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["warn", 4], + "@typescript-eslint/ban-ts-comment": ["warn", { "ts-expect-error": "allow-with-description" }], + "@typescript-eslint/explicit-function-return-type": [ + "warn", + { "allowExpressions": true } + ], + "indent": "off", + "no-unused-vars": "off", + "@typescript-eslint/no-unused-vars": [ + "warn", + { "args": "all", "argsIgnorePattern": "^_" } + ], + "@typescript-eslint/array-type": ["warn", { "default": "generic" }] + } + } + ] +} \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0c15975 --- /dev/null +++ b/.gitignore @@ -0,0 +1,70 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# TypeScript v1 declaration files +typings/ + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + +# dotenv environment variables file +.env + +# next.js build output +.next + +# other weird stuff +.DS_Store + +# Project related files +node_modules +public/bundle.* +public/app.* +public/confMat.* diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..c991377 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,71 @@ +# Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, nationality, personal +appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies within all project spaces, and it also applies when +an individual is representing the project or its community in public spaces. +Examples of representing a project or community include using an official +project e-mail address, posting via an official social media account, or acting +as an appointed representative at an online or offline event. Representation of +a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the open source team at [opensource-conduct@group.apple.com](mailto:opensource-conduct@group.apple.com). All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and appropriate to the circumstances. The project team is +obligated to maintain confidentiality with regard to the reporter of an incident. +Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 1.4, +available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct.html](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html) \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..a79135d --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,11 @@ +# Contribution Guide + +Thanks for your interest in contributing. This project was released to accompany a research paper for purposes of reproducability, and beyond its publication there are limited plans for future development of the repository. + +Nonetheless, we welcome new pull requests and issues and will do our best to respond timely. + +## Before you get started + +By submitting a pull request, you represent that you have the right to license your contribution to Apple and the community, and agree by submitting the patch that your contributions are licensed under the [LICENSE](LICENSE). + +We ask that all community members read and observe our [Code of Conduct](CODE_OF_CONDUCT.md). diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..8ce4f2e --- /dev/null +++ b/LICENSE @@ -0,0 +1,39 @@ +Copyright (C) 2020 Apple Inc. All Rights Reserved. + +IMPORTANT: This Apple software is supplied to you by Apple +Inc. ("Apple") in consideration of your agreement to the following +terms, and your use, installation, modification or redistribution of +this Apple software constitutes acceptance of these terms. If you do +not agree with these terms, please do not use, install, modify or +redistribute this Apple software. + +In consideration of your agreement to abide by the following terms, and +subject to these terms, Apple grants you a personal, non-exclusive +license, under Apple's copyrights in this original Apple software (the +"Apple Software"), to use, reproduce, modify and redistribute the Apple +Software, with or without modifications, in source and/or binary forms; +provided that if you redistribute the Apple Software in its entirety and +without modifications, you must retain this notice and the following +text and disclaimers in all such redistributions of the Apple Software. +Neither the name, trademarks, service marks or logos of Apple Inc. may +be used to endorse or promote products derived from the Apple Software +without specific prior written permission from Apple. Except as +expressly stated in this notice, no other rights or licenses, express or +implied, are granted by Apple herein, including but not limited to any +patent rights that may be infringed by your derivative works or by other +works in which the Apple Software may be incorporated. + +The Apple Software is provided by Apple on an "AS IS" basis. APPLE +MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION +THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY AND FITNESS +FOR A PARTICULAR PURPOSE, REGARDING THE APPLE SOFTWARE OR ITS USE AND +OPERATION ALONE OR IN COMBINATION WITH YOUR PRODUCTS. + +IN NO EVENT SHALL APPLE BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL +OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) ARISING IN ANY WAY OUT OF THE USE, REPRODUCTION, +MODIFICATION AND/OR DISTRIBUTION OF THE APPLE SOFTWARE, HOWEVER CAUSED +AND WHETHER UNDER THEORY OF CONTRACT, TORT (INCLUDING NEGLIGENCE), +STRICT LIABILITY OR OTHERWISE, EVEN IF APPLE HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..381ffb5 --- /dev/null +++ b/README.md @@ -0,0 +1,237 @@ +# Neo: Hierarchical Confusion Matrix + +The confusion matrix, a ubiquitous visualization for helping people evaluate machine learning models, is a tabular layout that compares predicted class labels against actual class labels over all data instances. Neo is a visual analytics system that enables practitioners to flexibly author and interact with hierarchical and multi-output confusion matrices, visualize derived metrics, renormalize confusions, and share matrix specifications. + +This code accompanies the research paper: + +**[Neo: Generalizing Confusion Matrix Visualization to Hierarchical and Multi-Output Labels](https://machinelearning.apple.com/research/generalizing-confusion-matrix)** +Jochen Görtler, Fred Hohman, Dominik Moritz, Kanit Wongsuphasawat, Donghao Ren, Rahul Nair, Marc Kirchner, Kayur Patel +*ACM Conference on Human Factors in Computing Systems (CHI), 2022.* + + +## Documentation + +You can embed our confusion matrix visualization into your own project. There are two ways to use it. + +### NPM + +Install with `npm install --save @apple/hierarchical-confusion-matrix` or `yarn add @apple/hierarchical-confusion-matrix`. + +Then you can import the module in your project + +```js +import confMat from "@apple/hierarchical-confusion-matrix"; + +const spec = { + classes: ['root'], +} + +const confusions = [ + { + actual: ['root:a'], + observed: ['root:a'], + count: 1, + }, + { + actual: ['root:a'], + observed: ['root:b'], + count: 2, + }, + { + actual: ['root:b'], + observed: ['root:a'], + count: 3, + }, + { + actual: ['root:b'], + observed: ['root:b'], + count: 4, + } +] + +confMat.embed('matContainer', spec, confusions); +``` + +### Embed the Compiled File + +If you prefer to load the compiled JavaScript directly, you have to compile it. To do this, run `yarn install` and copy the `public/confMat.js` into your project. Here is a simple example of a small confusion matrix: + +```html + + + + + + Neo: Hierarchical Confusion Matrix + + + +
