Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Development #467

Merged
merged 2 commits into from
Dec 16, 2023
Merged

Development #467

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4162517
feat (heart): simulator improvements
santanche Dec 7, 2023
fc22216
feat (annotation): new clustering metric
santanche Dec 16, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion src/adonisjs/public/editor/annotate/js/annotator.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -539,6 +539,9 @@ class Annotator {
o2html += '<tr><td>' + catList[g[0]-1] + '</td><td>' + g[2] + '</td></tr>'
}
const ctcategories = Object.keys(catIndex).length

const clustering = Math.round(AnnotationMetrics.i._clusteringFreeRecall(catOrder)*100) / 100

if (isAnnotations) {
document.querySelector('#memory-scores').innerHTML =
`<ul>
Expand All @@ -556,7 +559,8 @@ class Annotator {
<li><b>accuracy score (inferred):</b> ${(ctideas == 0) ? '' : ctinfright / ctideas}</li>
<li><b>encapsulated score:</b> ${(ctideas == 0) ? '' : (ctrightencap + ctwrongencap) / ctideas}</li>
<li><b>self order score:</b> ${selfOrder.score}</li>
<li><b>normalized self order score:</b> ${(ctideas == 0) ? 0 : selfOrder.score / ctideas}</li>
<li><b>normalized self order score:</b> ${(ctideas == 0) ? 0 : Math.round(selfOrder.score / ctideas * 100) / 100}</li>
<li><b>clustering in free recall:</b> ${clustering}</li>
<li> ${o1html} </li>
<li> ${o2html} </li>
</ul>`
Expand Down
52 changes: 52 additions & 0 deletions src/adonisjs/public/editor/annotate/js/metrics.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,58 @@ class AnnotationMetrics {
score: subs
}
}

/*
* Category clustering calculator for free recall
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665324/
*/
_clusteringFreeRecall (categoriesOrder) {
const n = categoriesOrder.length // number of recalled items

// sort by text position (second element)
const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])

const nc = {} // number of recalled items in each recalled category
let r = 0 // number of category repetition
for (let i = 0; i < sortedL.length; i++) {
const cat = sortedL[i][0]
if (!nc[cat])
nc[cat] = 1
else
nc[cat]++
let nextPos = i + 1
while (nextPos < sortedL.length && sortedL[nextPos][1] === sortedL[i][1])
nextPos++
if (nextPos < sortedL.length) {
let sp = nextPos
while (sp < sortedL.length && sortedL[sp][1] === sortedL[nextPos][1]) {
if (cat == sortedL[sp][0]) {
r++
break
}
sp++
}
}
}

const c = Object.keys(nc).length // number of recalled categories
const max = n - c // maximum possible number of category repetitions

let er = 0 // expected number of category repetitions
for (const cat in nc)
er += nc[cat] * nc[cat]
er = er / n - 1

const rr = r / (n - 1) // ratio of repetition

const mrr = r / max // modified ratio of repetition

const ds = r - er // deviation score

const arc = (r - er) / (max - er) // adjusted ratio of clustering

return arc
}
}

(function () {
Expand Down
1 change: 1 addition & 0 deletions src/adonisjs/public/editor/annotate/metrics/index.html
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
<!DOCTYPE html>
<html>
<body>
<textarea id="console" rows="50" style="width:100%" readonly></textarea>
<script type="text/javascript" src="metrics.js">
</script>
</body>
Expand Down
148 changes: 120 additions & 28 deletions src/adonisjs/public/editor/annotate/metrics/metrics.js
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
function sortSubstitutionCount(numbersList) {
const sortedL = numbersList.slice().sort((a, b) => a - b)
console.log(numbersList)
console.log(sortedL)
present(numbersList)
present(sortedL)
let subs = 0
for (let i = 0; i < numbersList.length; i++) {
if (numbersList[i] !== sortedL[i]) {
Expand All @@ -11,18 +11,18 @@ function sortSubstitutionCount(numbersList) {
return Math.ceil(subs/2)
}

// console.log(sortSubstitutionCount([1, 1, 1, 2, 3, 3, 4]))
// console.log(sortSubstitutionCount([1, 1, 1, 3, 2, 3, 4]))
// console.log(sortSubstitutionCount([1, 1, 1, 3, 3, 2, 4]))
// console.log(sortSubstitutionCount([1, 1, 1, 4, 3, 2, 3]))
// console.log(sortSubstitutionCount([1, 4, 1, 3, 3, 2, 1]))
// console.log(sortSubstitutionCount([4, 3, 3, 2, 1, 1, 1]))
// present(sortSubstitutionCount([1, 1, 1, 2, 3, 3, 4]))
// present(sortSubstitutionCount([1, 1, 1, 3, 2, 3, 4]))
// present(sortSubstitutionCount([1, 1, 1, 3, 3, 2, 4]))
// present(sortSubstitutionCount([1, 1, 1, 4, 3, 2, 3]))
// present(sortSubstitutionCount([1, 4, 1, 3, 3, 2, 1]))
// present(sortSubstitutionCount([4, 3, 3, 2, 1, 1, 1]))

function selfOrderCount(categoriesOrder) {
// sort by text position (second element)
const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])
console.log('Sorted by position')
console.log(sortedL)
present('Sorted by position')
present(sortedL)

// group by category (first element)
// group = [category, position, count]
Expand All @@ -46,13 +46,13 @@ function selfOrderCount(categoriesOrder) {
prev = i
}
}
console.log('Grouped by category')
console.log(JSON.parse(JSON.stringify(grouped)))
present('Grouped by category')
present(JSON.parse(JSON.stringify(grouped)))

