStructure)
-    targetAccessibility ← CalculateAccessibility(targetStructure)
-    features.append(gRNAAccessibility)
-    features.append(targetAccessibility)
-
-    // === Expression-based features ===
-
-    // 7. Target transcript expression level
-    transcriptExpression ← GetTranscriptExpression(candidateSite.transcriptId, alignedReads)
-    features.append(LOG(transcriptExpression + 1))  // Log-transformed TPM
-
-    // 8. Local read coverage at off-target site
-    localCoverage ← GetLocalCoverage(
-        candidateSite.transcriptId,
-        candidateSite.position,
-        window = 100,
-        alignedReads
-    )
-    features.append(LOG(localCoverage + 1))
-
-    // === Chromatin-based features (if available) ===
-
-    IF chromatinData != null THEN
-        // 9. Chromatin accessibility (DNase-seq, ATAC-seq)
-        chromatinAccessibility ← GetChromatinAccessibility(
-            candidateSite.transcriptId,
-            candidateSite.position,
-            chromatinData
-        )
-        features.append(chromatinAccessibility)
-    ELSE
-        features.append(0)  // Default value if not available
-    END IF
-
-    // === Evolutionary conservation features ===
-
-    // 10. PhyloP conservation score
-    conservationScore ← GetConservationScore(
-        candidateSite.transcriptId,
-        candidateSite.position
-    )
-    features.append(conservationScore)
-
-    // === Distance-based features ===
-
-    // 11. Distance to nearest exon junction
-    nearestJunctionDist ← GetDistanceToNearestJunction(
-        candidateSite.transcriptId,
-        candidateSite.position
-    )
-    features.append(MIN(nearestJunctionDist, 1000))  // Cap at 1000 bp
-
-    // === Thermodynamic features ===
-
-    // 12. Predicted binding affinity (simplified nearest-neighbor model)
-    bindingAffinity ← CalculateBindingAffinity(gRNA, candidateSite.targetSequence)
-    features.append(bindingAffinity)
-
-    RETURN features
-END
-
-SUBROUTINE: PredictRNAStructure
-INPUT: sequence (RNA string)
-OUTPUT: structure (Structure object)
-
-BEGIN
-    // Use Vienna RNA fold algorithm (simplified)
-    // Returns minimum free energy (MFE) structure
-
-    n ← length(sequence)
-
-    // Dynamic programming for MFE calculation
-    dp ← CREATE 2D array n × n, initialized to 0
-
-    FOR length ← 2 TO n DO
-        FOR i ← 0 TO n - length DO
-            j ← i + length
-
-            // Case 1: i unpaired
-            dp[i][j] ← dp[i+1][j]
-
-            // Case 2: i paired with k
-            FOR k ← i+1 TO j DO
-                IF CanPair(sequence[i], sequence[k]) THEN
-                    energy ← GetBasePairEnergy(sequence[i], sequence[k])
-
-                    IF k == j THEN
-                        dp[i][j] ← MIN(dp[i][j], dp[i+1][k-1] + energy)
-                    ELSE
-                        dp[i][j] ← MIN(dp[i][j], dp[i+1][k-1] + dp[k+1][j] + energy)
-                    END IF
-                END IF
-            END FOR
-        END FOR
-    END FOR
-
-    freeEnergy ← dp[0][n-1]
-
-    RETURN {
-        freeEnergy: freeEnergy,
-        structure: Traceback(dp, sequence)
-    }
-END
-
-SUBROUTINE: CalculateBindingAffinity
-INPUT: gRNA (string), target (string)
-OUTPUT: affinity (float, in kcal/mol)
-
-BEGIN
-    // Simplified nearest-neighbor thermodynamic model
-    // Real implementation would use full Turner parameters
-
-    affinity ← 0
-
-    FOR i ← 0 TO length(gRNA) - 2 DO
-        // Get dinucleotide pair
-        gRNADimer ← gRNA[i : i+2]
-        targetDimer ← target[i : i+2]
-
-        // Look up nearest-neighbor parameters
-        stackingEnergy ← GetStackingEnergy(gRNADimer, targetDimer)
-        affinity ← affinity + stackingEnergy
-
-        // Add penalty for mismatches
-        IF gRNA[i] != target[i] THEN
-            affinity ← affinity + 2.5  // Mismatch penalty (kcal/mol)
-        END IF
-    END FOR
-
-    // Add terminal penalties
-    affinity ← affinity + GetTerminalPenalty(gRNA[0], target[0])
-    affinity ← affinity + GetTerminalPenalty(gRNA[length(gRNA)-1], target[length(target)-1])
-
-    RETURN affinity
-END
-```
-
-**Complexity Analysis**:
-- **Time**: O(n²) for RNA structure prediction, O(n) for other features
-- **Space**: O(n²) for structure DP matrix
-- **Feature Vector Size**: 15-20 features
-- **Typical Performance**: 10-50 ms per candidate site
-
----
-
-## Algorithm 3: Gradient Boosting Model Training
-
-**Purpose**: Train gradient boosting classifier to predict off-target activity.