+ + + + +``` + +### Specification + +You can find all the options that you can pass via the `spec` argument in [`src/specification.ts`](src/specification.ts). + +### Loaders + +The different loaders can be found in [`src/loaders`](src/loaders), which include loading data from `json`, `csv`, `vega`, and a synthetic example `synth` for testing. + +### Confusion Data Format Examples + +#### Example 1: Conventional Confusions +The confusions for data with `actual` labels of `fruit:lemon` that are incorrectly predicted as `fruit:apple`, of which there are `count` 1 of them. + +``` +{ + "actual": [ + "fruit:lemon" + ], + "observed": [ + "fruit:apple" + ], + "count": 1 +} +``` + +#### Example 2: Hierarchical Confusions +The confusions for hierarchical data with `actual` labels of `fruit:citrus:lemon` that are incorrectly predicted as `fruit:pome:apple`, of which there are `count` 2 of them. Note `:` denotes hierarchies. + +``` +{ + "actual": [ + "fruit:citrus:lemon" + ], + "observed": [ + "fruit:pome:apple" + ], + "count": 2 +} +``` + +#### Example 3: Multi-output Confusions +The confusions for multi-output data with `actual` labels of `fruit:lemon,taste:sweet` that are incorrectly predicted as `fruit:apple,taste:sour`, of which there are `count` 3 of them. Note `,` denotes multi-ouput labels. + +``` +{ + "actual": [ + "fruit:lemon", + "taste:sweet" + ], + "observed": [ + "fruit:apple", + "taste:sour" + ], + "count": 3 +} +``` + +#### Example 4: Hierarchical and Multi-output Confusions +The confusions for hierarchical and multi-output data with `actual` labels of `fruit:citrus:lemon,taste:sweet,ripeness:ripe` that are incorrectly predicted as `fruit:pome:apple,taste:sour,ripeness:not-ripe`, of which there are `count` 4 of them. + +``` +{ + "actual": [ + "fruit:citrus:lemon", + "taste:sweet", + "ripeness:ripe" + ], + "observed": [ + "fruit:pome:apple", + "taste:sour" + "ripeness:not-ripe" + ], + "count": 4 +} +``` + +See [`fruit.json`](public/data/fruit.json) for a complete example of confusions for a hierarchical fruit, taste, and ripeness classification model. + +## Development + +Build: + +```sh +yarn install +yarn build +``` + +Test: + +```sh +yarn test +``` + +Start: + +```sh +yarn start +``` + +Dev Server: + +```sh +yarn dev +``` + +Lint & Fix: + +```sh +yarn format +``` + +## Contributing + +When making contributions, refer to the [`CONTRIBUTING`](CONTRIBUTING.md) guidelines and read the [`CODE OF CONDUCT`](CODE_OF_CONDUCT.md). + +## BibTeX + +To cite our paper, please use: + +```bibtex +@inproceedings{gortler2022neo, + title={Neo: Generalizing Confusion Matrix Visualization to Hierarchical and Multi-Output Labels}, + author={Görtler, Jochen and Hohman, Fred and Moritz, Dominik and Wongsuphasawat, Kanit and Ren, Donghao and Nair, Rahul and Kirchner, Marc and Patel, Kayur}, + booktitle={Proceedings of the SIGCHI Conference on Human Factors in Computing Systems}, + year={2022}, + organization={ACM}, + doi={10.1145/3491102.3501823} +} +``` + +## License + +This code is released under the [`LICENSE`](LICENSE) terms. diff --git a/babel.config.js b/babel.config.js new file mode 100644 index 0000000..9d06939 --- /dev/null +++ b/babel.config.js @@ -0,0 +1,3 @@ +module.exports = { + presets: ['@babel/preset-typescript'], +}; diff --git a/jest.config.js b/jest.config.js new file mode 100644 index 0000000..6d6062b --- /dev/null +++ b/jest.config.js @@ -0,0 +1,4 @@ +module.exports = { + preset: 'ts-jest', + testEnvironment: 'node', +}; diff --git a/package.json b/package.json new file mode 100644 index 0000000..3db69b1 --- /dev/null +++ b/package.json @@ -0,0 +1,70 @@ +{ + "name": "@apple/hierarchical-confusion-matrix", + "author": "Apple Inc.", + "version": "1.0.0", + "license": "Apple Sample Code", + "main": "public/confMat.js", + "files": [ + "src" + ], + "devDependencies": { + "@babel/core": "^7.17.5", + "@babel/preset-typescript": "^7.16.7", + "@rollup/plugin-commonjs": "^21.0.2", + "@rollup/plugin-json": "^4.1.0", + "@rollup/plugin-node-resolve": "^13.1.3", + "@rollup/plugin-typescript": "^8.3.1", + "@tsconfig/svelte": "^3.0.0", + "@types/cwise": "^1.0.4", + "@types/d3-array": "^3.0.2", + "@types/d3-dsv": "^3.0.0", + "@types/d3-scale": "^4.0.2", + "@types/jest": "^27.4.1", + "@types/lodash": 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--config .eslintrc.json --ext .js,.ts,.json .", + "format": "npm run lint -- --fix", + "test": "npm run lint && npm run svelte-check && jest", + "deploy": "npm run build && gh-pages -d public" + }, + "dependencies": { + "d3-array": "^2.11.0", + "d3-dsv": "^2.0.0", + "d3-scale": "^3.2.3", + "lodash": "^4.17.21", + "ndarray": "^1.0.19", + "ndarray-ops": "^1.2.2", + "vega-scale": "^7.1.1" + } +} diff --git a/public/data/beverages.json b/public/data/beverages.json new file mode 100644 index 0000000..d27e341 --- /dev/null +++ b/public/data/beverages.json @@ -0,0 +1,357 @@ +{ + "$schema": "https://vega.github.io/schema/vega-lite/v4.0.2.json", + "config": {"view": {"continuousHeight": 300, "continuousWidth": 400}}, + "data": { + "values": [ + { + "annotation_text": "[beverage:coke_zero,state:damaged]", + "occurence_log": 0, + "occurrence": 0, + "reference_text": "[beverage:coke_zero,state:damaged]" + }, + { + "annotation_text": "[beverage:coke_zero,state:open]", + "occurence_log": 1, + 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All Rights Reserved. + */ + +html { + display: block; +} + +body{ + padding: 0; + margin: 0; + font-size: 13px; + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"; +} +* { + box-sizing: border-box; +} +table, th, td { + border-collapse: collapse; +} + +h1 { + margin: 1em 0 1em 0; +} + +h2 { + margin:2em 0 1em 0; +} + +h3, h4, h5, h6 { + margin: 2em 0 1em 0; +} + +h1 { + font-size: 3em; +} +h2 { + font-size: 2em; +} + +.box { + margin: 0 0 1em 0; + padding: 2em; + border: 1px solid #ccc; + border-radius: 5px; + text-align: center; + min-width: 550px +} + +.box > div { + margin: 0 auto; + text-align: left; +} + diff --git a/public/index.html b/public/index.html new file mode 100644 index 0000000..694b69a --- /dev/null +++ b/public/index.html @@ -0,0 +1,17 @@ + + + + + + + Neo: Hierarchical Confusion Matrix + + + + + + + + + + diff --git a/rollup.config.js b/rollup.config.js new file mode 100644 index 0000000..dbb561b --- /dev/null +++ b/rollup.config.js @@ -0,0 +1,85 @@ +import autoPreprocess from 'svelte-preprocess'; +import commonjs from '@rollup/plugin-commonjs'; +import css from 'rollup-plugin-css-only'; +import json from '@rollup/plugin-json'; +import livereload from 'rollup-plugin-livereload'; +import pkg from './package.json'; +import resolve from '@rollup/plugin-node-resolve'; +import { Server } from 'http'; +import svelte from 'rollup-plugin-svelte'; +import { terser } from 'rollup-plugin-terser'; +import typescript from '@rollup/plugin-typescript'; + +const copyright = `// ${pkg.name} v${pkg.version} Copyright ${(new Date).getFullYear()} ${pkg.author.name}`; + +const production = !process.env.ROLLUP_WATCH; + +export default [ + // App + { + input: 'src/app.ts', + output: { + banner: copyright, + sourcemap: !production, + format: 'iife', + name: 'app', + file: 'public/app.js', + }, + plugins: [ + svelte({ + preprocess: autoPreprocess(), + compilerOptions: { + dev: !production, + }, + }), + css({ output: 'bundle.css' }), + typescript({ + noEmitOnError: false, + sourceMap: !production, + }), + json(), + resolve({ + browser: true, + dedupe: ['svelte'], + }), + commonjs(), + !production && Server(), + !production && livereload('public'), + production && terser({ output: { preamble: copyright } }), + ], + watch: { + clearScreen: false, + }, + }, + // Library + { + input: 'src/lib.ts', + output: { + banner: copyright, + sourcemap: !production, + format: 'umd', + name: 'confMat', + file: 'public/confMat.js', + }, + plugins: [ + svelte({ + preprocess: autoPreprocess(), + emitCss: false, + compilerOptions: { + dev: !production, + }, + }), + typescript({ + noEmitOnError: false, + sourceMap: !production, + }), + json(), + resolve({ + browser: true, + dedupe: ['svelte'], + }), + commonjs(), + terser({ output: { preamble: copyright } }), + ], + }, +]; diff --git a/src/app.ts b/src/app.ts new file mode 100644 index 0000000..7769590 --- /dev/null +++ b/src/app.ts @@ -0,0 +1,108 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import { csv, json, synth, vega, vegaCompressed } from './loaders'; +import App from './components/App.svelte'; +import type { Confusion } from './confusions'; +import { defaults } from './specification'; +import type { Spec } from './specification'; + +type Loader = () => Promise>; + +type Example = { + description: string; + loader: Loader; + spec: Spec; +} + +const examples: Array = [ + { + description: 'Fruit', + loader: () => json('data/fruit.json'), + spec: { + ...defaults, + classes: ['fruit'], + normalization: 'total', + }, + }, + { + description: 'Beverages', + loader: () => vega('data/beverages.json'), + spec: { + ...defaults, + classes: ['beverage'], + normalization: 'total', + }, + }, + { + description: 'Synthetic', + loader: async () => synth(), + spec: { + ...defaults, + classes: ['vehicle'], + normalization: 'total', + }, + }, + { + description: 'Synthetic (nested, filtered)', + loader: async () => synth(), + spec: { + ...defaults, + classes: ['vehicle', 'state'], + filter: ['vehicle:motorized'], + normalization: 'total', + }, + }, + { + description: 'Synthetic (conditioning)', + loader: async () => synth(), + spec: { + ...defaults, + classes: ['vehicle', 'animal'], + where: { qualifier: 'actual', label: 'state', is: 'state:moving' }, + normalization: 'total', + }, + }, + { + description: 'Case Study 1 (App Prediction)', + loader: () => csv('data/chi-paper/case-study-1.csv'), + spec: { + ...defaults, + classes: ['root'], + measures: ['accuracy', 'precision', 'recall'], + encoding: 'color', + normalization: 'total', + }, + }, + { + description: 'Case Study 2 (ImageNet)', + loader: () => vegaCompressed('data/chi-paper/case-study-2.json'), + spec: { + ...defaults, + classes: ['root'], + measures: ['precision', 'recall', 'countObserved'], + encoding: 'color', + normalization: 'total', + collapsed: ['', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:instrument:weapon-arm-weap:gun', 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entity:object-physical:whole-unit:artifact-artefa:instrumentality:equipment:gear-parapherna:rig:drill rig-drill', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:implement:bar', 'root:entity:physical entity:object-physical:geological form:natural elevati:ridge:bar', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:article:ware', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:clothing-articl:garment:overgarment-out', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:conveyance-tran:vehicle:craft:vessel-watercra:boat:sea boat', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:keyboard', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:memory device-s', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:passerine-passe:oscine-oscine b:thrush:nightingale-Lus', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:instrument:weapon-arm-weap:gun:firearm-piece-s', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:machine', 'root:entity:physical entity:matter:solid:food-solid food:produce-green g:vegetable-veggi:squash:winter squash', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:aquatic vertebr:fish:cartilaginous f:elasmobranch-se', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:ungulate-hoofed:even-toed ungul:ruminant:bovid:wild sheep', 'root:entity:physical entity:matter:substance:food-nutrient:foodstuff-food :ingredient-fixi:flavorer-flavou:condiment', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :invertebrate:arthropod:insect:lepidopterous i:butterfly:pierid-pierid b', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:article:ware:tableware:cutlery-eating :spoon', 'root:entity:physical entity:matter:solid:food-solid food:produce-green g', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:implement:rod', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:instrument:measuring instr:timepiece-timek:clock', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:structure-const:signboard-sign', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:restraint-const:brake:brake system-br', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:aquatic vertebr:fish:cartilaginous f:elasmobranch-se:ray', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:conveyance-tran:vehicle:craft:vessel-watercra:ship:warship-war ves:submersible-sub', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:instrument:optical instrum', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:aquatic vertebr:fish:bony fish:teleost fish-te:soft-finned fis:cypriniform