@datagrok/eda 1.3.4 → 1.4.0

package/dist/738.js

@@ -1,3 +1,3 @@
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n=[];e.forEach(((e,t,r)=>{n.push({value:e,row:t,col:r})})),n.sort(((e,n)=>e.row===n.row?e.col-n.col:e.row-n.row));const t=[],r=[],i=[];let a=-1;for(let e=0;e<n.length;e++){const{row:s,col:o,value:u}=n[e];s!==a&&(a=s,i.push(e)),t.push(o),r.push(u)}return{indices:t,values:r,indptr:i}}class Z{constructor(e,n,t,r){this.hyperplanes=e,this.offsets=n,this.children=t,this.indices=r}}function X(e,n,t,r){const i=Math.max(10,n),a=E(t).map(((n,t)=>function(e,n=30,t,r){return Q(e,E(e.length),n,t,r)}(e,i,t,r))),s=a.map((e=>function(e,n){const t=ee(e),r=ne(e),i=E(t).map((()=>e.hyperplane?1:0)),a=M(t),s=E(t).map((()=>[-1,-1])),o=E(r).map((()=>E(n).map((()=>-1))));return J(e,i,a,s,o,0,0),new Z(i,a,s,o)}(e,i)));return s}function Q(e,n,t=30,r,i){if(n.length>t){const a=function(e,n,t){const r=v(n.length,t);let i=v(n.length,t);i+=r===i?1:0,i%=n.length;const a=n[r],s=n[i];let o=0,u=0;u=e[a]-e[s],o-=u*(e[a]+e[s])/2;let l=0,c=0;const f=M(n.length);for(let r=0;r<n.length;r++){let 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r=0;for(;n.children[r][0]>0;)r=0===te(n.hyperplanes[r],n.offsets[r],e,t)?n.children[r][0]:n.children[r][1];const i=-1*n.children[r][0];return n.indices[i]}const ie=Object.prototype.toString;function ae(e){return ie.call(e).endsWith("Array]")}function se(e,n,t){let r=0;const i=t(n);for(let n=0;n<e.x.length;n++)r+=Math.abs(e.y[n]-i(e.x[n]));return r}var oe=t(5907);function ue(e,n,t,r,i){let a=t*r*r,s=oe.uq.eye(n.length,n.length,a);const o=i(n);let u=new Float64Array(e.x.length);for(let n=0;n<e.x.length;n++)u[n]=o(e.x[n]);let l=function(e,n,t,r,i){const a=t.length,s=e.x.length;let o=new Array(a);for(let u=0;u<a;u++){o[u]=new Array(s);let a=t.slice();a[u]+=r;let l=i(a);for(let t=0;t<s;t++)o[u][t]=n[t]-l(e.x[t])}return new oe.uq(o)}(e,u,n,r,i),c=function(e,n){const t=e.x.length;let r=new Array(t);for(let i=0;i<t;i++)r[i]=[e.y[i]-n[i]];return new oe.uq(r)}(e,u),f=(0,oe.DI)(s.add(l.mmul(l.transpose())));return(n=(n=new oe.uq([n])).sub(f.mmul(l).mmul(c).mul(r).transpose())).to1DArray()}const le=1e-5,ce=.001;class fe{get neighbors(){return this.nNeighbors}constructor(e={}){this.learningRate=1,this.localConnectivity=1,this.minDist=.1,this.nComponents=2,this.nEpochs=0,this.nNeighbors=15,this.negativeSampleRate=5,this.random=Math.random,this.repulsionStrength=1,this.setOpMixRatio=1,this.spread=1,this.transformQueueSize=4,this.targetMetric="categorical",this.targetWeight=.5,this.targetNNeighbors=15,this.distanceFn=he,this.isInitialized=!1,this.rpForest=[],this.embedding=[],this.optimizationState=new de;const n=n=>{void 0!==e[n]&&(this[n]=e[n])};n("distanceFn"),n("learningRate"),n("localConnectivity"),n("minDist"),n("nComponents"),n("nEpochs"),n("nNeighbors"),n("negativeSampleRate"),n("random"),n("repulsionStrength"),n("setOpMixRatio"),n("spread"),n("transformQueueSize"),this.targetNNeighbors=e.nNeighbors||this.nNeighbors||this.targetNNeighbors}fit(e){return this.initializeFit(e),this.optimizeLayout(),this.embedding}async fitAsync(e,n=()=>!0){return this.initializeFit(e),await this.optimizeLayoutAsync(n),this.embedding}setSupervisedProjection(e,n={}){this.Y=e,this.targetMetric=n.targetMetric||this.targetMetric,this.targetWeight=n.targetWeight||this.targetWeight,this.targetNNeighbors=n.targetNNeighbors||this.targetNNeighbors}setPrecomputedKNN(e,n){this.knnIndices=e,this.knnDistances=n}initializeFit(e){if(e.length<=this.nNeighbors)throw new Error(`Not enough data points (${e.length}) to create nNeighbors: ${this.nNeighbors}.  Add more data points or adjust the configuration.`);if(this.X===e&&this.isInitialized)return this.getNEpochs();if(this.X=e,!this.knnIndices&&!this.knnDistances){const n=this.nearestNeighbors(e);this.knnIndices=n.knnIndices,this.knnDistances=n.knnDistances}this.graph=this.fuzzySimplicialSet(e,this.nNeighbors,this.setOpMixRatio),this.makeSearchFns(),this.searchGraph=this.makeSearchGraph(e),this.processGraphForSupervisedProjection();const{head:n,tail:t,epochsPerSample:r}=this.initializeSimplicialSetEmbedding();return this.optimizationState.head=n,this.optimizationState.tail=t,this.optimizationState.epochsPerSample=r,this.initializeOptimization(),this.prepareForOptimizationLoop(),this.isInitialized=!0,this.getNEpochs()}makeSearchFns(){const{initFromTree:e,initFromRandom:n}=(t=this.distanceFn,{initFromRandom:function(e,n,r,i,a){for(let s=0;s<r.length;s++){const o=D(e,n.length,a);for(let e=0;e<o.length;e++)o[e]<0||U(i,s,t(n[o[e]],r[s]),o[e],1)}},initFromTree:function(e,n,r,i,a){for(let s=0;s<r.length;s++){const o=re(r[s],e,a);for(let e=0;e<o.length;e++){if(o[e]<0)return;U(i,s,t(n[o[e]],r[s]),o[e],1)}}}});var t;this.initFromTree=e,this.initFromRandom=n,this.search=function(e){return function(n,t,r,i){const{indices:a,indptr:s}=H(t);for(let t=0;t<i.length;t++){const o=new Set(r[0][t]);for(;;){const u=_(r,t);if(-1===u)break;const l=a.slice(s[u],s[u+1]);for(const a of l)a===u||-1===a||o.has(a)||(T(r,t,e(n[a],i[t]),a,1),o.add(a))}}return r}}(this.distanceFn)}makeSearchGraph(e){const n=this.knnIndices,t=this.knnDistances,r=[e.length,e.length],i=new L([],[],[],r);for(let e=0;e<n.length;e++){const r=n[e],a=t[e];for(let n=0;n<r.length;n++){const t=r[n],s=a[n];s>0&&i.set(e,t,s)}}return W(i,G(i),((e,n)=>e>n?e:n))}transform(e){const n=this.X;if(void 0===n||0===n.length)throw new Error("No data has been fit.");let t=Math.floor(this.nNeighbors*this.transformQueueSize);t=Math.min(n.length,t);const r=function(e,n,t,r,i,a,s){const o=k(t.length,r);if(i(r,n,t,o,s),e)for(const r of e)a(r,n,t,o,s);return o}(this.rpForest,n,e,t,this.initFromRandom,this.initFromTree,this.random),i=this.search(n,this.searchGraph,r,e);let{indices:a,weights:s}=O(i);a=a.map((e=>e.slice(0,this.nNeighbors))),s=s.map((e=>e.slice(0,this.nNeighbors)));const o=Math.max(0,this.localConnectivity-1),{sigmas:u,rhos:l}=this.smoothKNNDistance(s,this.nNeighbors,o),{rows:c,cols:f,vals:h}=this.computeMembershipStrengths(a,s,u,l),d=[e.length,n.length];let p=new L(c,f,h,d);const g=H(K(p,"l1")),m=e.length,y=function(e,n,t){const r=M(e.length).map((e=>M(t[0].length)));for(let i=0;i<e.length;i++)for(let a=0;a<e[0].length;a++)for(let s=0;s<t[0].length;s++){const o=e[i][a];r[i][s]+=n[i][a]*t[o][s]}return r}(C(g.indices,m,this.nNeighbors),C(g.values,m,this.nNeighbors),this.embedding),w=this.nEpochs?this.nEpochs/3:p.nRows<=1e4?100:30,b=p.getValues().reduce(((e,n)=>n>e?n:e),0);p=p.map((e=>e<b/w?0:e)),p=V(p);const x=this.makeEpochsPerSample(p.getValues(),w),v=p.getRows(),A=p.getCols();return this.assignOptimizationStateParameters({headEmbedding:y,tailEmbedding:this.embedding,head:v,tail:A,currentEpoch:0,nEpochs:w,nVertices:p.getDims()[1],epochsPerSample:x}),this.prepareForOptimizationLoop(),this.optimizeLayout()}processGraphForSupervisedProjection(){const{Y:e,X:n}=this;if(e){if(e.length!