@elarsaks/umap-wasm 0.1.0

package/LICENSE

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package/README.md

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+# UMAP-WASM: WebAssembly-Accelerated UMAP for JavaScript
+
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](LICENSE)
+
+A high-performance implementation of Uniform Manifold Approximation and Projection (UMAP) for JavaScript environments, featuring selective WebAssembly acceleration for compute-intensive operations.
+
+## 📚 Academic Context
+
+This project is part of a master's thesis:
+
+**Title:** *WebAssembly-Accelerated UMAP for Browser Environments*  
+**Author:** Elar Saks  
+**Institution:** Tampere University of Applied Sciences (TAMK)  
+**Year:** 2026
+
+### Research Objectives
+
+The thesis investigates hybrid JavaScript/WebAssembly architectures for scientific computing in browsers, specifically:
+
+- **Performance Analysis**: Quantifying speedup gains from selective Rust/WASM compilation of hot-path computational kernels
+- **Interoperability Patterns**: Evaluating efficient data marshalling between JavaScript and WebAssembly memory spaces
+- **Practical Implementation**: Maintaining API compatibility while optimizing performance-critical components
+- **Trade-off Analysis**: Assessing development complexity, bundle size, and runtime performance improvements
+
+## 🎯 Overview
+
+Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique used for visualization and general non-linear dimension reduction, offering advantages over t-SNE in speed and preservation of global structure.
+
+This implementation builds upon the PAIR-code `umap-js` library with strategic WebAssembly optimizations for:
+- Distance computations (implemented in Rust: `distances.rs`)
+- Nearest neighbour search (random projection trees) (implemented in Rust: `tree.rs`)
+- Matrix operations in optimization loops (implemented in Rust: `matrix.rs`)
+- Nearest‑neighbour graph refinement (NN‑Descent) *(TODO — JS implementation currently used)*
+- Gradient‑descent layout optimisation *(TODO — optimizer currently runs in JS)*
+
+### Key Features
+
+- **Hybrid Architecture**: JavaScript implementation with optional WASM acceleration for hot paths
+- **API Compatibility**: Drop-in replacement for standard `umap-js` usage patterns
+- **Flexible Execution**: Synchronous, asynchronous, and step-by-step fitting modes
+- **Supervised Learning**: Support for label-based projection
+- **Transform Capability**: Project new points into existing embeddings
+
+## 🏆 Attribution & Lineage
+
+This project is a research fork that extends the original UMAP implementations:
+
+### Upstream JavaScript Implementation
+- **Project**: [umap-js](https://github.com/PAIR-code/umap-js)
+- **Maintainer**: PAIR (People + AI Research) at Google
+- **License**: Apache 2.0
+
+### Original UMAP Algorithm
+- **Project**: [umap](https://github.com/lmcinnes/umap)  
+- **Authors**: Leland McInnes, John Healy, James Melville
+- **Reference**: McInnes, L., Healy, J., & Melville, J. (2018). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. *arXiv preprint arXiv:1802.03426*.
+
+**Credit**: The core UMAP algorithm implementation and JavaScript port are the work of the original and upstream authors. This thesis project focuses exclusively on performance optimization through selective WebAssembly compilation.
+
+## ⚡ Implementation Notes
+
+### Differences from Python UMAP
+
+- **Initialization**: Uses random embedding initialization instead of spectral embedding (eigenvalue computations are computationally prohibitive in JavaScript)
+- **Sparse Data**: No specialized sparse data structures (may be addressed in future work)
+- **Angular Distances**: Not currently implemented
+
+These differences result in comparable quality for most use cases, with the random initialization performing well on small to medium datasets.
+
+## 📦 Installation
+
+```bash
+npm install umap-wasm
+# or
+yarn add umap-wasm
+```
+
+## 🚀 Usage
+
+### Basic Usage (Synchronous)
+
+```javascript
+import { UMAP } from 'umap-wasm';
+
+const umap = new UMAP({
+  nComponents: 2,
+  nNeighbors: 15,
+  minDist: 0.1
+});
+
+const embedding = umap.fit(data);
+```
+
+### Asynchronous Fitting with Progress Tracking
+
+```javascript
+import { UMAP } from 'umap-wasm';
+
+const umap = new UMAP();
+const embedding = await umap.fitAsync(data, epochNumber => {
+  console.log(`Epoch ${epochNumber} complete`);
