@datagrok/eda 1.4.12 → 1.5.0

package/.eslintrc.json

@@ -17,7 +17,6 @@
   "rules": {
     "no-unused-vars": "off",
         "@typescript-eslint/no-unused-vars": ["warn", { "varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}],
-    "@typescript-eslint/require-array-sort-compare": "error",
     "indent": [
       "error",
       2

package/CHANGELOG.md

@@ -1,5 +1,15 @@
 # EDA changelog
 
+## 1.5.0 (2026-03-13)
+
+Probabilistic Multi-Parameter Optimization (pMPO) - Enhancements
+
+* Added support for both numeric and categorical desirability columns
+* Introduced automatic parameter tuning for streamlined configuration
+* Added option to run pMPO without sigmoidal correction
+* New ROC curve and confusion matrix visualizations for model evaluation
+* Expanded correctness test coverage
+
 ## 1.4.12 (2026-01-16)
 
 Implemented

package/CLAUDE.md

@@ -0,0 +1,185 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Overview
+
+EDA (Exploratory Data Analysis) is a Datagrok package providing statistical analysis and machine learning tools. It includes dimensionality reduction (PCA, UMAP, t-SNE, SPE), supervised learning (SVM, linear regression, softmax, PLS, gradient boosting via XGBoost), ANOVA, missing data imputation, Pareto optimization, and probabilistic multi-parameter optimization (pMPO).
+
+## Build Commands
+
+```bash
+npm install                # Install dependencies
+npm run build              # Full build: grok api && grok check --soft && webpack
+npm run build-eda          # Webpack only
+npm run build-all          # Build js-api, libraries, then this package
+
+npm run link-all           # Link local datagrok-api and libraries
+
+npm run debug-eda          # Build and publish to default server
+npm run debug-eda-local    # Build and publish to local server
+npm run release-eda        # Build and publish as release
+
+npm test                   # Run tests against localhost
+grok test                  # Run all tests
+grok test --test "TestName"      # Run specific test
+grok test --category "CategoryName"  # Run tests in category
+grok test --gui            # Run with visible browser
+```
+
+## Architecture
+
+### High-Level Structure
+
+The package combines TypeScript, WASM modules, and web workers for performance-critical computations:
+
+- **WASM Modules** (`wasm/`): C++ implementations compiled to WebAssembly for PCA, PLS, SVM, softmax regression, and XGBoost. These provide high-performance numerical computation.
+- **Web Workers** (`src/workers/`): JavaScript workers for t-SNE, UMAP, and softmax training to avoid blocking the UI thread.
+- **TypeScript API** (`src/`): High-level interfaces, UI components, and integration with Datagrok platform.
+
+### Core Modules
+
+#### Dimensionality Reduction
+- **PCA** (`eda-tools.ts`, `wasm/PCA/`): Principal Component Analysis via WASM
+- **UMAP/t-SNE** (`workers/umap-worker.ts`, `workers/tsne-worker.ts`): Manifold learning in workers
+- Uses `@datagrok-libraries/ml` for multi-column dimensionality reduction with custom distance metrics
+
+#### Partial Least Squares (`pls/`)
+- **PLS regression and analysis** (`pls-tools.ts`, `pls-ml.ts`): Multivariate analysis for high-dimensional data
+- **WASM backend** (`wasm/PLS/`): Performance-critical PLS computations
+- Supports both linear and quadratic PLS models
+
+#### Support Vector Machines (`svm.ts`)
+- **LS-SVM** implementation with multiple kernels (linear, RBF, polynomial, sigmoid)
+- Training/prediction via WASM (`wasm/svm.h`, `wasm/svmApi.cpp`)
+- Interactive model training with progress tracking
+
+#### XGBoost (`xgbooster.ts`)
+- **XGBoost** integration via WASM (`wasm/XGBoostAPI.wasm`)
+- Binary classification and regression
+- Requires initialization via `initXgboost()` in package init
+
+#### Other Supervised Machine Techniques
+- **Softmax Classifier** (`softmax-classifier.ts`): Multinomial logistic regression
+  - Training in web worker for non-blocking UI
+  - WASM backend for prediction
+- **Linear Regression** (`regression.ts`): Ordinary least squares
+
+#### Missing Values Imputation (`missing-values-imputation/`)
+- **K-Nearest Neighbors** imputation (`knn-imputer.ts`)
+- Handles both numerical and categorical features
+
+#### ANOVA (`anova/`)
+- **One-way ANOVA** (`anova-tools.ts`, `anova-ui.ts`)
+- Statistical analysis of variance with visual reports
+
+#### Pareto Optimization (`pareto-optimization/`)
+- **ParetoOptimizer** (`pareto-optimizer.ts`): Multi-objective optimization