==n.length)throw new Error("Length of X and y must be equal");if("categorical"===this.targetMetric){const n=this.targetWeight<1?1/(1-this.targetWeight)*2.5:1e12;this.graph=this.categoricalSimplicialSetIntersection(this.graph,e,n)}}}step(){const{currentEpoch:e}=this.optimizationState;return e<this.getNEpochs()&&this.optimizeLayoutStep(e),this.optimizationState.currentEpoch}getEmbedding(){return this.embedding}nearestNeighbors(e){const{distanceFn:n,nNeighbors:t}=this,r=function(e,n){return function(t,r,i,a=10,s=50,o=.001,u=.5,l=!0){const c=t.length,f=k(t.length,i);for(let r=0;r<t.length;r++){const a=R(i,t.length,n);for(let n=0;n<a.length;n++){const i=e(t[r],t[a[n]]);U(f,r,i,a[n],1),U(f,a[n],i,r,1)}}if(l)for(let n=0;n<r.length;n++)for(let i=0;i<r[n].length&&!(r[n][i]<0);i++)for(let a=i+1;a<r[n].length&&!(r[n][a]<0);a++){const s=e(t[r[n][i]],t[r[n][a]]);U(f,r[n][i],s,r[n][a],1),U(f,r[n][a],s,r[n][i],1)}for(let r=0;r<a;r++){const r=B(f,c,i,s,n);let a=0;for(let i=0;i<c;i++)for(let o=0;o<s;o++){const l=Math.floor(r[0][i][o]);if(!(l<0||A(n)<u))for(let n=0;n<s;n++){const s=Math.floor(r[0][i][n]),u=r[2][i][o],c=r[2][i][n];if(s<0||!u&&!c)continue;const h=e(t[l],t[s]);a+=U(f,l,h,s,1),a+=U(f,s,h,l,1)}}if(a<=o*i*t.length)break}return O(f)}}(n,this.random),i=5+Math.floor(.5==(a=e.length**.5/20)?0:Math.round(a));var a;const s=Math.max(5,Math.floor(Math.round((e=>Math.log(e)/Math.log(2))(e.length))));this.rpForest=X(e,t,i,this.random);const o=function(e){if(e.length>0){const n=[];for(const t of e)n.push(...t.indices);return n}return[[-1]]}(this.rpForest),{indices:u,weights:l}=r(e,o,t,s);return{knnIndices:u,knnDistances:l}}fuzzySimplicialSet(e,n,t=1){const{knnIndices:r=[],knnDistances:i=[],localConnectivity:a}=this,{sigmas:s,rhos:o}=this.smoothKNNDistance(i,n,a),{rows:u,cols:l,vals:c}=this.computeMembershipStrengths(r,i,s,o),f=[e.length,e.length],h=new L(u,l,c,f),d=G(h),p=$(h,d),g=j(F(h,d),p);return F(Y(g,t),Y(p,1-t))}categoricalSimplicialSetIntersection(e,n,t,r=1){let i=function(e,n,t=1,r=5){return e.map(((e,i,a)=>-1===n[i]||-1===n[a]?e*Math.exp(-t):n[i]!==n[a]?e*Math.exp(-r):e))}(e,n,r,t);return i=V(i),function(e){const n=G(e=K(e,"max"));return V(e=F(e,j(n,$(n,e))))}(i)}smoothKNNDistance(e,n,t=1,r=64,i=1){const a=Math.log(n)/Math.log(2)*i,s=M(e.length),o=M(e.length);for(let n=0;n<e.length;n++){let i=0,u=1/0,l=1;const c=e[n],f=c.filter((e=>e>0));if(f.length>=t){const e=Math.floor(t),r=t-e;e>0?(s[n]=f[e-1],r>le&&(s[n]+=r*(f[e]-f[e-1]))):s[n]=r*f[0]}else f.length>0&&(s[n]=P(f));for(let t=0;t<r;t++){let t=0;for(let r=1;r<e[n].length;r++){const i=e[n][r]-s[n];t+=i>0?Math.exp(-i/l):1}if(Math.abs(t-a)<le)break;t>a?(u=l,l=(i+u)/2):(i=l,u===1/0?l*=2:l=(i+u)/2)}if(o[n]=l,s[n]>0){const e=N(c);o[n]<ce*e&&(o[n]=ce*e)}else{const t=N(e.map(N));o[n]<ce*t&&(o[n]=ce*t)}}return{sigmas:o,rhos:s}}computeMembershipStrengths(e,n,t,r){const i=e.length,a=e[0].length,s=M(i*a),o=M(i*a),u=M(i*a);for(let l=0;l<i;l++)for(let i=0;i<a;i++){let c=0;-1!==e[l][i]&&(c=e[l][i]===l?0:n[l][i]-r[l]<=0?1:Math.exp(-(n[l][i]-r[l])/t[l]),s[l*a+i]=l,o[l*a+i]=e[l][i],u[l*a+i]=c)}return{rows:s,cols:o,vals:u}}initializeSimplicialSetEmbedding(){const e=this.getNEpochs(),{nComponents:n}=this,t=this.graph.getValues();let r=0;for(let e=0;e<t.length;e++){const n=t[e];r<t[e]&&(r=n)}const i=this.graph.map((n=>n<r/e?0:n));this.embedding=M(i.nRows).map((()=>M(n).map((()=>20*A(this.random)-10))));const a=[],s=[],o=[],u=i.getAll();for(let e=0;e<u.length;e++){const n=u[e];n.value&&(a.push(n.value),o.push(n.row),s.push(n.col))}return{head:s,tail:o,epochsPerSample:this.makeEpochsPerSample(a,e)}}makeEpochsPerSample(e,n){const t=I(e.length,-1),r=P(e),i=e.map((e=>e/r*n));return i.forEach(((e,r)=>{e>0&&(t[r]=n/i[r])})),t}assignOptimizationStateParameters(e){Object.assign(this.optimizationState,e)}prepareForOptimizationLoop(){const{repulsionStrength:e,learningRate:n,negativeSampleRate:t}=this,{epochsPerSample:r,headEmbedding:i,tailEmbedding:a}=this.optimizationState,s=i[0].length,o=i.length===a.length,u=r.map((e=>e/t)),l=[...u],c=[...r];this.assignOptimizationStateParameters({epochOfNextSample:c,epochOfNextNegativeSample:l,epochsPerNegativeSample:u,moveOther:o,initialAlpha:n,alpha:n,gamma:e,dim:s})}initializeOptimization(){const e=this.embedding,n=this.embedding,{head:t,tail:r,epochsPerSample:i}=this.optimizationState,a=this.getNEpochs(),s=this.graph.nCols,{a:o,b:u}=function(e,n){const t=function(e,n){return S(300).map(((e,t)=>0+t*((n-0)/299)))}(0,3*e).map((e=>e<n?1:e)),r=M(t.length).map(((r,i)=>t[i]>=n?Math.exp(-(t[i]-n)/e):r)),i={x:t,y:r},{parameterValues:a}=function(e,n,t={}){let{maxIterations:r=100,gradientDifference:i=.1,damping:a=0,errorTolerance:s=.01,minValues:o,maxValues:u,initialValues:l}=t;if(a<=0)throw new Error("The damping option must be a positive number");if(!e.x||!e.y)throw new Error("The data parameter must have x and y elements");if(!ae(e.x)||e.x.length<2||!ae(e.y)||e.y.length<2)throw new Error("The data parameter elements must be an array with more than 2 points");if(e.x.length!==e.y.length)throw new Error("The data parameter elements must have the same size");let c=l||new Array(n.length).fill(1),f=c.length;if(u=u||new Array(f).fill(Number.MAX_SAFE_INTEGER),o=o||new Array(f).fill(Number.MIN_SAFE_INTEGER),u.length!