+  // Return false to stop early if needed
+  return true;
+});
+```
+
+### Step-by-Step Fitting
+
+For fine-grained control over the optimization process:
+
+```javascript
+import { UMAP } from 'umap-wasm';
+
+const umap = new UMAP();
+const nEpochs = umap.initializeFit(data);
+
+for (let i = 0; i < nEpochs; i++) {
+  umap.step();
+  // Update UI, check convergence, etc.
+}
+
+const embedding = umap.getEmbedding();
+```
+
+### Supervised Projection
+
+Use label information to guide the embedding:
+
+```javascript
+import { UMAP } from 'umap-wasm';
+
+const labels = [0, 0, 1, 1, 2, 2]; // Category labels for each data point
+const umap = new UMAP();
+umap.setSupervisedProjection(labels);
+const embedding = umap.fit(data);
+```
+
+### Transforming New Points
+
+Project additional data points into an existing embedding space:
+
+```javascript
+import { UMAP } from 'umap-wasm';
+
+const umap = new UMAP();
+const embedding = umap.fit(trainingData);
+
+// Transform new points into the same embedding space
+const newEmbedding = umap.transform(newData);
+```
+
+## 🔧 Configuration Parameters
+
+The UMAP constructor accepts a `UMAPParameters` object with the following options:
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `nComponents` | `number` | `2` | Target dimensionality of the embedding |
+| `nNeighbors` | `number` | `15` | Number of nearest neighbors for manifold approximation |
+| `nEpochs` | `number` | *auto* | Number of optimization iterations (computed if not specified) |
+| `minDist` | `number` | `0.1` | Minimum distance between embedded points |
+| `spread` | `number` | `1.0` | Effective scale of embedded points |
+| `random` | `() => number` | `Math.random` | PRNG for reproducibility |
+| `distanceFn` | `DistanceFn` | `euclidean` | Distance metric for input space |
+| `useWasmDistance` | `boolean` | `false` | Whether to use Rust/WASM distance functions when available |
+| `useWasmTree` | `boolean` | `false` | Whether to use Rust/WASM random projection tree construction when available |
+| `useWasmMatrix` | `boolean` | `false` | Whether to use Rust/WASM sparse matrix operations when available |
+
+### WASM Components & Status
+
+The project exposes configuration flags to selectively enable WASM-accelerated components. The table below maps the high-level operations to the available configuration flags and current implementation status.
+
+| Component | Config Flag | Status | Notes |
+|-----------|-------------|--------|-------|
+| Distance computations | `useWasmDistance` | Implemented | WASM provides `euclidean` and `cosine` implementations (via `wasmBridge`). These are implemented in `distances.rs`.
+| Nearest neighbour search (random projection trees) | `useWasmTree` | Implemented | WASM-accelerated random projection tree construction is available and can be enabled with `useWasmTree` (see `tree.rs`).
+| Matrix operations in optimization loops | `useWasmMatrix` | Implemented | Sparse-matrix operations (transpose, element-wise ops, CSR conversion, normalization) are implemented in WASM (see `matrix.rs`).
+| Nearest‑neighbour graph refinement (NN‑Descent) | — | TODO | NN‑Descent (graph refinement / approximate nearest neighbours) currently uses the JS implementation; WASM integration is planned.
+| Gradient‑descent layout optimisation | — | TODO | The optimization loop runs in JS; a WASM-accelerated optimizer is under investigation.
+
+
+### Example with Custom Parameters
+
+```typescript
+import { UMAP } from 'umap-wasm';
+
+const umap = new UMAP({
+  nComponents: 3,          // 3D embedding
+  nNeighbors: 30,          // Larger neighborhood
+  minDist: 0.3,            // More spread out
+  spread: 2.0,             // Wider scale
+  nEpochs: 500,            // More optimization steps
+  random: seedrandom('42') // Reproducible results
+});
+```
+
+## 🛠️ Development
+
+### Prerequisites
+
+- **Node.js** 18+ and **Yarn** 4.12.0
+- **Rust** toolchain with `wasm32-unknown-unknown` target
+- **wasm-pack** for WebAssembly builds
+
+### Setup
+
+```bash
+# Install dependencies
+yarn install
+
+# Install Rust target (if not already installed)
+rustup target add wasm32-unknown-unknown
+
+# Install wasm-pack
+curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh
+```
+
+### Build Commands
+
+```bash
+# Build TypeScript and bundle
+yarn build
+
+# Build WebAssembly modules (both web and node targets)
+yarn build:wasm
+
+# Run tests
+yarn test
+
