Memory-efficient TCA - #5

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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Memory-efficient TCA - #5

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quannfa:Memory-efficient-TCA
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Memory-efficient TCA#5
quannfa wants to merge 1 commit into
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quannfa:Memory-efficient-TCA

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Memory-efficient TCA - #5

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quannfa:Memory-efficient-TCA
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Memory-efficient TCA#5
quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Memory-efficient TCA - #5

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quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA
Open

Memory-efficient TCA#5
quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
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Memory-efficient TCA - #5

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ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA
Open

Memory-efficient TCA#5
quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA

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@quannfa

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Memory-efficient TCA - #5

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ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA
Open

Memory-efficient TCA#5
quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA

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@quannfa

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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1 participant

@quannfa
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Memory-efficient TCA - #5

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ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA
Open

Memory-efficient TCA#5
quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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1 participant

@quannfa
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
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Memory-efficient TCA - #5

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quannfa:Memory-efficient-TCA
Open

Memory-efficient TCA#5
quannfa wants to merge 1 commit into
ZJUFanLab:masterfrom
quannfa:Memory-efficient-TCA

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This PR improves the memory efficiency of TCA on large datasets and fixes a normalization edge case that could produce NaN values. The changes are focused on the TCA fit implementation.

Background

In the original implementation, the primal mode explicitly constructs n×n M and H matrices. With large sample sizes (for example, around 56k samples), this leads to very high memory usage and can cause OOM failures.
Also, column normalization did not handle zero-norm columns, which could result in NaN values.

What Changed

Reworked the primal-kernel computation path to avoid explicitly building n×n M/H matrices.
Replaced matrix products with low-rank equivalent forms:
K·M·Kᵀ is computed via an outer product based on Xe.
K·H·Kᵀ is computed as XXᵀ minus a rank-1 centering update.
Added safe normalization for both input X and projected Z, normalizing only columns with norm > 0.
Kept the non-primal branches (linear/rbf) as fallback with the original logic.

Expected Impact

Significantly lower memory usage in primal mode, from O(n²) to approximately O(m·n + m²).
Better scalability and reduced OOM risk on large datasets.
Improved numerical stability by preventing NaN generation from zero columns.

Compatibility

No public API changes.
Primal branch internal computation path changed but remains mathematically equivalent.
Linear/RBF branches preserve existing behavior.

Validation Notes

The commit modifies only the TCA implementation file.
Full end-to-end regression/training was not run in this step; it is recommended to run a full pipeline check on representative datasets.

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