==o.length)throw new Error("minValues and maxValues must be the same size");if(!ae(c))throw new Error("initialValues must be an array");let h,d=se(e,c,n),p=d<=s;for(h=0;h<r&&!p;h++){c=ue(e,c,a,i,n);for(let e=0;e<f;e++)c[e]=Math.min(Math.max(o[e],c[e]),u[e]);if(d=se(e,c,n),isNaN(d))break;p=d<=s}return{parameterValues:c,parameterError:d,iterations:h}}(i,(([e,n])=>t=>1/(1+e*t**(2*n))),{damping:1.5,initialValues:[.5,.5],gradientDifference:.1,maxIterations:100,errorTolerance:.01}),[s,o]=a;return{a:s,b:o}}(this.spread,this.minDist);this.assignOptimizationStateParameters({headEmbedding:e,tailEmbedding:n,head:t,tail:r,epochsPerSample:i,a:o,b:u,nEpochs:a,nVertices:s})}optimizeLayoutStep(e){const{optimizationState:n}=this,{head:t,tail:r,headEmbedding:i,tailEmbedding:a,epochsPerSample:s,epochOfNextSample:o,epochOfNextNegativeSample:u,epochsPerNegativeSample:l,moveOther:c,initialAlpha:f,alpha:h,gamma:d,a:p,b:g,dim:m,nEpochs:y,nVertices:w}=n;for(let n=0;n<s.length;n++){if(o[n]>e)continue;const f=t[n],y=r[n],b=i[f],x=a[y],A=ge(b,x);let S=0;A>0&&(S=-2*p*g*Math.pow(A,g-1),S/=p*Math.pow(A,g)+1);for(let e=0;e<m;e++){const n=pe(S*(b[e]-x[e]),4);b[e]+=n*h,c&&(x[e]+=-n*h)}o[n]+=s[n];const E=Math.floor((e-u[n])/l[n]);for(let e=0;e<E;e++){const e=v(w,this.random),n=a[e],t=ge(b,n);let r=0;if(t>0)r=2*d*g,r/=(.001+t)*(p*Math.pow(t,g)+1);else if(f===e)continue;for(let e=0;e<m;e++){let t=4;r>0&&(t=pe(r*(b[e]-n[e]),4)),b[e]+=t*h}}u[n]+=E*l[n]}return n.alpha=f*(1-e/y),n.currentEpoch+=1,i}optimizeLayoutAsync(e=()=>!0){return new Promise(((n,t)=>{const r=async()=>{try{const{nEpochs:t,currentEpoch:i}=this.optimizationState;this.embedding=this.optimizeLayoutStep(i);const a=this.optimizationState.currentEpoch,s=!1===e(a),o=a===t;if(s||o)return n(o);setTimeout((()=>r()),0)}catch(e){t(e)}};setTimeout((()=>r()),0)}))}optimizeLayout(e=()=>!0){let n=!1,t=[];for(;!n;){const{nEpochs:r,currentEpoch:i}=this.optimizationState;t=this.optimizeLayoutStep(i);const a=this.optimizationState.currentEpoch,s=!1===e(a);n=a===r||s}return t}getNEpochs(){const e=this.graph;if(this.nEpochs>0)return this.nEpochs;if(!e)return 200;const n=e.nRows;return n<=2500?500:n<=5e3?400:n<=7500?300:200}}function he(e,n){return Math.abs(e-n)}class de{constructor(){this.currentEpoch=0,this.headEmbedding=[],this.tailEmbedding=[],this.head=[],this.tail=[],this.epochsPerSample=[],this.epochOfNextSample=[],this.epochOfNextNegativeSample=[],this.epochsPerNegativeSample=[],this.moveOther=!0,this.initialAlpha=1,this.alpha=1,this.gamma=1,this.a=1.5769434603113077,this.b=.8950608779109733,this.dim=2,this.nEpochs=500,this.nVertices=0}}function pe(e,n){return e>n?n:e<-n?-n:e}function ge(e,n){let t=0;for(let r=0;r<e.length;r++)t+=Math.pow(e[r]-n[r],2);return t}var me=t(5731),ye=t(8774),we=t(7391),be=t.n(we);class xe{assert(e,n){if(!e)throw n||"Assertion failed"}getopt(e,n,t){return e.hasOwnProperty(n)?e[n]:t}gaussRandom(){if(this.returnV)return this.returnV=!1,this.vValue;const e=2*this.random()-1,n=2*this.random()-1,t=e*e+n*n;if(0===t||t>1)return this.gaussRandom();const r=Math.sqrt(-2*Math.log(t)/t);return this.vValue=n*r,this.returnV=!0,e*r}randn(e,n){return e+this.gaussRandom()*n}zeros(e){if(void 0===e||isNaN(e))return new Float32Array;if("undefined"==typeof ArrayBuffer){const n=new Float32Array(e);for(let t=0;t<e;t++)n[t]=0;return n}return new Float32Array(e)}randn2d(e,n,t){const r=void 0!==t,i=new Array(e).fill(null).map((()=>new Float32Array(n)));if(r)for(let r=0;r<e;r++)i[r]=new Float32Array(n).fill(t);else for(let t=0;t<e;t++)for(let e=0;e<n;e++)i[t][e]=this.randn(0,1e-4);return i}l2(e,n){const t=e.length;let r=0;for(let i=0;i<t;i++){const t=e[i],a=n[i];r+=(t-a)*(t-a)}return r}xtod(e){const n=e.length,t=this.zeros(n*n);for(let r=0;r<n;r++)for(let i=r+1;i<n;i++){const a=this.l2(e[r],e[i]);t[r*n+i]=a,t[i*n+r]=a}return t}getIterSize(e){return e<=2e3?100:e<=3e3?90:e<=5e3?80:70}d2p(e,n,t,r){const i=(s=r,(e,n)=>s*e+n-Math.floor((e+2)*(e+1)/2)),a=new Float32Array(r*r);var s;for(let n=0;n<r;n++)for(let t=n+1;t<r;t++)a[n*r+t]=a[t*r+n]=e[i(n,t)];const o=r,u=Math.log(n),l=this.zeros(o*o),c=this.zeros(o);for(let e=0;e<o;e++){let n=-1/0,i=1/0,s=1,f=!1;const h=Math.floor(this.getIterSize(r)/5);let d=0;for(;!f;){let r=0;for(let n=0;n<o;n++){const t=e===n?0:Math.exp(-a[e*o+n]*s);c[n]=t,r+=t}let l=0;for(let e=0;e<o;e++){let n;n=0===r?0:c[e]/r,c[e]=n,n>1e-7&&(l-=n*Math.log(n))}l>u?(n=s,i===1/0?s*=2:s=(s+i)/2):(i=s,n===-1/0?s/=2:s=(s+n)/2),d++,Math.abs(l-u)<t&&(f=!0),d>=h&&(f=!0)}for(let n=0;n<o;n++)l[e*o+n]=c[n]}const f=this.zeros(o*o),h=2*o;for(let e=0;e<o;e++)for(let n=0;n<o;n++)f[e*o+n]=Math.max((l[e*o+n]+l[n*o+e])/h,1e-100);return f}sign(e){return e>0?1:e<0?-1:0}constructor(e){this.iter=0,this.random=Math.random,this.returnV=!1,this.vValue=0,e=e||{},this.perplexity=this.getopt(e,"perplexity",30),this.dim=this.getopt(e,"dim",2),this.epsilon=this.getopt(e,"epsilon",10),this.random=this.getopt(e,"random",Math.random)}initDataRaw(e){const n=e.length,t=e[0].length;this.assert(n>0," X is empty? You must have some data!"),this.assert(t>0," X[0] is empty? Where is the data?");const r=this.xtod(e);this.P=this.d2p(r,this.perplexity,1e-4,t),this.N=n,this.initSolution()}initDataDist(e,n){const t=e.length;this.assert(t>0," X is empty? You must have some data!"),console.time("distances to matrix"),this.P=this.d2p(e,this.perplexity,1e-4,n),console.timeEnd("distances to matrix"),this.N=n,this.initSolution()}initSolution(){this.Y=this.randn2d(this.N,this.dim),this.gains=this.randn2d(this.N,this.dim,1),this.ystep=this.randn2d(this.N,this.dim,0),this.iter=0}getSolution(){return this.Y}step(){this.iter+=1;const e=this.N,n=this.costGrad(this.Y),t=n.cost,r=n.grad,i=this.zeros(this.dim);for(let n=0;n<e;n++)for(let e=0;e<this.dim;e++){const t=r[n][e],a=this.ystep[n][e],s=this.gains[n][e];let o=this.sign(t)===this.sign(a)?.8*s:s+.2;o<.01&&(o=.01),this.gains[n][e]=o;const u=(this.iter<250?.5:.8)*a-this.epsilon*o*r[n][e];this.ystep[n][e]=u,this.Y[n][e]+=u,i[e]+=this.Y[n][e]}for(let n=0;n<e;n++)for(let t=0;t<this.dim;t++)this.Y[n][t]-=i[t]/e;return t}debugGrad(){const e=this.N,n=this.costGrad(this.Y).grad,t=1e-5;for(let r=0;r<e;r++)for(let e=0;e<this.dim;e++){const i=this.Y[r][e];this.Y[r][e]=i+t;const a=this.costGrad(this.Y);this.Y[r][e]=i-t;const s=this.costGrad(this.Y),o=n[r][e],u=(a.cost-s.cost)/(2*t);console.log(r+","+e+": gradcheck analytic: "+o+" vs. numerical: "+u),this.Y[r][e]=i}}costGrad(e){const n=this.N,t=this.dim,r=this.P,i=this.iter<100?4:1;this.quArr??(this.quArr=this.zeros(n*n));let a=0;for(let r=0;r<n;r++)for(let i=r+1;i<n;i++){const s=1/(1+new Array(t).reduce(((n,t,a)=>n+Math.pow(e[r][a]-e[i][a],2)),0));this.quArr[r*n+i]=s,this.quArr[i*n+r]=s,a+=2*s}let s=0;const o=new Array(n).fill(null).map((()=>new Float32Array(t).fill(0)));for(let u=0;u<n;u++)for(let l=u+1;l<n;l++){const c=Math.max(this.quArr[u*n+l]/a,1e-100);s+=-r[u*n+l]*Math.log(c)*2;const f=4*(i*r[u*n+l]-c)*this.quArr[u*n+l];for(let n=0;n<t;n++)o[u][n]+=f*(e[u][n]-e[l][n]),o[l][n]+=f*(e[l][n]-e[u][n])}return{cost:s,grad:o}}}t(5540);var ve=function(e,n,t,r){return new(t||(t=Promise))((function(i,a){function s(e){try{u(r.next(e))}catch(e){a(e)}}function o(e){try{u(r.throw(e))}catch(e){a(e)}}function u(e){var n;e.done?i(e.value):(n=e.value,n instanceof t?n:new t((function(e){e(n)}))).then(s,o)}u((r=r.apply(e,n||[])).next())}))};let Ae=null,Se=null;function Ee(){return ve(this,void 0,void 0,(function*(){if(!navigator.gpu)return console.error("WebGPU is not supported in this browser"),null;if(!Ae&&(Ae=yield