+- **ParetoFrontViewer** (`pareto-front-viewer.ts`): Custom JsViewer for visualizing Pareto fronts
+- Computes Pareto-optimal solutions from multiple objectives (minimize/maximize)
+
+#### Probabilistic Scoring (`probabilistic-scoring/`)
+- **pMPO** (`prob-scoring.ts`): Probabilistic Multi-Parameter Optimization for drug discovery
+- Based on https://pmc.ncbi.nlm.nih.gov/articles/PMC4716604/
+- Features:
+  - Training with descriptor statistics and correlation filtering
+  - Sigmoid-corrected desirability functions
+  - ROC curve analysis and confusion matrix
+  - Model evaluation and auto-tuning via Nelder-Mead optimization (`nelder-mead.ts`)
+  - Export to MPO desirability profiles (integration with `@datagrok-libraries/statistics`)
+- Sample data in `files/` directory for testing and demos
+
+### WASM Integration
+
+WASM modules are initialized asynchronously in `PackageFunctions.init()`:
+- `_initEDAAPI()` from `wasm/EDAAPI.js`
+- `initXgboost()` from `wasm/xgbooster.js`
+
+WASM source files (`wasm/*.cpp`, `wasm/*.h`) are C++ implementations compiled to WebAssembly. Do not modify generated `.js` and `.wasm` files directly.
+
+### Function Registration
+
+Functions are registered via JSDoc-style metadata comments (not TypeScript decorators):
+
+```typescript
+@grok.decorators.func({
+  'top-menu': 'ML | Analyze | PCA...',
+  'description': 'Principal component analysis (PCA)',
+  'helpUrl': '/help/explore/dim-reduction#pca',
+})
+static async PCA(
+  @grok.decorators.param({'type': 'dataframe', 'options': {'caption': 'Table'}}) table: DG.DataFrame,
+  // ...
+) { }
+```
+
+Run `grok api` to generate `package.g.ts` and `package-api.ts` from these annotations.
+
+### External Dependencies
+
+Key library integrations:
+- **@datagrok-libraries/ml**: Distance metrics, dimensionality reduction, MCL clustering
+- **@datagrok-libraries/statistics**: Statistical functions, MPO profile editor
+- **@datagrok-libraries/math**: DBSCAN, mathematical utilities
+- **@datagrok-libraries/test**: Test framework
+
+External packages (must be in webpack externals):
+- `mathjs`: Matrix operations and numerical computation
+- `jstat`: Statistical distributions
+- `umap-js`: UMAP implementation
+- `@keckelt/tsne`: t-SNE implementation
+
+## Testing
+
+Tests are organized by feature in `src/tests/`:
+- `dim-reduction-tests.ts`: PCA, UMAP, t-SNE, SPE
+- `linear-methods-tests.ts`: Linear regression, PLS
+- `classifiers-tests.ts`: SVM, softmax, XGBoost
+- `mis-vals-imputation-tests.ts`: KNN imputation
+- `anova-tests.ts`: One-way ANOVA
+- `pmpo-tests.ts`: Probabilistic scoring
+- `pareto-tests.ts`: Pareto optimization
+
+Test framework from `@datagrok-libraries/test`:
+```typescript
+import {category, expect, test} from '@datagrok-libraries/test/src/test';
+
+category('Feature Name', () => {
+  test('Test description', async () => {
+    // test code
+  }, {timeout: 30000});
+});
+```
+
+## Scripts and Files
+
+- **`scripts/`**: Python scripts for exporting TypeScript constants from Python implementations
+- **`files/`**: Demo/test data for pMPO (drugs-props-train.csv, drugs-props-test.csv, scores)
+- **`css/`**: Custom stylesheets (pmpo.css for pMPO UI)
+
+## Key Workflows
+
+### Adding a New ML Method
+
+1. Implement the algorithm in TypeScript (or C++ for WASM)
+2. Add function registration with `@grok.decorators.func()`
+3. Create tests in appropriate test file
+4. Run `grok api` to generate wrappers
+5. Add to package menu structure in `package.json` meta.menu
+
+### Working with WASM
+
+- WASM sources in `wasm/*.cpp` and `wasm/*.h`
+- Generated files: `wasm/*.js`, `wasm/*.wasm`
+- Initialization required in `PackageFunctions.init()`
+- Web workers have separate WASM entry points (e.g., `EDAForWebWorker.js`)
+
+### pMPO Model Development
+
+The probabilistic scoring module is complex and tightly integrated:
+- Model training in `Pmpo` class (`prob-scoring.ts`)
+- Statistical computations in `stat-tools.ts`
+- UI utilities and serialization in `pmpo-utils.ts`
+- Optimization via Nelder-Mead in `nelder-mead.ts`
+- All constants and types in `pmpo-defs.ts`
+- Integration with `@datagrok-libraries/statistics` for MPO profile export

package/css/pmpo.css

@@ -23,4 +23,13 @@
   transform: translate(-50%, -50%);
   pointer-events: none;
   white-space: nowrap;
+}
+
+.eda-pmpo-centered-text {
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  height: 100%;
+  width: 100%;
+  text-align: center;
 }

package/dist/111.js

@@ -1,2 +1,2 @@
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package/dist/111.js.map