-
-```
-ALGORITHM: TrainOffTargetModel
-INPUT: trainingData (array of {features, label} pairs),
-       config (ModelConfig object)
-OUTPUT: trainedModel (GradientBoostingModel)
-
-CONSTANTS:
-    NUM_TREES = 100
-    MAX_DEPTH = 6
-    LEARNING_RATE = 0.1
-    MIN_SAMPLES_SPLIT = 20
-    SUBSAMPLE_RATIO = 0.8
-
-BEGIN
-    model ← {
-        trees: [],
-        learningRate: LEARNING_RATE,
-        featureImportances: [],
-        baseScore: 0
-    }
-
-    // Step 1: Initialize base prediction (mean of labels)
-    model.baseScore ← MEAN(label for {features, label} in trainingData)
-
-    // Initialize predictions with base score
-    predictions ← [model.baseScore] × length(trainingData)
-
-    // Step 2: Build trees iteratively
-    FOR treeIndex ← 0 TO NUM_TREES - 1 DO
-        // Calculate residuals (negative gradient for squared loss)
-        residuals ← []
-        FOR i ← 0 TO length(trainingData) - 1 DO
-            residual ← trainingData[i].label - predictions[i]
-            residuals.append(residual)
-        END FOR
-
-        // Subsample training data for stochastic gradient boosting
-        subsampleSize ← FLOOR(length(trainingData) × SUBSAMPLE_RATIO)
-        subsampledIndices ← RandomSample(0 to length(trainingData)-1, subsampleSize)
-        subsampledData ← [trainingData[i] for i in subsampledIndices]
-        subsampledResiduals ← [residuals[i] for i in subsampledIndices]
-
-        // Build regression tree to predict residuals
-        tree ← BuildRegressionTree(
-            subsampledData,
-            subsampledResiduals,
-            maxDepth = MAX_DEPTH,
-            minSamplesSplit = MIN_SAMPLES_SPLIT
-        )
-
-        model.trees.append(tree)
-
-        // Update predictions
-        FOR i ← 0 TO length(trainingData) - 1 DO
-            treePrediction ← tree.Predict(trainingData[i].features)
-            predictions[i] ← predictions[i] + LEARNING_RATE × treePrediction
-        END FOR
-
-        // Calculate training loss
-        trainingLoss ← CalculateMSE(predictions, [data.label for data in trainingData])
-
-        IF (treeIndex + 1) MOD 10 == 0 THEN
-            LogInfo("Tree {treeIndex + 1}/{NUM_TREES}, Training Loss: {trainingLoss}")
-        END IF
-    END FOR
-
-    // Step 3: Calculate feature importances
-    model.featureImportances ← CalculateFeatureImportances(model.trees)
-
-    LogInfo("Training complete. Top features: {model.featureImportances[:5]}")
-
-    RETURN model
-END
-
-SUBROUTINE: BuildRegressionTree
-INPUT: data (array), targets (array of residuals), maxDepth, minSamplesSplit
-OUTPUT: tree (DecisionTree object)
-
-BEGIN
-    tree ← {
-        isLeaf: false,
-        splitFeature: null,
-        splitThreshold: null,
-        leftChild: null,
-        rightChild: null,
-        prediction: null
-    }
-
-    // Base case: create leaf node
-    IF maxDepth == 0 OR length(data) < minSamplesSplit THEN
-        tree.isLeaf ← true
-        tree.prediction ← MEAN(targets)
-        RETURN tree
-    END IF
-
-    // Find best split
-    bestSplit ← FindBestSplit(data, targets)
-
-    IF bestSplit == null THEN
-        // No improvement possible, create leaf
-        tree.isLeaf ← true
-        tree.prediction ← MEAN(targets)
-        RETURN tree
-    END IF
-
-    tree.splitFeature ← bestSplit.feature