navigator.gpu.requestAdapter({powerPreference:"high-performance"}),null==Ae))return null;let e=!1;if(Se&&(Se.lost.then((()=>{e=!0})),yield new Promise((e=>setTimeout(e,10)))),!Se||e){const e=1e9,n=Ae.limits,t=n.maxBufferSize,r=n.maxStorageBufferBindingSize;try{return Se=yield Ae.requestDevice({requiredLimits:{maxBufferSize:Math.min(t,e),maxStorageBufferBindingSize:Math.min(r,e)}}),Se}catch(e){return console.error("Failed to create device with required limits",e),Se=yield Ae.requestDevice(),Se}}return Se}))}var Ie,Me;(Me=Ie||(Ie={})).EUCLIDEAN="EUCLIDEAN",Me.MANHATTAN="MANHATTAN";const Ne={[Ie.EUCLIDEAN]:function(e){return`\n        var sum = 0.0;\n        for (var i = 0u; i < ${e}; i = i + 1u) {\n            sum = sum + distances[i] * distances[i] * computeInfo.weights[i] * computeInfo.weights[i];\n        }\n        return sqrt(sum);\n    `},[Ie.MANHATTAN]:function(e){return`\n        var sum = 0.0;\n        for (var i = 0u; i < ${e}; i = i + 1u) {\n            sum = sum + abs(distances[i]) * computeInfo.weights[i];\n        }\n        return sum;\n    `}};var Pe,De;(De=Pe||(Pe={})).HAMMING="Hamming",De.EUCLIDEAN="Euclidean",De.MANHATTAN="Manhattan",De.TANIMOTO="Tanimoto",De.LEVENSTEIN="Levenshtein",De.NEEDLEMAN_WUNSCH="Needlemann-Wunsch",De.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",De.SOKAL="Sokal",De.COSINE="Cosine",De.ASYMMETRIC="Asymmetric",De.Difference="Difference",De.OneHot="One-Hot";const Ce={[Pe.HAMMING]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n  let sizeDiff: u32 = maxLength - minLength;\n  \n  let maxIntDistance = ceil(maxDistance * f32(maxLength)) - f32(sizeDiff);\n\n  var diff: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n      diff = diff + f32(a[i] != b[i]);\n      if (diff > maxIntDistance) {\n            return 1.0;\n        }\n  }\n  diff += f32(sizeDiff);\n  return diff / ${e};\n  `},[Pe.EUCLIDEAN]:function(e,n){return`\n  var dist: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n    dist = dist + f32(a[i] - b[i]) * f32(a[i] - b[i]);\n  }\n  return sqrt(dist);\n  `},[Pe.MANHATTAN]:function(e,n){return`\n  var dist: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n    dist = dist + abs(f32(a[i] - b[i]));\n  }\n  return dist;\n  `},[Pe.TANIMOTO]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n\n  if (onBitsa == 0u && onBitsb == 0u) {\n      return 0.0;\n  }\n\n  let totalOnBits = onBitsa + onBitsb;\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n\n  return 1.0 - f32(commonBits) / f32(totalOnBits - commonBits);\n  `},[Pe.LEVENSTEIN]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n\n  let maxIntDistance = ceil(maxDistance * f32(maxLength));\n\n  // we will store two arrays as matrix and swap the working indices per pass.\n  // this way we can reduce memory usage per computation to just O(aLength)\n  // the grid will have aLength + 1 columns and bLength + 1 rows\n  // this will be guaranteed by iteration, but the array sizes must be known at compile time, so we will use a fixed size of maxArraySize\n  var dynamicPassMat: array<array<f32, ${e+1}u>, 2>; // initialize to 0\n  \n  var prevIndex: u32 = 0;\n  var curIndex: u32 = 1; // we will swap these indices per pass\n\n  // initialize the first row\n  for (var i = 0u; i <= aLength; i = i + 1u) {\n      dynamicPassMat[prevIndex][i] = f32(i);\n  }\n\n  // iterate over the rows\n  for (var i = 1u; i <= bLength; i = i + 1u) {\n      dynamicPassMat[curIndex][0] = f32(i);\n      var minEntry: f32 = f32(maxLength);\n      let prevRow = &dynamicPassMat[prevIndex];\n      let curRow = &dynamicPassMat[curIndex];\n      let bMon = u32(b[i - 1]);\n      for (var j = 1u; j <= aLength; j = j + 1u) {\n          var cost: f32 = f32(a[j - 1] != bMon);\n          var res: f32 = min(\n              min(\n                (*prevRow)[j] + 1.0, // deletion\n                (*curRow)[j - 1] + 1.0, // insertion\n              ),\n              (*prevRow)[j - 1] + cost // substitution\n              );\n              (*curRow)[j] = res;\n          if (res < minEntry) {\n              minEntry = res;\n          }\n      }\n      // swap the indices\n      let temp: u32 = prevIndex;\n      prevIndex = curIndex;\n      curIndex = temp;\n      if (minEntry > maxIntDistance) {\n          return 1.0;\n      }\n  }\n\n  return dynamicPassMat[prevIndex][aLength] / f32(maxLength);\n  `},[Pe.NEEDLEMAN_WUNSCH]:function(e,n){return`\n      let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n      let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n      let maxLength: u32 = max(aLength, bLength);\n      let minLength: u32 = min(aLength, bLength);\n  \n      let maxIntDistance = ceil(maxDistance * f32(maxLength));\n      // we will store two arrays as matrix and swap the working indices per pass.\n      // this way we can reduce memory usage per computation to just O(aLength)\n      // the grid will have aLength + 1 columns and bLength + 1 rows\n      // this will be guaranteed by iteration, but the array sizes must be known at compile time, so we will use a fixed size of maxArraySize\n      var dynamicPassMat: array<array<f32, ${e+1}u>, 2>; // initialize to 0\n      \n      // we need to keep track of which operation led to the current cell\n      // i.e. whether we came from the left, top or diagonal to assign gap open/gap extend penalty\n      var verticalGaps: array<u32, ${e+1}u>;\n      var horizontalGaps: array<u32, ${e+1}u>;\n\n      let gapOpenPenalty: f32 = suppInfo.gapOpenPenalty${n};\n      let gapExtensionPenalty: f32 = suppInfo.gapExtensionPenalty${n};\n      var prevIndex: u32 = 0;\n      var curIndex: u32 = 1; // we will swap these indices per pass\n      // initialize the first row\n      for (var i = 0u; i <= aLength; i = i + 1u) {\n          dynamicPassMat[prevIndex][i] = gapExtensionPenalty + f32(i - 1) * gapExtensionPenalty; // accounting for the fact that left and right gaps are less costly\n          dynamicPassMat[curIndex][i] = 0.0;\n      }\n      dynamicPassMat[0][0] = 0.0;\n\n      let simMatrix = &suppInfo.similarityMatrix${n}; // using pointers make things faster\n      // iterate over the rows\n      for (var i = 1u; i <= bLength; i = i + 1u) {\n          let prevRow = &dynamicPassMat[prevIndex];\n          let curRow = &dynamicPassMat[curIndex];\n          (*curRow)[0] = gapExtensionPenalty + f32(i - 1) * gapExtensionPenalty;\n          var minEntry: f32 = f32(maxLength);\n          let monB = u32(b[i - 1]);\n          for (var j = 1u; j <= aLength; j = j + 1u) {\n              let monA = u32(a[j - 1]);\n              \n              let cost: f32 = (*prevRow)[j - 1] + 1f - (*simMatrix)[monA][monB];\n              var top = (*prevRow)[j]; // deletion\n              if (verticalGaps[j] > 0 || i == 1 || i == bLength) {\n                  top = top + gapExtensionPenalty;\n              } else {\n                  top = top + gapOpenPenalty;\n              }\n              var left = (*curRow)[j - 1]; // insertion\n              if (horizontalGaps[j - 1] > 0 || j == 1 || j == aLength) {\n                  left = left + gapExtensionPenalty;\n              } else {\n                  left = left + gapOpenPenalty;\n              }\n              var res: f32 = min(\n                  min(\n                      top, // deletion\n                      left, // insertion\n                  ),\n                  cost // substitution\n                  );\n                  (*curRow)[j] = res;\n              if (res < minEntry) {\n                  minEntry = res;\n              }\n              // update the horizontal and vertical gaps\n              if (res == cost) {\n                  verticalGaps[j] = 0;\n                  horizontalGaps[j] = 0;\n              } else if (res == left) {\n                  verticalGaps[j] = 0;\n                  horizontalGaps[j] = 1;\n              } else {\n                  verticalGaps[j] = 1;\n                  horizontalGaps[j] = 0;\n              }\n          }\n          // swap the indices\n          let temp: u32 = prevIndex;\n          prevIndex = curIndex;\n          curIndex = temp;\n          if (minEntry > maxIntDistance) {\n              return 1.0;\n          }\n      }\n      return dynamicPassMat[prevIndex][aLength] / f32(minLength);\n\n  `},[Pe.MONOMER_CHEMICAL_DISTANCE]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n  let sizeDiff: u32 = maxLength - minLength;\n  \n  let maxIntDistance = ceil(maxDistance * f32(maxLength)) - f32(sizeDiff);\n\n  let simMatrix = &(suppInfo.similarityMatrix${n}); // using pointers make things faster\n  var diff: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n      diff = diff + 1.0 - (*simMatrix)[u32(a[i])][u32(b[i])];\n      if (diff > maxIntDistance) {\n            return 1.0;\n        }\n  }\n  diff += f32(sizeDiff);\n  return diff / ${e};\n  `},[Pe.SOKAL]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let total = onBitsa + onBitsb;\n  if (total == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / f32(total * 2 - commonBits * 3);\n  `},[Pe.COSINE]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let total = onBitsa * onBitsb; // p.s. here total is taken by multiplying\n  if (total == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / sqrt(f32(total));\n  `},[Pe.ASYMMETRIC]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let min = min(onBitsa, onBitsb);\n  if (min == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / f32(min);\n  `},[Pe.Difference]:function(e,n){return`\n    let range = suppInfo.range${n};\n    return f32(abs(f32(a[0]) - f32(b[0])) / range);\n  `},[Pe.OneHot]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  if (aLength != bLength) {\n    return 1.0;\n  }\n  for (var i = 0u; i < aLength; i = i + 1u) {\n    if(a[i] != b[i]) {\n      return 1.0;\n    }\n  }\n  return 0.0;\n  `}},ke={[Pe.HAMMING]:e=>Math.ceil(e/30),[Pe.EUCLIDEAN]:e=>Math.ceil(e/30),[Pe.MANHATTAN]:e=>Math.ceil(e/30),[Pe.TANIMOTO]:e=>Math.ceil(e/30),[Pe.SOKAL]:e=>Math.ceil(e/30),[Pe.COSINE]:e=>Math.ceil(e/30),[Pe.ASYMMETRIC]:e=>Math.ceil(e/30),[Pe.LEVENSTEIN]:e=>Math.ceil(e*e/60),[Pe.NEEDLEMAN_WUNSCH]:e=>Math.ceil(e*e/60),[Pe.MONOMER_CHEMICAL_DISTANCE]:e=>Math.ceil(e/25),[Pe.Difference]:e=>1,[Pe.OneHot]:e=>Math.ceil(e/40)},Re={STRING:new Set([Pe.HAMMING,Pe.LEVENSTEIN,Pe.NEEDLEMAN_WUNSCH,Pe.MONOMER_CHEMICAL_DISTANCE,Pe.OneHot]),UINT32ARRAY:new Set([Pe.HAMMING,Pe.EUCLIDEAN,Pe.MANHATTAN,Pe.MONOMER_CHEMICAL_DISTANCE,Pe.LEVENSTEIN,Pe.NEEDLEMAN_WUNSCH,Pe.TANIMOTO,Pe.COSINE,Pe.SOKAL,Pe.ASYMMETRIC,Pe.OneHot,Pe.Difference]),INT32ARRAY:new Set([Pe.EUCLIDEAN,Pe.MANHATTAN,Pe.OneHot,Pe.Difference]),FLOAT32ARRAY:new Set([Pe.EUCLIDEAN,Pe.MANHATTAN,Pe.Difference]),NUMBER:new Set([Pe.EUCLIDEAN,Pe.MANHATTAN,Pe.Difference]),BITARRAY:new Set([Pe.TANIMOTO,Pe.COSINE,Pe.SOKAL,Pe.ASYMMETRIC])};var Ue,Te,Be;function Oe(e,n=15,t,r,i,a){return s=this,o=void 0,l=function*(){if(a.length!==e.length||a.length!==t.length||a.length!==i.length)throw new Error("Options, weigths and distance functions must be provided for each column");if(e.some((n=>n.length!==e[0].length)))throw new Error("All entry lists must be the same length");const s=Object.values(Pe);if(t.some((e=>!s.includes(e))))throw new Error("Invalid distance metrics provided: "+t.join(", "));if(!Object.values(Ie).includes(r))throw new Error("Invalid aggregation function provided: "+r);const o=e.length;if(0===o)throw new Error("No columns provided. Please provide at least one column of data.");const u=yield Ee();if(!u)return null;let l=!1;u.lost.then((()=>{l=!0}));const c=e[0].length,f=e.map(((e,n)=>function(e,n=Pe.HAMMING,t,r={gapOpenPenalty:1,gapExtensionPenalty:.6}){var i,a;let s=null;const o=e.some((e=>"string"==typeof e))?(s="STRING",e.map((e=>new Uint32Array(e.split("").map((e=>e.charCodeAt(0))))))):e.some((e=>"number"==typeof e))?(s="NUMBER",e.map((e=>new Float32Array([e])))):"object"==typeof e[0]&&e.some((e=>"_data"in e&&"_length"in e))?(s="BITARRAY",e.map((e=>e._data))):e.some((e=>e instanceof Float32Array))?(s="FLOAT32ARRAY",e):e.some((e=>e instanceof Uint32Array))?(s="UINT32ARRAY",e):e.some((e=>e instanceof Int32Array))?(s="INT32ARRAY",e):void 0;if(!o||!s)throw new Error("Invalid entry type, could not determine entry type from input list");const u=o[0]instanceof Int32Array?"INT32ARRAY":o[0]instanceof Float32Array?"FLOAT32ARRAY":"UINT32ARRAY",l=new Uint32Array(o.map((e=>e.length)));if(!Re[s]||!Re[s].has(n))throw new Error(`Distance metric '${n}' not supported for entry type '${s}'`);const c=l.reduce(((e,n)=>Math.max(e,n)),0),f=ke[n](c),h="INT32ARRAY"===u?Int32Array:"FLOAT32ARRAY"===u?Float32Array:Uint32Array,d=new h(o.length*c);o.forEach(((e,n)=>{d.set(e,n*c)}));let p="",g=0,m="FLOAT32ARRAY",y=null;if(n===Pe.NEEDLEMAN_WUNSCH||n===Pe.MONOMER_CHEMICAL_DISTANCE){let e=r.scoringMatrix&&r.alphabetIndexes?Object.keys(r.alphabetIndexes).reduce(((e,n)=>Math.max(e,n.charCodeAt(0))),0):-1;if(!r.alphabetIndexes||!r.scoringMatrix){for(let n=0;n<d.length;n++)d[n]>e&&(e=d[n]);r.scoringMatrix=new Array(e+1).fill(null).map((()=>new Array(e+1).fill(0))),r.alphabetIndexes={};for(let e=0;e<r.scoringMatrix.length;e++)r.scoringMatrix[e][e]=1,r.alphabetIndexes[String.fromCharCode(e)]=e}const n=(e+1)*(e+1),s=new Array(e+1).fill(null).map((()=>new Float32Array(e+1)));for(let n=0;n<e+1;n++)s[n][n]=1;const o=r.alphabetIndexes;for(const e of Object.keys(o))for(const n of Object.keys(o))e!