fis', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :invertebrate:arthropod:insect:orthopterous in', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:clothing-articl:uniform', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:musical instrum:wind instrument', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:aquatic vertebr:fish:bony fish:teleost fish-te:spiny-finned fi:plectognath-ple', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:aquatic bird:seabird-sea bir:sphenisciform s', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:protective cove:sheath', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:aquatic vertebr:fish:bony fish:teleost fish-te:soft-finned fis:salmonid:salmon', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:conveyance-tran:vehicle:wheeled vehicle:self-propelled :motor vehicle-a', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:fabric-cloth-ma', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:mechanism:rotating mechan', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:plant-flora-pla', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :invertebrate:worm', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :invertebrate:echinoderm', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:electrical devi:transducer', 'root:entity:physical entity:matter:substance:food-nutrient:nutriment-nouri:course', 'root:entity:physical entity:matter:substance:food-nutrient:nutriment-nouri:dish', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:aquatic bird:wading bird-wad:shorebird-shore:plover:turnstone', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:ungulate-hoofed:even-toed ungul:ruminant:bovid:bovine:cattle-cows-kin', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:clothing-articl:garment', 'root:entity:physical entity:matter:substance:agent', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:carnivore:canine-canid:dog-domestic do:toy dog-toy:toy spaniel:English toy spa', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:implement:tool:cutting impleme:cutter-cutlery-:edge tool', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:reptile-reptili:anapsid-anapsid', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:runner', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:aquatic bird:wading bird-wad:shorebird-shore:plover', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:edentate', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:implement:sharpener', 'root:entity:abstraction-abs:attribute:shape-form:round shape:sphere:ball-globe-orb', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:parrot', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:toiletry-toilet:cream-ointment-', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:aquatic bird:waterfowl-water', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:aquatic mammal:pinniped mammal:seal', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:prototherian', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:carnivore:canine-canid:dog-domestic do:working dog:watchdog-guard :pinscher', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :invertebrate:arthropod:insect:lepidopterous i:butterfly', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:clothing-articl:apparel-wearing', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:excavation', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:ungulate-hoofed:odd-toed ungula:equine-equid:horse-Equus cab', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:lagomorph-gnawi', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:airfoil-aerofoi', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:floor cover-flo:mat', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:structure-const:memorial-monume', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:restraint-const:safety belt-lif', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:musical instrum:keyboard instru', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:structure-const:establishment:institution', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:aquatic bird:waterfowl-water:anseriform bird', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:musical instrum:wind instrument:free-reed instr', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:instrument:scientific inst:magnifier:microscope', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:mammal-mammalia:placental-place:aquatic mammal:cetacean-cetace:whale:toothed whale', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:commodity-trade:consumer goods', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:conveyance-tran:vehicle:wheeled vehicle:trailer-house t', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:piciform bird', 'root:entity:physical entity:object-physical:whole-unit:living thing-an:organism-being:animal-animate :chordate:vertebrate-cran:bird:cuculiform bird:cuckoo', 'root:entity:physical entity:object-physical:whole-unit:natural object:plant part-plan:plant organ:reproductive st:fruit:edible fruit', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:structure-const:building comple:plant-works-ind:factory-mill-ma', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:covering:clothing-articl:attire-garb-dre:hairpiece-false', 'root:entity:physical entity:object-physical:whole-unit:artifact-artefa:instrumentality:device:musical instrum:stringed instru:chordophone'], + }, + }, + { + description: 'Case Study 3 (Toxicity)', + loader: () => json('data/chi-paper/case-study-3.json'), + spec: { + ...defaults, + classes: ['toxic_mild'], + measures: ['accuracy', 'countObserved', 'countActual', 'precision', 'recall', 'falsePositives', 'falseNegatives'], + encoding: 'color', + normalization: 'total', + }, + }, +]; + +new App({ + target: document.body, + props: { examples }, +}); diff --git a/src/components/App.svelte b/src/components/App.svelte new file mode 100644 index 0000000..056f350 --- /dev/null +++ b/src/components/App.svelte @@ -0,0 +1,181 @@ + + + + + + +
+
+ +
+
+ +
+ {#if specVisible} +
+ +
+ SpecificationAll the configuration and state of the confusion matrix is stored in an easily shareable JSON format. Changing values in the textarea updates the visualization. + +
+
+ {/if} + + {#await confusionPromise} +

...waiting

+ {:then confusions} + + {:catch error} +

{error.message}

+ {/await} +