-    tree.splitThreshold ← bestSplit.threshold
-
-    // Split data into left and right children
-    leftIndices ← [i for i in 0 to length(data)-1
-                   WHERE data[i].features[bestSplit.feature] <= bestSplit.threshold]
-    rightIndices ← [i for i in 0 to length(data)-1
-                    WHERE data[i].features[bestSplit.feature] > bestSplit.threshold]
-
-    leftData ← [data[i] for i in leftIndices]
-    leftTargets ← [targets[i] for i in leftIndices]
-    rightData ← [data[i] for i in rightIndices]
-    rightTargets ← [targets[i] for i in rightIndices]
-
-    // Recursively build children
-    tree.leftChild ← BuildRegressionTree(leftData, leftTargets, maxDepth - 1, minSamplesSplit)
-    tree.rightChild ← BuildRegressionTree(rightData, rightTargets, maxDepth - 1, minSamplesSplit)
-
-    RETURN tree
-END
-
-SUBROUTINE: FindBestSplit
-INPUT: data (array), targets (array)
-OUTPUT: bestSplit (object) or null
-
-BEGIN
-    bestGain ← 0
-    bestSplit ← null
-
-    numFeatures ← length(data[0].features)
-
-    // Try splitting on each feature
-    FOR featureIdx ← 0 TO numFeatures - 1 DO
-        // Extract feature values
-        featureValues ← [sample.features[featureIdx] for sample in data]
-
-        // Get unique values as potential split thresholds
-        sortedValues ← Sort(UNIQUE(featureValues))
-
-        // Try each threshold
-        FOR i ← 0 TO length(sortedValues) - 2 DO
-            threshold ← (sortedValues[i] + sortedValues[i+1]) / 2
-
-            // Split data
-            leftIndices ← [j for j in 0 to length(data)-1
-                          WHERE featureValues[j] <= threshold]
-            rightIndices ← [j for j in 0 to length(data)-1
-                           WHERE featureValues[j] > threshold]
-
-            IF length(leftIndices) < 5 OR length(rightIndices) < 5 THEN
-                CONTINUE  // Skip splits that create very small nodes
-            END IF
-
-            // Calculate variance reduction (information gain for regression)
-            leftTargets ← [targets[j] for j in leftIndices]
-            rightTargets ← [targets[j] for j in rightIndices]
-
-            parentVariance ← Variance(targets)
-            leftVariance ← Variance(leftTargets)
-            rightVariance ← Variance(rightTargets)
-
-            weightedVariance ← (length(leftIndices) × leftVariance +
-                               length(rightIndices) × rightVariance) / length(data)
-
-            gain ← parentVariance - weightedVariance
-
-            IF gain > bestGain THEN
-                bestGain ← gain
-                bestSplit ← {
-                    feature: featureIdx,
-                    threshold: threshold,
-                    gain: gain
-                }
-            END IF
-        END FOR
-    END FOR
-
-    IF bestGain < 1e-7 THEN
-        RETURN null  // No meaningful split found
-    END IF
-
-    RETURN bestSplit
-END
-```
-
-**Complexity Analysis**:
-- **Time**: O(T × N × F × log N) where T = trees, N = samples, F = features
-- **Space**: O(T × D) where D = max depth
-- **Training Time**: 1-5 minutes for 10,000 samples on CPU
-- **Model Size**: 1-10 MB for 100 trees
-
----
-
-## Algorithm 4: Off-Target Scoring and Ranking
-
-**Purpose**: Predict off-target scores and rank by biological significance.