+# Run tests in watch mode
+yarn test:watch
+
+# Run tests with UI
+yarn test:ui
+
+# Run tests with coverage
+yarn test:coverage
+```
+
+### Project Structure
+
+```
+umap-wasm/
+├── src/               # TypeScript implementation
+│   ├── umap.ts       # Main UMAP class
+│   ├── matrix.ts     # Matrix operations
+│   ├── tree.ts       # KD-tree for nearest neighbors
+│   └── wasmBridge.ts # WASM interop layer
+├── wasm/             # Rust/WASM implementation
+│   ├── src/          # Rust source code
+│   └── pkg/          # Built WASM artifacts
+│       ├── web/      # Web target (ES modules)
+│       └── node/     # Node target (CommonJS)
+├── test/             # Test suites (Vitest)
+└── lib/              # Output bundles
+```
+
+### WebAssembly Development
+
+The Rust core is located in the `wasm/` directory. To modify WASM components:
+
+```bash
+cd wasm
+cargo build --target wasm32-unknown-unknown
+
+# Build for web (ES modules)
+wasm-pack build --target web --out-dir pkg/web
+
+# Build for Node.js (CommonJS)
+wasm-pack build --target nodejs --out-dir pkg/node
+```
+
+The build artifacts are generated in `wasm/pkg/web/` and `wasm/pkg/node/`. The TypeScript bridge automatically detects the runtime environment and loads the appropriate build.
+
+## 🧪 Testing
+
+This project uses [Vitest](https://vitest.dev/) for fast unit testing.
+
+```bash
+# Run all tests
+yarn test
+
+# Run specific test suite
+yarn test matrix.test.ts
+
+# Watch mode for development
+yarn test:watch
+
+# UI mode (visual test runner)
+yarn test:ui
+
+# Generate coverage report
+yarn test:coverage
+```
+
+## 📊 Benchmarking
+
+Performance benchmarks are available in the companion `umap-bench` repository, which includes:
+
+- Comparative analysis (pure JS vs WASM-accelerated)
+- Dataset size scaling tests
+- Browser compatibility tests
+- Memory profiling
+
+See [../umap-bench/README.md](../umap-bench/README.md) for details.
+
+## 🤝 Contributing
+
+This is a thesis research project with specific academic goals. While external contributions are not actively solicited during the research phase, feedback and bug reports are welcome.
+
+Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+## 📄 License
+
+Apache License 2.0 - see [LICENSE](LICENSE) for details.
+
+This project inherits the Apache 2.0 license from the upstream `umap-js` project.
+
+## 📚 References
+
+### Academic Publications
+
+1. **McInnes, L., Healy, J., & Melville, J.** (2018). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. *arXiv preprint arXiv:1802.03426*. [https://arxiv.org/abs/1802.03426](https://arxiv.org/abs/1802.03426)
+
+2. **McInnes, L., & Healy, J.** (2017). Accelerated Hierarchical Density Based Clustering. *IEEE International Conference on Data Mining Workshops (ICDMW)*, 33-42.
+
+### Related Projects
+
+- **umap-js**: [https://github.com/PAIR-code/umap-js](https://github.com/PAIR-code/umap-js)
+- **umap (Python)**: [https://github.com/lmcinnes/umap](https://github.com/lmcinnes/umap)
+- **UMAP Documentation**: [https://umap-learn.readthedocs.io/](https://umap-learn.readthedocs.io/)
+
+## 🙏 Acknowledgments
+
+- **PAIR team at Google** for the original JavaScript implementation
+- **Leland McInnes** and collaborators for the UMAP algorithm
+- **TAMK** thesis advisors and reviewers
+
+## 📧 Contact
+
+For thesis-related inquiries or research collaboration:
+
+**Elar Saks**  
+Master's Thesis Project  
+Tampere University of Applied Sciences
+
+---
+
+*This README is maintained as part of academic research. Last updated: January 2026*

package/dist/src/heap.d.ts

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+import { RandomFn } from './umap';
+export type Heap = number[][][];
+export declare function makeHeap(nPoints: number, size: number): Heap;
+export declare function rejectionSample(nSamples: number, poolSize: number, random: RandomFn): number[];
+export declare function heapPush(heap: Heap, row: number, weight: number, index: number, flag: number): number;
+export declare function uncheckedHeapPush(heap: Heap, row: number, weight: number, index: number, flag: number): number;
+export declare function buildCandidates(currentGraph: Heap, nVertices: number, nNeighbors: number, maxCandidates: number, random: RandomFn): Heap;
+export declare function deheapSort(heap: Heap): {
+    indices: number[][];
+    weights: number[][];
+};
+export declare function smallestFlagged(heap: Heap, row: number): number;