diff --git a/src/components/CellBlank.svelte b/src/components/CellBlank.svelte new file mode 100644 index 0000000..eea2ac8 --- /dev/null +++ b/src/components/CellBlank.svelte @@ -0,0 +1,40 @@ + + + + + \ No newline at end of file diff --git a/src/components/CellColor.svelte b/src/components/CellColor.svelte new file mode 100644 index 0000000..2b2d9f0 --- /dev/null +++ b/src/components/CellColor.svelte @@ -0,0 +1,48 @@ + + + + + + + \ No newline at end of file diff --git a/src/components/CellSquare.svelte b/src/components/CellSquare.svelte new file mode 100644 index 0000000..76423c0 --- /dev/null +++ b/src/components/CellSquare.svelte @@ -0,0 +1,64 @@ + + + + + + + + \ No newline at end of file diff --git a/src/components/CellStat.svelte b/src/components/CellStat.svelte new file mode 100644 index 0000000..ca4033c --- /dev/null +++ b/src/components/CellStat.svelte @@ -0,0 +1,28 @@ + + + + + + + +{statistic[1]} + + + + diff --git a/src/components/CellZero.svelte b/src/components/CellZero.svelte new file mode 100644 index 0000000..3e1018f --- /dev/null +++ b/src/components/CellZero.svelte @@ -0,0 +1,53 @@ + + + + + + + + \ No newline at end of file diff --git a/src/components/Label.svelte b/src/components/Label.svelte new file mode 100644 index 0000000..fd07751 --- /dev/null +++ b/src/components/Label.svelte @@ -0,0 +1,103 @@ + + + + + + +{#if node.isLeaf()} + + {truncate(node.data.name)} + +{:else if $spec.collapsed.includes(node.data.id)} + { + const index = $spec.collapsed.indexOf(node.data.id); + if (index > -1) { + $spec.collapsed.splice(index, 1); + $spec = $spec; + } + }} + class={$currentCell && $currentCell[direction] === node ? 'label active' : 'label'}> + {'>'} + {truncate(node.data.name)} + +{:else} + + { + $spec.collapsed.push(node.data.id); + $spec = $spec; + }}> + ⋁ + + {truncate(node.data.name)} + + + {#if $spec.filter?.includes(node.data.id)} + { + const filterSet = new Set($spec.filter); + filterSet.delete(node.data.id); + $spec.filter = [...filterSet]; + $spec = $spec; + }}> + ❌ + + {:else} + { + if (!$spec.filter || $spec.filter.length === 0) { + $spec.filter = [node.data.id]; + } else { + const filterSet = new Set($spec.filter); + filterSet.add(node.data.id); + $spec.filter = [...filterSet]; + } + $spec = $spec; + }}> + 🔎 + + {/if} + +{/if} diff --git a/src/components/LegendColor.svelte b/src/components/LegendColor.svelte new file mode 100644 index 0000000..e801552 --- /dev/null +++ b/src/components/LegendColor.svelte @@ -0,0 +1,47 @@ + + + + + + + + + {#each [...Array(steps).keys()] as s} + + {/each} + + + + + +{#each ticks as tick,i} + {format(tick, 1)} +{/each} \ No newline at end of file diff --git a/src/components/LegendSize.svelte b/src/components/LegendSize.svelte new file mode 100644 index 0000000..67260a7 --- /dev/null +++ b/src/components/LegendSize.svelte @@ -0,0 +1,49 @@ + + + + + + +{#each ticks as tick,i} + + + {format(tick, 1)} +{/each} \ No newline at end of file diff --git a/src/components/Matrix.svelte b/src/components/Matrix.svelte new file mode 100644 index 0000000..4da4e77 --- /dev/null +++ b/src/components/Matrix.svelte @@ -0,0 +1,224 @@ + + + + + + +
+ {#if $currentCell} + {$currentCell[0].data.name.substring(0, 21)} was labeled as {$currentCell[1].data.name.substring(0, 21)} + in {matrix.frequency($currentCell[0], $currentCell[1])} instances. + {:else}Hover over cells to show more information.{/if} +
+ + + + + + {#if $spec.filter?.length > 0} + {'< go back'} + {/if} + + + {$spec.normalization === 'total' ? 'Counts' : `${$spec.normalization} Probabilities`} + + {#if $spec.encoding === 'color'} + + {:else if $spec.encoding === 'size'} + + {/if} + + + + + {#if highlightRow} + + {/if} + {#if highlightCol} + + {/if} + + + Observed + {#each layout as { node: predict, pos: predictPos }} + + + + + + {/each} + + + Actual + + {#each layout as { node: actual, pos: actualPos, span }} + + {#if span > 0} + $currentCell && n.data.id === $currentCell[0].data.id) ? "black" : "#cccccc"} /> + {/if} + + + {/each} + + + + {#each layout as { node: actual, pos: actualPos }} + + {#each layout as { node: predict, pos: predictPos }} + {#if !isFrontier(predict) || !isFrontier(actual)} + + {:else if matrix.frequency(actual, predict) === 0} + + {:else if $spec.encoding === 'color'} + + {:else if $spec.encoding === 'size'} + + {/if} + {/each} + + {/each} + + + + {#each columns as statistic, i} + + {statistic.name()} + {#each layout as { node: row, pos: rowPos }} + + + + {/each} + + {/each} + + + diff --git a/src/components/MatrixWithUI.svelte b/src/components/MatrixWithUI.svelte new file mode 100644 index 0000000..9a26049 --- /dev/null +++ b/src/components/MatrixWithUI.svelte @@ -0,0 +1,18 @@ + + + + + + + \ No newline at end of file diff --git a/src/components/UIOptions.svelte b/src/components/UIOptions.svelte new file mode 100644 index 0000000..945ff8d --- /dev/null +++ b/src/components/UIOptions.svelte @@ -0,0 +1,68 @@ + + + + + + +
+
+ Encoding + {#each [...encodingChoices.entries()] as [name, enc]} + + {/each} +
+
+ Normalization + {#each [...mappingChoices.entries()] as [name, mapping]} + + {/each} +
+
\ No newline at end of file diff --git a/src/components/UIShelf.svelte b/src/components/UIShelf.svelte new file mode 100644 index 0000000..d0833a9 --- /dev/null +++ b/src/components/UIShelf.svelte @@ -0,0 +1,197 @@ + + + + + + +

Dimensions

+
+
+ {#each active as d, i} +
+ deactivate(d)}>{d} + 0 ? 'activeArrow' : 'inactiveArrow'} on:click={() => moveLeft(i)}>◁ + moveRight(i)}>▷ +
+ {/each} + {#each inactive as d} + {#if where?.label !== d} +
+ activate(d)}>{d} activate +
+ {/if} + {/each} +
+
+ Shelf + Enable and disable different dimensions of the data. The order of dimension defines the nesting level. +
+
+ +
+
+ {#if where} +
+ +
+
+ {where.label} + removeWhere(0)}>× +
+
+ +
+ {:else} + {#if inactive.length > 0} + {#each inactive as label, i} +
+ { + $spec.where = {qualifier: 'actual', label, is: options(confusions, label)[0]}; + $spec = $spec; + }}>{label} +
+ {/each} + {:else} + All dimensions are already in use. + {/if} + {/if} +
+
+ Where + Condition the confusion matrix on the value of a given label. +
+