-
-```
-ALGORITHM: ScoreOffTargetSites
-INPUT: candidateSites (array), trainedModel (GradientBoostingModel),
-       gRNA (string), config (ScoringConfig)
-OUTPUT: rankedSites (array of scored OffTargetSite objects)
-
-BEGIN
-    scoredSites ← []
-
-    // Step 1: Extract features and predict scores
-    FOR EACH candidate IN candidateSites DO
-        // Extract feature vector
-        features ← ExtractOffTargetFeatures(
-            gRNA,
-            candidate,
-            config.alignedReads,
-            config.chromatinData
-        )
-
-        // Predict off-target activity score
-        rawScore ← PredictGradientBoosting(trainedModel, features)
-
-        // Convert to probability using sigmoid
-        probability ← 1 / (1 + EXP(-rawScore))
-
-        // Calculate confidence interval (optional)
-        confidenceInterval ← CalculateConfidenceInterval(trainedModel, features)
-
-        scoredSites.append({
-            site: candidate,
-            offTargetScore: probability,
-            confidenceLower: confidenceInterval.lower,
-            confidenceUpper: confidenceInterval.upper,
-            features: features
-        })
-    END FOR
-
-    // Step 2: Apply biological filters
-    filteredSites ← []
-    FOR EACH scored IN scoredSites DO
-        // Filter by score threshold
-        IF scored.offTargetScore >= config.minScoreThreshold THEN
-            // Filter by expression level
-            expression ← GetTranscriptExpression(scored.site.transcriptId, config.alignedReads)
-            IF expression >= config.minExpressionThreshold THEN
-                filteredSites.append(scored)
-            END IF
-        END IF
-    END FOR
-
-    // Step 3: Rank by composite score
-    FOR EACH scored IN filteredSites DO
-        // Composite score = off-target probability × expression weight
-        expression ← GetTranscriptExpression(scored.site.transcriptId, config.alignedReads)
-        expressionWeight ← LOG(expression + 1) / 10  // Normalize
-
-        scored.compositeScore ← scored.offTargetScore × (1 + expressionWeight)
-
-        // Add biological context annotations
-        scored.annotations ← {
-            geneSymbol: GetGeneSymbol(scored.site.transcriptId),
-            biotype: GetBiotype(scored.site.transcriptId),
-            isEssentialGene: IsEssentialGene(scored.site.transcriptId),
-            pathways: GetAssociatedPathways(scored.site.transcriptId)
-        }
-    END FOR
-
-    // Step 4: Sort by composite score (descending)
-    rankedSites ← Sort(filteredSites, by = compositeScore, descending = true)
-
-    // Step 5: Apply top-k filtering if requested
-    IF config.maxReturnedSites > 0 THEN
-        rankedSites ← rankedSites[0 : config.maxReturnedSites]
-    END IF
-
-    LogInfo("Scored and ranked {length(rankedSites)} off-target sites")
-
-    RETURN rankedSites
-END
-
-SUBROUTINE: PredictGradientBoosting
-INPUT: model (GradientBoostingModel), features (array of floats)
-OUTPUT: prediction (float)
-
-BEGIN
-    prediction ← model.baseScore
-
-    FOR EACH tree IN model.trees DO
-        treePrediction ← PredictTree(tree, features)