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priority];\n\t\treturn;\n\t}\n\tvar notFulfilled = Infinity;\n\tfor (var i = 0; i < deferred.length; i++) {\n\t\tvar [chunkIds, fn, priority] = deferred[i];\n\t\tvar fulfilled = true;\n\t\tfor (var j = 0; j < chunkIds.length; j++) {\n\t\t\tif ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {\n\t\t\t\tchunkIds.splice(j--, 1);\n\t\t\t} else {\n\t\t\t\tfulfilled = false;\n\t\t\t\tif(priority < notFulfilled) notFulfilled = priority;\n\t\t\t}\n\t\t}\n\t\tif(fulfilled) {\n\t\t\tdeferred.splice(i--, 1)\n\t\t\tvar r = fn();\n\t\t\tif (r !== undefined) result = r;\n\t\t}\n\t}\n\treturn result;\n};","var next = __webpack_require__.x;\n__webpack_require__.x = () => {\n\treturn Promise.all([\n\t\t__webpack_require__.e(242),\n\t\t__webpack_require__.e(589)\n\t]).then(next);\n};","import { DistanceAggregationMethods } from './types';\nexport const isNil = (x) => x === null || x === undefined;\nexport function insertSmaller(distancesAr, indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num < v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n    if (num < distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num > v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function getAggregationFunction(aggregationMethod, weights) {\n    switch (aggregationMethod) {\n        case DistanceAggregationMethods.MANHATTAN:\n            return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n        default:\n            return (vs) => {\n                // euclidean\n                const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n                return Math.sqrt(sum);\n            };\n    }\n}\n//# 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{ getAggregationFunction, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, threshold, fnNames, opts, aggregationMethod, weights } = event.data;\n    try {\n        const i = [];\n        const j = [];\n        const distances = [];\n        const chunkSize = endIdx - startIdx;\n        //const mi = startRow;\n        //const mj = startCol;\n        const aggregate = getAggregationFunction(aggregationMethod, weights);\n        values.forEach((v, colIdx) => {\n            if (isBitArrayMetric(fnNames[colIdx])) {\n                for (let i = 0; i < v.length; ++i) {\n                    if (isNil(v[i]))\n                        continue;\n                    values[colIdx][i] = new BitArray(values[colIdx][i]._data, values[colIdx][i]._length);\n                }\n            }\n        });\n        let cnt = 0;\n        const distanceFns = new Array(fnNames.length).fill(null).map((_, i) => new Measure(fnNames[i]).getMeasure(opts[i]));\n        const startRow = values[0].length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values[0].length * (values[0].length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values[0].length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n        let mi = startRow;\n        let mj = startCol;\n        while (cnt < chunkSize) {\n            //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n            const distanceValues = distanceFns.map((fn, idx) => !isNil(values[idx][mi]) && !isNil(values[idx][mj]) ?\n                fn(values[idx][mi], values[idx][mj]) : 1);\n            const value = distanceValues.length === 1 ? distanceValues[0] : aggregate(distanceValues);\n            if (1 - value >= threshold) {\n                i.push(mi);\n                j.push(mj);\n                distances.push(value);\n  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{ getAggregationFunction, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, threshold, fnNames, opts, aggregationMethod, weights } = event.data;\n    try {\n        const i = [];\n        const j = [];\n        const distances = [];\n        const chunkSize = endIdx - startIdx;\n        //const mi = startRow;\n        //const mj = startCol;\n        const aggregate = getAggregationFunction(aggregationMethod, weights);\n        values.forEach((v, colIdx) => {\n            if (isBitArrayMetric(fnNames[colIdx])) {\n                for (let i = 0; i < v.length; ++i) {\n                    if (isNil(v[i]))\n                        continue;\n                    values[colIdx][i] = new BitArray(values[colIdx][i]._data, values[colIdx][i]._length);\n                }\n            }\n        });\n        let cnt = 0;\n        const distanceFns = new Array(fnNames.length).fill(null).map((_, i) => new Measure(fnNames[i]).getMeasure(opts[i]));\n        const startRow = values[0].length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values[0].length * (values[0].length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values[0].length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n        let mi = startRow;\n        let mj = startCol;\n        while (cnt < chunkSize) {\n            //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n            const distanceValues = distanceFns.map((fn, idx) => !isNil(values[idx][mi]) && !isNil(values[idx][mj]) ?\n                fn(values[idx][mi], values[idx][mj]) : 1);\n            const value = distanceValues.length === 1 ? distanceValues[0] : aggregate(distanceValues);\n            if (1 - value >= threshold) {\n                i.push(mi);\n                j.push(mj);\n                distances.push(value);\n            }\n            cnt++;\n            mj++;\n            if (mj === values[0].length) {\n                mi++;\n                mj = mi + 1;\n            }\n        }\n        const iArray = new Int32Array(i);\n        const jArray = new Int32Array(j);\n        const distanceArray = new Float32Array(distances);\n        postMessage({ i: iArray, j: jArray, distance: distanceArray });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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