diff --git a/src/components/stores.js b/src/components/stores.js new file mode 100644 index 0000000..f8995a0 --- /dev/null +++ b/src/components/stores.js @@ -0,0 +1,10 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import { writable } from 'svelte/store'; + +export const currentCell = writable(null); +export const spec = writable(null); diff --git a/src/confusions.ts b/src/confusions.ts new file mode 100644 index 0000000..877d4de --- /dev/null +++ b/src/confusions.ts @@ -0,0 +1,259 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import type { Condition, Spec } from './specification'; +import { Entry, Matrix } from './matrix'; +import { rollup, sum } from 'd3-array'; +import { cloneDeep } from 'lodash'; +import ndarray from 'ndarray'; +import { Node } from './node'; +import { parseTagString as parse } from './parser'; + +// TODO: Add testcases to these methods! +// TODO: Consider working on strings as long as possible to get rid of `replacer` and `revivier`. +// Ideally, we would want to have this backed by some more elaborate (database-like) system, +// that provides these operations as queries. + +type Path = string; + +/** Captures a single confusion. */ +export interface Confusion { + actual: Array; + observed: Array; + count: number; +} + +function topLevel(path: Path): string { + return path.split(':')[0]; +} + +export function dimensions(confusions: Array): Set { + const labelNames = new Set(); + for (const { actual, observed } of confusions) { + for (const l of actual) { + labelNames.add(topLevel(l)); + } + for (const l of observed) { + labelNames.add(topLevel(l)); + } + } + return labelNames; +} + +export function paths(node: Node): Set { + const result: Set = new Set(); + const curr: Array = []; + node.fullorder( + n => curr.push(n.data), + n => { + if (n.isLeaf()) { + result.add(curr.join(':')); + } + curr.pop(); + }, + ); + return result; +} + +export function options(confusions: Array, label: string): Array { + const options: Set = new Set(); + for (const { actual, observed } of confusions) { + const foundA = actual.find(l => topLevel(l) === label); + if (foundA) { + options.add(foundA); + } + const foundB = observed.find(l => topLevel(l) === label); + if (foundB) { + options.add(foundB); + } + } + return [...options]; +} + +function addMissingLabels(confusions: Array): void { + const labels = new Set(); + for (const { actual, observed } of confusions) { + actual.forEach(p => labels.add(topLevel(p))); + observed.forEach(p => labels.add(topLevel(p))); + } + for (const { actual, observed } of confusions) { + for (const l of labels) { + if (!actual.find(c => topLevel(c) === l)) { + actual.push(`${l}:none`); + } + if (!observed.find(c => topLevel(c) === l)) { + observed.push(`${l}:none`); + } + } + } +} + +function hasPathFromRoot(full: string, sub: string): boolean { + return full.includes(`${sub}:`) || (full === sub); +} + +function filter( + confusions: Array, + filters: Array, +): Array { + return confusions.filter(c => { + return filters.some(s => c.actual.some(p => hasPathFromRoot(p, s))) + && filters.some(s => c.actual.some(p => hasPathFromRoot(p, s))); + }); +} + +function condition(confusions: Array, cond: Condition): Array { + const newConfs = confusions.filter(c => c[cond.qualifier].some(l => l.includes(cond.is))); + for (const c of newConfs) { + c[cond.qualifier] = c[cond.qualifier].filter(l => !l.includes(cond.label)); + } + return newConfs.filter(c => c.actual.length !== 0 && c.observed.length !== 0); +} + +function marginalize(confusions: Array, keep: string): Map> { + const mmap: Map> = rollup( + confusions, + v => sum(v, d => d.count), + (d: Confusion) => d.actual.find(p => topLevel(p) === keep) ?? 'none', + (d: Confusion) => d.observed.find(p => topLevel(p) === keep) ?? 'none', + ); + return mmap; +} + +export function nest(paths: Array, parent: string, sub: string): void { + const parentIndex = paths.findIndex(p => topLevel(p) === parent); + const subIndex = paths.findIndex(p => topLevel(p) === sub); + if (subIndex > -1) { + paths[parentIndex] = paths[parentIndex].concat(`:${paths[subIndex]}`); + paths.splice(subIndex, 1); + } +} + +export function linearize(paths: Array): Array { + const root = new Node('root'); + paths.forEach(p => parse(p).forEach(l => root.merge(l))); + for (const label of root.children) { + label.preorder(n => { + if (n.children.length > 1) { + n.children = [ + new Node(`{${n.leaves() + .map(c => c.data) + .join(',')}}`), + ]; + } + }); + } + return root.children.map(c => stringify(c)); +} + +export function stringify(choices: Node): string { + const result = []; + choices.preorder(n => result.push(n.data)); + return result.join(':'); +} + +// TODO: Could become part of `Node` as a `pruneWith` function. +export function prune(root: Entry): void { + root.postorder(n => { + if (n.children.length === 1 && n.children[0].isLeaf()) { + n.data.name = `${n.data.name}:${n.children[0].data.name}`; + n.children = []; + } + }); +} + +// TODO: Don't export this and write test for the complete pipeline. +export function buildHierarchy(labels: Array): Entry { + const paths = labels.map(str => { + const levels = str.split(':'); + const tl = new Node({ name: levels[0], id: levels[0], start: 0, end: 0 }); + let curr = tl; + for (let i = 1; i < levels.length; ++i) { + const tmp = new Node({ + name: levels[i], + id: curr.data.id.concat(`:${levels[i]}`), + start: 0, + end: 0, + }); + curr.children.push(tmp); + curr = tmp; + } + return tl; + }); + + const root = paths.reduce( + (acc, p) => acc.merge(p, (a, b) => a.data.id === b.data.id), + new Node({ name: 'root', id: 'root', start: 0, end: 0 }), + ); + + return addRangeIndex(root); +} + +export function addRangeIndex(root: Entry): Entry { + let leafCounter = 0; + root.postorder(n => { + if (n.isLeaf()) { + const range = { start: leafCounter, end: leafCounter + 1 }; + n.data = { ...n.data, ...range }; + leafCounter++; + } else { + const start = n.children[0].data.start; + const end = n.children[n.children.length - 1].data.end; + const range = { start, end }; + n.data = { ...n.data, ...range }; + } + }); + return root; +} + +export function buildMatrix(spec: Spec, confusions: Array): Matrix { + let cloned = cloneDeep(confusions); + addMissingLabels(cloned); + + // Condition + if (spec.where && spec.where instanceof Array) { + throw new Error('Multiple conditions are currently not supported.'); + } else if (spec.where && !(spec.where instanceof Array)) { + cloned = condition(cloned, spec.where); + } + + // Filter + if (spec.filter && spec.filter.length > 0) { + cloned = filter(cloned, spec.filter); + } + + // Powerset + for (const { actual, observed } of cloned) { + linearize(actual); + linearize(observed); + } + + // Nest + for (let i = 1; i < spec.classes.length; ++i) { + for (const conf of cloned) { + nest(conf.actual, spec.classes[0], spec.classes[i]); + nest(conf.observed, spec.classes[0], spec.classes[i]); + } + } + + // Marginalize + const map = marginalize(cloned, spec.classes[0]); + + const hierarchy = buildHierarchy([...map.keys()]); + const entries = hierarchy.leaves(); + const shape = [entries.length, entries.length]; + const freqs = ndarray(new Int32Array(shape.reduce((acc, x) => acc * x, 1)), shape); + + entries.forEach((actual, i) => { + entries.forEach((observed, j) => { + freqs.set(i, j, map.get(actual.data.id).get(observed.data.id)); + }); + }); + + prune(hierarchy.children[0]); + + return new Matrix(freqs, hierarchy.children[0]); // TODO: Get rid of unneeded nesting +} diff --git a/src/layout.ts b/src/layout.ts new file mode 100644 index 0000000..b254b15 --- /dev/null +++ b/src/layout.ts @@ -0,0 +1,83 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import