-        prediction ← prediction + model.learningRate × treePrediction
-    END FOR
-
-    RETURN prediction
-END
-
-SUBROUTINE: PredictTree
-INPUT: tree (DecisionTree), features (array)
-OUTPUT: prediction (float)
-
-BEGIN
-    IF tree.isLeaf THEN
-        RETURN tree.prediction
-    END IF
-
-    featureValue ← features[tree.splitFeature]
-
-    IF featureValue <= tree.splitThreshold THEN
-        RETURN PredictTree(tree.leftChild, features)
-    ELSE
-        RETURN PredictTree(tree.rightChild, features)
-    END IF
-END
-
-SUBROUTINE: CalculateConfidenceInterval
-INPUT: model (GradientBoostingModel), features (array)
-OUTPUT: interval (object with lower and upper bounds)
-
-BEGIN
-    // Use bootstrap aggregation to estimate uncertainty
-    NUM_BOOTSTRAP_SAMPLES ← 100
-    predictions ← []
-
-    FOR i ← 0 TO NUM_BOOTSTRAP_SAMPLES - 1 DO
-        // Randomly sample trees with replacement
-        sampledTrees ← RandomSampleWithReplacement(model.trees, length(model.trees))
-
-        // Create temporary model
-        tempModel ← {
-            trees: sampledTrees,
-            learningRate: model.learningRate,
-            baseScore: model.baseScore
-        }
-
-        pred ← PredictGradientBoosting(tempModel, features)
-        predictions.append(pred)
-    END FOR
-
-    // Calculate percentiles
-    sortedPredictions ← Sort(predictions)
-    lowerIdx ← FLOOR(NUM_BOOTSTRAP_SAMPLES × 0.025)
-    upperIdx ← FLOOR(NUM_BOOTSTRAP_SAMPLES × 0.975)
-
-    RETURN {
-        lower: sortedPredictions[lowerIdx],
-        upper: sortedPredictions[upperIdx],
-        median: sortedPredictions[FLOOR(NUM_BOOTSTRAP_SAMPLES / 2)]
-    }
-END
-```
-
-**Complexity Analysis**:
-- **Time**: O(K × T × D) where K = candidates, T = trees, D = depth
-- **Space**: O(K × F) where F = feature dimensions
-- **Inference Time**: 0.1-1 ms per candidate site
-
----
-
-## Algorithm 5: Off-Target Prediction Pipeline
-
-**Purpose**: Main pipeline orchestrating all off-target prediction steps.
-
-```
-ALGORITHM: PredictOffTargets
-INPUT: gRNA (string), transcriptomeFile (path), alignedReadsFile (path),
-       modelFile (path), config (PipelineConfig)
-OUTPUT: predictionResults (OffTargetPredictionResults)
-
-BEGIN
-    startTime ← GetCurrentTime()
-
-    // Step 1: Load resources
-    LogInfo("Loading transcriptome and model...")
-    transcriptome ← LoadTranscriptome(transcriptomeFile)
-    trainedModel ← LoadModel(modelFile)
-    alignedReads ← OpenBAM(alignedReadsFile)
-
-    // Step 2: Discover candidate sites
-    LogInfo("Discovering candidate off-target sites...")
-    candidateSites ← DiscoverOffTargetSites(
-        gRNA,
-        transcriptome,
-        maxMismatches = config.maxMismatches
-    )
-
-    LogInfo("Found {length(candidateSites)} candidates")
-
-    IF length(candidateSites) == 0 THEN
-        LogWarning("No candidate sites found")
-        RETURN {
-            gRNA: gRNA,
-            offTargetSites: [],
-            statistics: {totalCandidates: 0, totalPredicted: 0}
-        }
-    END IF
-
-    // Step 3: Score candidates (parallelized)
-    LogInfo("Scoring candidate sites...")