==n&&(s[e.charCodeAt(0)][n.charCodeAt(0)]=r.scoringMatrix[o[e]][o[n]]);g=2+n,m="FLOAT32ARRAY",y=new Float32Array(g),y[0]=null!==(i=r.gapOpenPenalty)&&void 0!==i?i:1,y[1]=null!==(a=r.gapExtensionPenalty)&&void 0!==a?a:.6;let u=2;for(let e=0;e<s.length;e++)y.set(s[e],u),u+=s[e].length;p=`\n            gapOpenPenalty${t}: f32,\n            gapExtensionPenalty${t}: f32,\n            similarityMatrix${t}: array<array<f32, ${e+1}>, ${e+1}>`}else if(n===Pe.Difference){if(!r.range||"number"!=typeof r.range||r.range<=0){const e=d.reduce(((e,n)=>Math.min(e,n)),d[0]),n=d.reduce(((e,n)=>Math.max(e,n)),d[0]);r.range=n-e}r.range<=0&&(r.range=1),g=1,m="FLOAT32ARRAY",y=new Float32Array([r.range]),p=`\n            range${t}: f32`}const w=d instanceof Int32Array?"i32":d instanceof Float32Array?"f32":"u32",b=`data${t}: array<array<${w}, ${c}>, ${o.length}>`;return{flatSourceArray:d,sourceArraySize:d.length,maxEntryLen:c,arraySizes:l,complexity:f,suppInfoBuffer:y,suppInfoSize:g,suppInfoType:m,suppInfoStructWgsl:p,entryType:s,dataTypeWGSL:w,dataStructWgsl:b,EncodedArrayConstructor:h}}(e,t[n],n,a[n])));1===o&&(r=Ie.MANHATTAN);let h=f.map((e=>e.suppInfoStructWgsl)).filter((e=>!!e&&""!=e)).join(",\n"),d=!1;h&&""!=h.trim()||(d=!0,h="\ndummy: f32\n");const p=f.reduce(((e,n)=>e+n.complexity),0),g=f.map((e=>e.dataStructWgsl)).filter((e=>!!e&&""!=e)).join(",\n"),m=new Uint32Array(o*c);f.forEach(((e,n)=>{m.set(e.arraySizes,n*c)}));const y=1e4,w=Math.ceil(1e4/p),b=Math.ceil(Math.sqrt(Math.ceil(100))),x=10*b,v=new Array(c).fill(null).map((()=>new Uint32Array(n))),A=new Array(c).fill(null).map((()=>new Float32Array(n))),S=u.createShaderModule({label:"KNN compute shader",code:`\n          // this struct will contain all the info about the computation, startAtEndAt will contain the start and end of the knnDistances and knnIndexes.\n          // array of sizes for each entries, and the main data as arrays of arrays called data0, data1 and so on. good thing is that because the first entry is vec4<u32>,\n          // there will be no paddings, so no need to worry about padding data. also, arrays and matrices get stucked together, so no padding there as well.\n          // what we need to worry about is the padding of overall struct. the size of overall struct will be factor of 16 bytes, so keep that in mind.\n          struct ComputeInfo {\n            // the x coordinate will contain the start index of the knnDistances and knnIndexes, while y will contain the end index   \n            // the z coordinate will contain the start of the pair comparisons, while w will contain the end of the pair comparisons\n            // just keep in mind that this vec4 will be in first 16 bytes of corresponding buffer.\n            startAtEndAt: vec4<u32>,\n            // the ACTUALLY sizes of each entry\n            entrySizes: array<array<u32, ${c}>, ${o}>,\n            // the weights for each entry\n            weights: array<f32, ${o}>,\n            // the data for each entry\n            ${g} // an example of the dataWgsl would be:\n            //data0: array<array<u32,20>,100>,\n            //data1: array<array<u32,20>,100>\n          };\n\n          struct SuppInfo {\n            // struct containing all the supplementary info, like scoring matrix, alphabet indexes, range, etc.\n            ${h}\n          };\n    \n          @group(0) @binding(0) var<storage, read_write> knnIndexes: array<array<u32, ${n}>, 10000>;\n          @group(0) @binding(1) var<storage, read_write> knnDistances: array<array<f32, ${n}>, 10000>; // each time just compute for a subset of the list\n          @group(0) @binding(2) var<storage, read_write> computeInfo: ComputeInfo;\n          @group(0) @binding(3) var<storage, read_write> suppInfo: SuppInfo;\n          \n          @compute @workgroup_size(10, 10) fn calcKNN(\n            @builtin(global_invocation_id) id: vec3<u32>\n          ) {\n            ${d?"let otherDummy = suppInfo.dummy * 2;":""} // just to make sure that the suppInfo is not optimized out\n            let col = id.x; //* 10 + localId.x;\n            let row = id.y; //* 10 + localId.y;\n            let graphIndex = row * ${x} + col;\n            let index = graphIndex + computeInfo.startAtEndAt.x; // add the starting index of the knnDistances and knnIndexes\n    \n            if (index >= min(${c}u, computeInfo.startAtEndAt.y)) {return;}\n    \n            let pairComparisonStartAt = computeInfo.startAtEndAt.z;\n            let pairComparisonEndAt = min(computeInfo.startAtEndAt.w, ${c}u);\n    \n    \n            // only clear the knnDistances and knnIndexes if we are at the start of the pair comparison\n            if (pairComparisonStartAt == 0u) {\n              for (var i = 0u; i < ${n}; i = i + 1u) {\n                knnDistances[graphIndex][i] = 99999.0;\n                knnIndexes[graphIndex][i] = 0u;\n              }\n            }\n    \n            for (var i: u32 = pairComparisonStartAt; i < pairComparisonEndAt; i = i + 1u) {\n              if (i == index) {continue;}\n              let dist = combinedDistance(index, i);\n              insertKnn(graphIndex, dist, i);\n            }\n            \n          }\n          // this will generate the distance script for each distance metric and then combine them into one\n          ${ze(t,f.map((e=>e.maxEntryLen)),n,r)}\n    \n          fn insertKnn(knnIndex: u32, dist: f32, index: u32) {\n            // small optimization, if the distance is larger than the last element in the knnDistances, we can skip\n            if (dist >= knnDistances[knnIndex][${n} - 1u]) {return;}\n            for (var i = 0u; i < ${n}; i = i + 1u) {\n              if (dist < knnDistances[knnIndex][i]) {\n                for (var j = ${n} - 1u; j > i; j = j - 1u) {\n                  knnDistances[knnIndex][j] = knnDistances[knnIndex][j - 1u];\n                  knnIndexes[knnIndex][j] = knnIndexes[knnIndex][j - 1u];\n                }\n                knnDistances[knnIndex][i] = dist;\n                knnIndexes[knnIndex][i] = index;\n                return;\n              }\n            }\n          }\n        `}),E=u.createComputePipeline({label:"hamming compute pipeline",layout:"auto",compute:{module:S,entryPoint:"calcKNN"}}),I=4+o*c+o+f.reduce(((e,n)=>e+n.sourceArraySize),0),M=f.reduce(((e,n)=>e+n.suppInfoSize),0),N=I*Uint32Array.BYTES_PER_ELEMENT;let P=N;const D=15&N;0!