// sort groups by position (second element)
const sortedG = grouped.sort((a, b) => a[1] - b[1])
console.log('Group sorted by position')
console.log(JSON.parse(JSON.stringify(sortedG)))
present('Group sorted by position')
present(JSON.parse(JSON.stringify(sortedG)))

// count order change to group together categories
let subs = 0
Expand All @@ -75,21 +75,113 @@ function selfOrderCount(categoriesOrder) {
}
}
}
console.log('Final group after ordering')
console.log(sortedG)
present('Final group after ordering')
present(sortedG)

return subs
}

console.log(selfOrderCount(
[[1, 10], [2, 20], [1, 20], [2, 30]]))
console.log(selfOrderCount(
[[1, 10], [2, 20], [1, 25], [2, 30]]))
console.log(selfOrderCount(
[[1, 10], [2, 20], [1, 20], [3, 20], [1, 30], [2, 30], [3, 30]]))
console.log(selfOrderCount(
[[2, 71], [2, 96], [3, 98], [2, 100], [5, 120], [5, 130], [5, 135], [3, 140], [5, 180]]))
console.log(selfOrderCount(
[[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]]))
console.log(selfOrderCount(
[[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]]))
// present(selfOrderCount(
// [[1, 10], [2, 20], [1, 20], [2, 30]]))
// present(selfOrderCount(
// [[1, 10], [2, 20], [1, 25], [2, 30]]))
// present(selfOrderCount(
// [[1, 10], [2, 20], [1, 20], [3, 20], [1, 30], [2, 30], [3, 30]]))
// present(selfOrderCount(
// [[2, 71], [2, 96], [3, 98], [2, 100], [5, 120], [5, 130], [5, 135], [3, 140], [5, 180]]))
// present(selfOrderCount(
// [[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]]))
// present(selfOrderCount(
// [[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]]))

/*
* Category clustering calculator for free recall
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665324/
* tested here and traferred to /editor/annotate/js/metrics.js
*/
function clusteringFreeRecall(categoriesOrder, console) {

const n = categoriesOrder.length // number of recalled items

// sort by text position (second element)
const sortedL = categoriesOrder.sort((a, b) => a[1] - b[1])

const nc = {} // number of recalled items in each recalled category
let r = 0 // number of category repetition
for (let i = 0; i < sortedL.length; i++) {
const cat = sortedL[i][0]
if (!nc[cat])
nc[cat] = 1
else
nc[cat]++
let nextPos = i + 1
while (nextPos < sortedL.length && sortedL[nextPos][1] === sortedL[i][1])
nextPos++
if (nextPos < sortedL.length) {
let sp = nextPos
while (sp < sortedL.length && sortedL[sp][1] === sortedL[nextPos][1]) {
if (cat == sortedL[sp][0]) {
r++
break
}
sp++
}
}
}

const c = Object.keys(nc).length // number of recalled categories
const max = n - c // maximum possible number of category repetitions

let er = 0 // expected number of category repetitions
for (const cat in nc)
er += nc[cat] * nc[cat]
er = er / n - 1

const rr = r / (n - 1) // ratio of repetition

const mrr = r / max // modified ratio of repetition

const ds = r - er // deviation score

const arc = (r - er) / (max - er) // adjusted ratio of clustering

if (console) {
present('\n\n=== Clustering Free Recall ===')
present(JSON.stringify(categoriesOrder))
present('--- n = ' + n)
present('--- sorted by position')
present(JSON.stringify(sortedL))
present('--- c = ' + c)
present('--- ni')
present(nc)
present('--- r = ' + r)
present('--- max = ' + max)
present('--- E(r) = ' + Math.round(er * 100) / 100)
present('--- RR = ' + Math.round(rr * 100) / 100)
present('--- MRR = ' + Math.round(mrr * 100) / 100)
present('--- DS = ' + Math.round(ds * 100) / 100)
present('--- ARC = ' + Math.round(arc * 100) / 100)
}

return arc
}

function present (output) {
document.querySelector('#console').value += output + '\n'
}

present(clusteringFreeRecall(
[[2, 1], [4, 2], [4, 3], [3, 4], [2, 5], [3, 6], [1, 7], [4, 8], [4, 9]], true
))
present(clusteringFreeRecall(
[[3, 1], [4, 2], [4, 3], [3, 4], [1, 5], [1, 6], [3, 7], [1, 8], [1, 9], [2, 10], [2, 11], [2, 12], [4, 13], [4, 14], [3, 15]], true
))
present(clusteringFreeRecall(
[[2, 1], [2, 2], [3, 3], [1, 4], [1, 5], [1, 6], [1, 7], [2, 8], [3, 9], [3, 10], [2, 11], [1, 12], [4, 13], [4, 14], [4, 15], [4, 16], [2, 17], [2, 18], [3, 19], [1, 20]], true
))
present(clusteringFreeRecall(
[[5, 135], [2, 100], [2, 71], [2, 96], [5, 130], [3, 98], [5, 180], [5, 120], [3, 140]], true))
present(clusteringFreeRecall(
[[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [5, 130], [5, 135], [3, 140], [5, 180]], true))
present(clusteringFreeRecall(
[[2, 71], [2, 96], [3, 98], [2, 98], [5, 98], [7,98], [5, 130], [5, 135], [3, 140], [5, 180]], true))
Loading
Loading