-    rankedSites ← ScoreOffTargetSites(
-        candidateSites,
-        trainedModel,
-        gRNA,
-        config
-    )
-
-    // Step 4: Generate summary statistics
-    statistics ← {
-        totalCandidates: length(candidateSites),
-        totalPredicted: length(rankedSites),
-        highConfidenceSites: COUNT(site for site in rankedSites
-                                   WHERE site.offTargetScore >= 0.7),
-        mediumConfidenceSites: COUNT(site for site in rankedSites
-                                     WHERE site.offTargetScore >= 0.3 AND site.offTargetScore < 0.7),
-        lowConfidenceSites: COUNT(site for site in rankedSites
-                                  WHERE site.offTargetScore < 0.3),
-        meanScore: MEAN(site.offTargetScore for site in rankedSites),
-        medianScore: MEDIAN(site.offTargetScore for site in rankedSites),
-        processingTime: GetCurrentTime() - startTime
-    }
-
-    // Step 5: Create result object
-    results ← {
-        gRNA: gRNA,
-        offTargetSites: rankedSites,
-        statistics: statistics,
-        modelInfo: {
-            modelPath: modelFile,
-            numTrees: length(trainedModel.trees),
-            featureImportances: trainedModel.featureImportances
-        },
-        timestamp: GetCurrentTime()
-    }
-
-    LogInfo("Off-target prediction complete in {statistics.processingTime}s")
-    LogInfo("Found {statistics.highConfidenceSites} high-confidence off-targets")
-
-    RETURN results
-END
-```
-
-**Complexity Analysis**:
-- **Time**: O(T × L + K × log K + K × F × D) for full pipeline
-- **Space**: O(T × L + K × F) where K = candidates
-- **End-to-End Performance**: 1-10 seconds per gRNA
-
----
-
-## Error Handling
-
-### 1. Invalid Input Validation
-
-```
-FUNCTION: ValidateGRNA
-INPUT: gRNA (string)
-OUTPUT: boolean (valid or not)
-
-BEGIN
-    // Check length
-    IF length(gRNA) < 18 OR length(gRNA) > 28 THEN
-        LogError("Invalid gRNA length: {length(gRNA)} (expected 18-28)")
-        RETURN false
-    END IF
-
-    // Check valid RNA bases
-    validBases ← {'A', 'U', 'C', 'G'}
-    FOR EACH base IN gRNA DO
-        IF base NOT IN validBases THEN
-            LogError("Invalid base '{base}' in gRNA (must be A, U, C, or G)")
-            RETURN false
-        END IF
-    END FOR
-
-    // Check for excessive homopolymers
-    maxHomopolymer ← FindMaxHomopolymerLength(gRNA)
-    IF maxHomopolymer >= 6 THEN
-        LogWarning("gRNA contains homopolymer run of length {maxHomopolymer}")
-    END IF
-
-    // Check GC content
-    gcContent ← CalculateGCContent(gRNA)
-    IF gcContent < 0.2 OR gcContent > 0.8 THEN
-        LogWarning("Extreme GC content: {gcContent × 100}%")
-    END IF
-
-    RETURN true
-END
-```
-
-### 2. Model Loading Error Handling
-
-```
-FUNCTION: LoadModelSafely
-INPUT: modelPath (string)
-OUTPUT: model (GradientBoostingModel) or error
-
-BEGIN
-    TRY
-        IF NOT FileExists(modelPath) THEN
-            RETURN error("MODEL_NOT_FOUND", "Model file not found: {modelPath}")
-        END IF
-
-        model ← DeserializeModel(modelPath)
-
-        // Validate model structure
-        IF model.trees == null OR length(model.trees) == 0 THEN
-            RETURN error("INVALID_MODEL", "Model has no trees")
-        END IF
-
-        IF model.learningRate <= 0 OR model.learningRate > 1 THEN
-            RETURN error("INVALID_MODEL", "Invalid learning rate: {model.learningRate}")
-        END IF
-
-        LogInfo("Loaded model with {length(model.trees)} trees")
-        RETURN model
-
-    CATCH IOException AS e DO
-        RETURN error("IO_ERROR", "Failed to read model file: {e.message}")
-    CATCH DeserializationError AS e DO
-        RETURN error("DESERIALIZATION_ERROR", "Corrupted model file: {e.message}")
-    END TRY
-END
-```
-
-### 3. Resource Exhaustion Handling
-
-```