type { Node, PredFn } from './node'; + +export interface LayoutedNode { + node: Node; + pos: [number, number]; + span: number; +} + +export function layoutCompact(pred: PredFn, hierarchy: Node): Array> { + const currPos = [0, 0]; + const numChilds = new Map(); + const layout = []; + const isBottom = (node: Node): boolean => node.isLeaf() || !pred(node); + hierarchy.fullorder( + n => { // pre-order + layout.push({ node: n, pos: [currPos[0], currPos[1]] }); + currPos[0] += 1; + + if (isBottom(n)) { + numChilds.set(n, 1); + } + }, + n => { // post-order + if (!isBottom(n)) { + const nc = n.children.reduce((acc, c) => acc + numChilds.get(c), 0); + numChilds.set(n, nc); + } + currPos[0] -= 1; + + if (isBottom(n)) { + currPos[1] += 1; + } + }, + pred, + ); + layout.forEach(l => { + l.span = numChilds.get(l.node); + return l; + }); + return layout; +} + +export function layoutClassic(pred: PredFn, hierarchy: Node): Array> { + const currPos = [0, 0]; + const numDescend = new Map(); + const layout = []; + const isBottom = (node: Node): boolean => node.isLeaf() || !pred(node); + hierarchy.fullorder( + n => { // pre-order + layout.push({ node: n, pos: [currPos[0], currPos[1]] }); + currPos[0] += 1; + currPos[1] += 1; + + if (isBottom(n)) { + numDescend.set(n, 0); + } + }, + n => { // post-order + if (!isBottom(n)) { + const nc = n.children.length + + n.children.reduce((acc, c) => acc + numDescend.get(c), 0); + numDescend.set(n, nc); + } + currPos[0] -= 1; + }, + pred, + ); + layout.forEach(l => { + l.span = numDescend.get(l.node); + return l; + }); + return layout; +} + +export function flip(layout: Array>): Array> { + return layout.map(({ node, pos, span }) => ({ node, pos: [pos[1], pos[0]], span })); +} diff --git a/src/lib.ts b/src/lib.ts new file mode 100644 index 0000000..c658641 --- /dev/null +++ b/src/lib.ts @@ -0,0 +1,74 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import type { Confusion } from './confusions'; +import { defaults } from './specification'; +import Matrix from './components/Matrix.svelte'; +import MatrixWithUI from './components/MatrixWithUI.svelte'; +import type { Spec } from './specification'; +import { spec as specStore } from './components/stores.js'; + +export function embed( + id: string, + spec: Spec, + confusions: Array, +): void { + const ref = document.getElementById(id); + if (!ref) { + console.warn(`Could not find container "${id}"`); + } + + specStore.set({ ...defaults, ...spec }); + + new MatrixWithUI({ + target: ref, + props: { confusions }, + }); +} + +export function embedElement( + element: HTMLElement, + spec: Spec, + confusions: Array, +): void { + specStore.set({ ...defaults, ...spec }); + + new MatrixWithUI({ + target: element, + props: { confusions }, + }); +} + +export function embedWithoutUI( + id: string, + spec: Spec, + confusions: Array, +): void { + const ref = document.getElementById(id); + if (!ref) { + console.warn(`Could not find container "${id}"`); + } + + specStore.set({ ...defaults, ...spec }); + + new Matrix({ + target: ref, + props: { confusions }, + }); +} + +export function embedElementWithoutUI( + element: HTMLElement, + spec: Spec, + confusions: Array, +): void { + specStore.set({ ...defaults, ...spec }); + + new Matrix({ + target: element, + props: { confusions }, + }); +} diff --git a/src/loaders/csv.ts b/src/loaders/csv.ts new file mode 100644 index 0000000..ec43689 --- /dev/null +++ b/src/loaders/csv.ts @@ -0,0 +1,28 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import { Confusion, stringify } from '../confusions'; +import { csvParse } from 'd3-dsv'; +import { parseTagString as parse } from '../parser'; + +interface ConfusionInterface { + 'Ground Truth': string; + 'Prediction': string; + 'Count': string; +} + +export async function csv(filename: string): Promise> { + const response = await fetch(filename); + const text = await response.text(); + const data: Array = csvParse(text); + + return data.map(d => ({ + // TODO: Find a better solution than adding virtual nodes + actual: parse(d['Ground Truth']).map(l => `root:${stringify(l)}`), + observed: parse(d.Prediction).map(l => `root:${stringify(l)}`), + count: Number(d.Count), + })); +} diff --git a/src/loaders/index.ts b/src/loaders/index.ts new file mode 100644 index 0000000..5628603 --- /dev/null +++ b/src/loaders/index.ts @@ -0,0 +1,11 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +export { csv } from './csv'; +export { vega } from './vega'; +export { synth } from './synth'; +export { vegaCompressed } from './vega-compressed'; +export { json } from './json'; diff --git a/src/loaders/json.ts b/src/loaders/json.ts new file mode 100644 index 0000000..52d65a5 --- /dev/null +++ b/src/loaders/json.ts @@ -0,0 +1,16 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import type { Confusion } from '../confusions'; + +// TODO: Write test case +export async function json(filename: string): Promise> { + const response = await fetch(filename); + const json = await response.json(); + const data = json.data.values; + + return data; +} diff --git a/src/loaders/synth.ts b/src/loaders/synth.ts new file mode 100644 index 0000000..380b2f2 --- /dev/null +++ b/src/loaders/synth.ts @@ -0,0 +1,41 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import type { Confusion } from '../confusions'; +import { powerset } from '../setops'; + +function allChoices(): Array> { + const vehicles = [ + 'vehicle:motorized:car', + 'vehicle:motorized:motorcycle', + 'vehicle:airplane', + ]; + const states = [ + 'state:parked', + 'state:moving', + ]; + const animals = [ + 'animal:flying:bird', + 'animal:walking:cat', + ]; + + return powerset([...vehicles, ...states, ...animals]); +} + +export function synth(): Array { + const choices = allChoices(); + const result: Array = []; + for (const actual of choices) { + for (const observed of choices) { + result.push({ + actual: [...actual], + observed: [...observed], + count: Math.floor(Math.random() * 2), + }); + } + } + return result; +} diff --git a/src/loaders/vega-compressed.ts b/src/loaders/vega-compressed.ts new file mode 100644 index 0000000..3205b19 --- /dev/null +++ b/src/loaders/vega-compressed.ts @@ -0,0 +1,27 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import { Confusion, stringify } from '../confusions'; +import { parseTagString as parse } from '../parser'; + +interface ConfusionInterface { + rt: string; // eslint-disable-line camelcase + at: string; // eslint-disable-line camelcase + oc: number; +} + +// TODO: Write test case +export async function vegaCompressed(filename: string): Promise> { + const response = await fetch(filename); + const json = await response.json(); + const data = json.data.values; + + return data.map((d: ConfusionInterface): Confusion => ({ + actual: parse(d.rt).map(l => stringify(l)), + observed: parse(d.at).map(l => stringify(l)), + count: d.oc, + })); +} diff --git a/src/loaders/vega.ts b/src/loaders/vega.ts new file mode 100644 index 0000000..b766bb2 --- /dev/null +++ b/src/loaders/vega.ts @@ -0,0 +1,29 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import { Confusion, stringify } from '../confusions'; +import { parseTagString as parse } from '../parser'; + +interface ConfusionInterface { + reference_text: string; // eslint-disable-line camelcase + annotation_text: string; // eslint-disable-line camelcase + occurrence: number; +} + +// TODO: Write test case +export async function vega(filename: string): Promise> { + const response = await fetch(filename); + const json = await response.json(); + const data = json.data.values; + + return data.map((d: ConfusionInterface): Confusion => { + return { + actual: parse(d.reference_text).map(l => stringify(l)), + observed: parse(d.annotation_text).map(l => stringify(l)), + count: d.occurrence, + }; + }); +} diff --git a/src/matrix.ts b/src/matrix.ts new file mode 100644 index 0000000..090fe36 --- /dev/null +++ b/src/matrix.ts @@ -0,0 +1,101 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import type { NdArray } from 'ndarray'; +import type { Node } from './node'; +import ops from 'ndarray-ops'; + +export interface RangeIndex { + start: number; + end: number; +} + +export interface Data { + id: string; + name: string; +} + +export type Entry = Node; + +// TODO: use `ndarray-sum` to speed up these ops. +// TODO: Consider using prefix sum; +export class Matrix { + constructor( + readonly freqs: NdArray, + readonly axis: Entry, + ) { } + + slice(actual: RangeIndex, observed: RangeIndex): NdArray { + return this.freqs + .lo(actual.start, observed.start) + .hi(actual.end - actual.start, observed.end - observed.start); + } + + classes(): Array { + const result = []; + this.axis.preorder(n => result.push(n)); + return result; + } + + frequency(actual: Entry, observed: Entry): number { + const slice = this.slice(actual.data, observed.data); + return ops.sum(slice); + } + + total(): number { + return ops.sum(this.freqs); + } + + totalRow(row: Entry): number { + const slice = this.slice(row.data, { start: 0, end: this.freqs.shape[1] }); + return ops.sum(slice); + } + + totalColumn(col: Entry): number { + const slice = this.slice({ start: 0, end: this.freqs.shape[0] }, col.data); + return ops.sum(slice); + } + + truePositives(forClass: Entry): number { + return forClass + .leaves() + .reduce((acc, c) => acc + this.frequency(c, c), 0); + } + + falsePositives(forClass: Entry): number { + const tpfp = this.totalColumn(forClass); + return tpfp - this.truePositives(forClass); + } + + trueNegatives(forClass: Entry): number { + const completeDiag = this.axis + .leaves() + .reduce((acc, c) => acc + this.frequency(c, c), 0); + return completeDiag - this.truePositives(forClass); + } + + falseNegatives(forClass: Entry): number { + const tnfn = this.totalRow(forClass); + return tnfn - this.truePositives(forClass); + } +} + +export function precision(matrix: Matrix, forClass: Entry): number { + return matrix.truePositives(forClass) / matrix.totalColumn(forClass); +} + +export function recall(matrix: Matrix, forClass: Entry): number { + return matrix.truePositives(forClass) / matrix.totalRow(forClass); +} + +// TODO: This could probably be simplified +export function accuracy(matrix: Matrix, forClass: Entry): number { + const tp = matrix.truePositives(forClass); + const tn = matrix.trueNegatives(forClass); + const fp = matrix.falsePositives(forClass); + const fn = matrix.falseNegatives(forClass); + return (tp + tn) / (tp + tn + fp + fn); +} diff --git a/src/node.ts b/src/node.ts new file mode 100644 index 0000000..93f643d --- /dev/null +++ b/src/node.ts @@ -0,0 +1,111 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +import { nop } from './util'; + +// I keep on looking this up, so I'll put that here once and for all. +// Height of a node: longest number of edges to a leaf +// Depth of a node: number of edges to root + +export type PredFn = (n: Node) => boolean; +export type VisitFn = (n: Node) => void; +export type IdentityFn = (a: Node, b: Node) => boolean; + +function id(a: Node, b: Node): boolean { + return a.data === b.data; +} + +export class Node { + children?: Array>; + constructor( + public data: T, + ...children: Array> + ) { + this.data = data; + this.children = children ? children : []; + } + + isLeaf(): boolean { + return this.children.length === 0; + } + + fullorder(pre: VisitFn, post: VisitFn, pred?: PredFn): void { + pre(this); + if (!pred || pred(this)) { + for (const c of this.children) { + c.fullorder(pre, post, pred); + } + } + post(this); + } + + preorder(visit: VisitFn, pred?: PredFn): void { + this.fullorder(visit, nop, pred); + } + + postorder(visit: VisitFn, pred?: PredFn): void { + this.fullorder(nop, visit, pred); + } + + leaves(pred?: PredFn): Array> { + const leafs = []; + this.preorder( + n => { + if (n.isLeaf() || (pred && !pred(n))) { + leafs.push(n); + } + }, + pred, + ); + return leafs; + } + + merge(other: Node, identity: IdentityFn = id): this { + const match = this.children.find(own => identity(own, other)); + if (match) { + other.children.forEach(c => match.merge(c, identity)); + } else { + this.children.push(other); + } + return this; + } + + has(subtree: Node, identity: IdentityFn = id): boolean { + const match = this.children.find(own => identity(own, subtree)); + if (match) { + return subtree.children.every(c => match.has(c, identity)); + } else { + return false; + } + } + + // TODO: Consider a `Path` type here (we don't allow branches) + find(node: Node, identity: IdentityFn = id): Node | undefined { + if (node.isLeaf()) { + return this.children.find(own => identity(own, node)); + } else { + const match = this.children.find(own => identity(own, node)); + if (match) { + return match.find(node.children[0], identity); + } + } + } + + // TODO: Consider a `Path` type here (we don't allow branches) + remove(node: Node, identity: IdentityFn = id): Node | undefined { + if (node.isLeaf()) { + const index = this.children.findIndex(own => identity(own, node)); + if (index > -1) { + return this.children.splice(index, 1)[0]; + } + } else { + const match = this.children.find(own => identity(own, node)); + if (match) { + return match.remove(node, identity); + } + } + } +} diff --git a/src/parser.ts b/src/parser.ts new file mode 100644 index 0000000..38e8222 --- /dev/null +++ b/src/parser.ts @@ -0,0 +1,125 @@ +/* + * For licensing see accompanying LICENSE file. + * + * Copyright (C) 2022 Apple Inc. All Rights Reserved. + */ + +/** + * Labels may use the following grammar: + * + * ::=