-FUNCTION: DiscoverOffTargetsWithLimits
-INPUT: gRNA, transcriptome, maxMismatches, memoryLimitMB
-OUTPUT: candidateSites (array)
-
-BEGIN
-    candidateSites ← []
-    currentMemoryMB ← GetProcessMemoryUsage()
-
-    IF currentMemoryMB > memoryLimitMB × 0.9 THEN
-        LogWarning("Approaching memory limit, using stricter filtering")
-        // Reduce candidate set aggressively
-        maxMismatches ← MIN(2, maxMismatches)
-    END IF
-
-    candidateSites ← DiscoverOffTargetSites(gRNA, transcriptome, maxMismatches)
-
-    // If still too many candidates, filter by expression
-    IF length(candidateSites) > 10000 THEN
-        LogInfo("Too many candidates ({length(candidateSites)}), filtering by expression")
-        candidateSites ← FilterByExpression(candidateSites, minExpression = 1.0)
-    END IF
-
-    RETURN candidateSites
-END
-```
-
----
-
-## Performance Optimization
-
-### 1. Parallel Feature Extraction
-
-```
-FUNCTION: ExtractFeaturesBatch
-INPUT: candidates (array), gRNA, config, numThreads
-OUTPUT: featureMatrix (2D array)
-
-BEGIN
-    batchSize ← CEILING(length(candidates) / numThreads)
-
-    featureMatrix ← ParallelMap(
-        candidates,
-        FUNCTION(candidate)
-            RETURN ExtractOffTargetFeatures(gRNA, candidate, config)
-        END FUNCTION,
-        numThreads = numThreads
-    )
-
-    RETURN featureMatrix
-END
-```
-
-### 2. Caching Strategy
-
-```
-DATA STRUCTURE: TranscriptomeCache
-    kmerIndex: LRU Cache (size = 10GB)
-    expressionData: Hash table
-    structureData: LRU Cache (size = 1GB)
-
-FUNCTION: GetCachedKmerIndex
-INPUT: transcriptomeFile (path)
-OUTPUT: kmerIndex
-
-BEGIN
-    cacheKey ← Hash(transcriptomeFile)
-
-    IF cacheKey IN TranscriptomeCache.kmerIndex THEN
-        LogInfo("Using cached k-mer index")
-        RETURN TranscriptomeCache.kmerIndex[cacheKey]
-    ELSE
-        transcriptome ← LoadTranscriptome(transcriptomeFile)
-        kmerIndex ← BuildKmerIndex(transcriptome)
-        TranscriptomeCache.kmerIndex[cacheKey] ← kmerIndex
-        RETURN kmerIndex
-    END IF
-END
-```
-
----
-
-## Testing and Validation
-
-### 1. Unit Tests
-
-```
-TEST: FeatureExtractionConsistency
-BEGIN
-    gRNA ← "GUUUUAGAGCUAUGCUGUUUUG"
-    target ← "GUUUUAGAGCUAUGCUGUUUUA"  // 1 mismatch at end
-
-    candidate ← CreateMockCandidate(target)
-    features ← ExtractOffTargetFeatures(gRNA, candidate, mockConfig)
-
-    ASSERT features[0] == 1  // Total mismatches
-    ASSERT features[1] == 1  // Seed mismatches
-    ASSERT length(features) == 15  // Expected feature count
-END
-
-TEST: GradientBoostingPrediction
-BEGIN
-    model ← CreateMockModel(numTrees = 10)
-    features ← [0.5, 1.0, 0.3, 2.1, 0.8]
-
-    prediction ← PredictGradientBoosting(model, features)
-
-    ASSERT prediction >= 0 AND prediction <= 1
-END
-```
-
-### 2. Integration Tests
-
-```
-TEST: EndToEndOffTargetPrediction
-BEGIN
-    // Use small test dataset
-    gRNA ← "GUUUUAGAGCUAUGCUGUUUUG"
-    transcriptome ← LoadTestTranscriptome("test_data/small_transcriptome.fa")
-    model ← LoadTestModel("test_data/test_model.gbm")
-
-    results ← PredictOffTargets(gRNA, transcriptome, model, testConfig)
-
-    ASSERT results.statistics.totalCandidates > 0
-    ASSERT results.statistics.totalPredicted <= results.statistics.totalCandidates
-    ASSERT ALL(site.offTargetScore >= 0 AND site.offTargetScore <= 1
-               for site in results.offTargetSites)
-END
-```
-
----
-
-## References
-
-1. Haeussler, M., et al. (2016). Evaluation of off-target and on-target scoring algorithms. *Genome Biology*.
-2. Friedman, J. H. (2001). Greedy function approximation: A gradient boosting machine. *Annals of Statistics*.
-3. Doench, J. G., et al. (2016). Optimized sgRNA design to maximize activity and minimize off-target effects. *Nature Biotechnology*.
-
----
-
-**Next Module**: Differential Expression Analysis Module