==D&&(P+=16-D);const C=u.createBuffer({label:"compute info buffer",size:P,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),k=C.getMappedRange();let R=0,U=y,T=0,B=w,O=0;new Uint32Array(k,O,4).set([R,U,T,B]),O+=4*Uint32Array.BYTES_PER_ELEMENT,new Uint32Array(k,O,m.length).set(m),O+=m.byteLength,new Float32Array(k,O,o).set(i),O+=o*Float32Array.BYTES_PER_ELEMENT;for(const e of f){const n=e.EncodedArrayConstructor,t=e.sourceArraySize;new n(k,O,t).set(e.flatSourceArray),O+=t*n.BYTES_PER_ELEMENT}C.unmap();const z=M*Uint32Array.BYTES_PER_ELEMENT;let _=z;const L=15&z;0!==L&&(_+=16-L),_=Math.max(_,16);const G=u.createBuffer({label:"supp info buffer",size:_,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),$=G.getMappedRange();let F=0;for(const e of f)e.suppInfoBuffer&&e.suppInfoBuffer.byteLength>0&&e.suppInfoSize>0&&(new("UINT32ARRAY"===e.suppInfoType?Uint32Array:Float32Array)($,F,e.suppInfoBuffer.length).set(e.suppInfoBuffer),F+=e.suppInfoBuffer.byteLength);0===F&&new Uint32Array($,0,4).set([1,1,1,1]),G.unmap();const j=n*Uint32Array.BYTES_PER_ELEMENT*y,Y=u.createBuffer({label:"buffer distances",size:j,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),V=u.createBuffer({label:"buffer indexes",size:j,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),K=n*Uint32Array.BYTES_PER_ELEMENT,q=u.createBindGroup({label:"bindGroup for knn buffer",layout:E.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:V}},{binding:1,resource:{buffer:Y}},{binding:2,resource:{buffer:C}},{binding:3,resource:{buffer:G}}]}),W=u.createBuffer({label:"result buffer distances",size:Y.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST}),H=u.createBuffer({label:"result buffer indexes",size:V.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});for(let e=0;e<Math.ceil(c/y);e++){R=e*y,U=Math.min((e+1)*y,c);const t=Math.ceil(c/w);for(let e=0;e<t;e++){T=e*w,B=Math.min((e+1)*w,c),u.queue.writeBuffer(C,0,new Uint32Array([R,U,T,B]));const r=u.createCommandEncoder({label:"distance encoder"}),i=r.beginComputePass({label:"distance compute pass"});if(i.setPipeline(E),i.setBindGroup(0,q),i.dispatchWorkgroups(b,Math.ceil(y/b/100)),i.end(),e===t-1){r.copyBufferToBuffer(Y,0,W,0,W.size),r.copyBufferToBuffer(V,0,H,0,H.size);const e=r.finish();u.queue.submit([e]),yield u.queue.onSubmittedWorkDone(),yield W.mapAsync(GPUMapMode.READ),yield H.mapAsync(GPUMapMode.READ);const t=H.getMappedRange(),i=W.getMappedRange();for(let e=0;e<U-R;e++){const r=new Uint32Array(t,e*K,n),a=new Float32Array(i,e*K,n);v[R+e].set(r),A[R+e].set(a)}H.unmap(),W.unmap()}else{const e=r.finish();u.queue.submit([e]),yield u.queue.onSubmittedWorkDone()}if(l)return null}}return Y.destroy(),V.destroy(),C.destroy(),G.destroy(),W.destroy(),H.destroy(),l?null:{knnIndexes:v,knnDistances:A}},new((u=void 0)||(u=Promise))((function(e,n){function t(e){try{i(l.next(e))}catch(e){n(e)}}function r(e){try{i(l.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof u?i:new u((function(e){e(i)}))).then(t,r)}i((l=l.apply(s,o||[])).next())}));var s,o,u,l}function ze(e,n,t,r){return e.map(((e,r)=>`\n        fn distanceScript${r}(aIndex: u32, bIndex: u32) -> f32 {\n          let a = computeInfo.data${r}[aIndex];\n          let b = computeInfo.data${r}[bIndex];\n          let maxDistance: f32 = knnDistances[aIndex - computeInfo.startAtEndAt.x][${t} - 1u];\n          ${Ce[e](n[r],r)}\n        }\n      `)).join("\n")+"\n"+`\n      fn combinedDistance(aIndex: u32, bIndex: u32) -> f32 {\n        var distances: array<f32, ${e.length}>;\n        ${e.map(((e,n)=>`distances[${n}] = distanceScript${n}(aIndex, bIndex);`)).join("\n")}\n        ${Ne[r](e.length)}\n      }\n    \n    `}!function(e){e.ADD="ADD",e.SUB="SUB",e.MULT="MULT"}(Ue||(Ue={})),function(e){e.SQUARE="SQUARE",e.INVERSE="INVERSE",e.TRANSPOSE="TRANSPOSE",e.NORM="NORM",e.COLUMN_NORM="COLUMN_NORM"}(Te||(Te={})),function(e){e.SCALARMULT="SCALARMULT",e.SCALARADD="SCALARADD",e.SCALARPOW="SCALARPOW"}(Be||(Be={}));var _e=function(e,n,t,r){return new(t||(t=Promise))((function(i,a){function s(e){try{u(r.next(e))}catch(e){a(e)}}function o(e){try{u(r.throw(e))}catch(e){a(e)}}function u(e){var n;e.done?i(e.value):(n=e.value,n instanceof t?n:new t((function(e){e(n)}))).then(s,o)}u((r=r.apply(e,n||[])).next())}))};function Le(e,n,t,r,i,a,s,o,u){return _e(this,void 0,void 0,(function*(){const l=Math.ceil(s/100),c=Math.ceil(Math.sqrt(l)),f=10*c,h=t[t.length-1],d=a[a.length-1],p=o[o.length-1],g=`\n        struct SparseKNNStorage1 {\n            indexes:array<i32, ${h}>,\n            knnDistances: array<f32, ${h}>,\n            offsets: array<u32, ${s+1}>\n        }\n\n        struct SparseKNNStorage2 {\n            indexes:array<i32, ${d}>,\n            knnDistances: array<f32, ${d}>,\n            offsets: array<u32, ${s+1}>\n        }\n\n        struct ResKnn {\n            knnIndexes: array<i32, ${p}>,\n            knnDistances: array<f32, ${p}>\n        }\n\n        @group(0) @binding(0) var<storage, read_write> source1: SparseKNNStorage1;\n        @group(0) @binding(1) var<storage, read_write> source2: SparseKNNStorage2;\n        @group(0) @binding(2) var<storage, read_write> result: ResKnn;\n        @group(0) @binding(3) var<storage, read_write> unionMatrixOffsets: array<u32, ${s+1}>;\n        @compute @workgroup_size(10, 10) fn pairwiseOp(\n            @builtin(global_invocation_id) id: vec3<u32>,\n        ) {\n\n            let col: u32 = id.x;\n            let row: u32 = id.y;\n            let workingIndex: u32 = row * ${f} + col;\n\n            if (workingIndex >= ${s}) {\n                return;\n            }\n            var curUnionOffset: u32 = unionMatrixOffsets[workingIndex]; // offset at which to start writing in union matrix\n\n            let start1 = source1.offsets[workingIndex];\n            let end1 = source1.offsets[workingIndex + 1];\n            let start2 = source2.offsets[workingIndex];\n            let end2 = source2.offsets[workingIndex + 1];\n            // TODO: sort a copy of these arrays, will make operation faster\n            for (var i: u32 = start1; i < end1; i++) {\n                let val1: f32 = source1.knnDistances[i];\n                var val2: f32 = 0.0;\n                let curIndex: i32 = source1.indexes[i];\n                for (var j: u32 = start2; j < end2; j++) {\n                    if (source2.indexes[j] == curIndex) {\n                        val2 = source2.knnDistances[j];\n                        break;\n                    }\n                }\n                \n                result.knnIndexes[curUnionOffset] = curIndex;\n                result.knnDistances[curUnionOffset] = val1 ${u} val2;\n                curUnionOffset += 1;\n            }\n\n            if (curUnionOffset >= unionMatrixOffsets[workingIndex + 1]) {\n                // small optimization applicable only to our case, but saves a good amount of time\n                return;\n            }\n\n            // do the same for source2 but skip the indexes where they are already present in source1\n            for (var i: u32 = start2; i < end2; i++) {\n                let val1: f32 = source2.knnDistances[i];\n                let curIndex: i32 = source2.indexes[i];\n                var found = false;\n                for (var j: u32 = start1; j < end1; j++) {\n                    if (source1.indexes[j] == curIndex) {\n                        found = true;\n                        break;\n                    }\n                }\n                if (!found) {\n                    result.knnIndexes[curUnionOffset] = curIndex;\n                    result.knnDistances[curUnionOffset] = val1 ${u} 0.0;\n                    curUnionOffset += 1;\n                }\n            }\n        }\n`;let m=4*(2*h+s+1);const y=15&m;0!==y&&(m+=16-y);let w=4*(2*d+s+1);const b=15&w;0!==b&&(w+=16-b);let x=2*p*4;const v=15&x;0!==v&&(x+=16-v);const A=yield Ee();if(null==A)return;const S=A.createShaderModule({label:"pairwiseOpShader",code:g}),E=A.createComputePipeline({label:"pairwiseOpPipeline",layout:"auto",compute:{module:S,entryPoint:"pairwiseOp"}}),I=A.createBuffer({label:"source 1 buffer",size:m,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),M=I.getMappedRange();new Int32Array(M,0,h).set(e),new Float32Array(M,4*h,h).set(n),new Uint32Array(M,8*h,s+1).set(t),I.unmap();const N=A.createBuffer({label:"source 2 buffer",size:w,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),P=N.getMappedRange();new Int32Array(P,0,d).set(r),new Float32Array(P,4*d,d).set(i),new Uint32Array(P,8*d,s+1).set(a),N.unmap();const D=A.createBuffer({label:"res buffer",size:x,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST}),C=A.createBuffer({label:"union matrix offsets 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MIN_K_DIST_SCALE: f32 = 1e-3;\n        var<private> nNeighbors: u32 = ${r};\n        var<private> localConnectivity: f32 = ${i}; \n        var<private> nIter: u32 = ${a};\n        var<private> bandwidth: u32 = ${s};\n        var<private> meanDistances: f32 = ${u/o};\n        var<private> targetValue: f32 = ${Math.log(r)/Math.log(2)*s};\n        @group(0) @binding(0) var<storage, read_write> sigmas: array<f32, ${o}>;\n        @group(0) @binding(1) var<storage, read_write> rhos: array<f32, ${o}>;\n        @group(0) @binding(2) var<storage, read> distances: array<array<f32, ${r}>, ${o}>;\n        @compute @workgroup_size(${e}, ${e}) fn smoothKNNDistance(\n            @builtin(global_invocation_id) id: vec3<u32>,\n        ) {\n            let col: u32 = id.x;\n            let row: u32 = id.y;\n            let workingIndex: u32 = row * ${n} + col;\n\n            if (workingIndex >= ${o}) {\n                return;\n            }\n\n            var lo: f32 = 0.0;\n            var hi: f32 = 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{\n                    rhos[workingIndex] = interpolation * nonZeroDists[0];\n                }\n            }\n            else if (nonZeroDistsSize > 0u) {\n                var maxDist: f32 = 0.0;\n                for (var j = 0u; j < nonZeroDistsSize; j = j + 1u) {\n                    maxDist = max(nonZeroDists[j], maxDist);\n                }\n                rhos[workingIndex] = maxDist;\n            }\n\n            for (var n = 0u; n < nIter; n = n + 1u) {\n                var psum: f32 = 0.0;\n                for (var j = 1u; j < ${r}; j = j + 1u) {\n                    let d: f32 = distances[workingIndex][j] - rhos[workingIndex];\n                    if (d > 0.0) {\n                        psum += exp(0.0 - (d / mid));\n                    }\n                    else {\n                        psum += 1.0;\n                    }\n                }\n\n                if (abs(psum - targetValue) < SMOOTH_K_TOLERANCE) {\n                    break;\n                }\n\n                if (psum > targetValue) {\n                    hi = mid;\n                    mid = (lo + hi) / 2.0;\n                }\n                else {\n                    lo = mid;\n                    if (hi == 1.0e+30) {\n                        mid *= 2.0;\n                    }\n                    else {\n                        mid = (lo + hi) / 2.0;\n                    }\n                }\n            }\n\n            sigmas[workingIndex] = mid;\n\n            if (rhos[workingIndex] > 0.0) {\n                var sum: f32 = 0.0;\n                for (var j = 0u; j < ${r}; j = j + 1u) {\n                    sum += distances[workingIndex][j];\n                }\n                let meanIthDistances: f32 = sum / ${r}.0;\n                if (sigmas[workingIndex] < MIN_K_DIST_SCALE * meanIthDistances) {\n                    sigmas[workingIndex] = MIN_K_DIST_SCALE * meanIthDistances;\n                }\n            }\n            else {\n                if (sigmas[workingIndex] < MIN_K_DIST_SCALE * meanDistances) {\n                    sigmas[workingIndex] = MIN_K_DIST_SCALE * meanDistances;\n                }\n            }\n        }\n    `}(10,10*o,e,n,t,r,i),l=a*e[0].length,c=yield Ee();if(null==c)return;const f=new Float32Array(a),h=new Float32Array(a),d=c.createShaderModule({label:"sigmaRhoCalulation",code:u}),p=c.createComputePipeline({label:"sigmaRhoPipeline",layout:"auto",compute:{module:d,entryPoint:"smoothKNNDistance"}}),g=c.createBuffer({label:"distance buffer",size:4*l,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),m=g.getMappedRange(),y=new Float32Array(m);for(let n=0;n<e.length;n++)y.set(e[n],n*e[n].length);g.unmap();const w=c.createBuffer({label:"buffer sigmas",size:4*a,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),b=c.createBuffer({label:"buffer Rhos",size:4*a,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),x=c.createBindGroup({label:"bindGroup for sigmarho buffers",layout:p.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:w}},{binding:1,resource:{buffer:b}},{binding:2,resource:{buffer:g}}]}),v=c.createCommandEncoder({label:"sigmarho encoder"}),A=v.beginComputePass({label:"sigmarho compute pass"});A.setPipeline(p),A.setBindGroup(0,x),A.dispatchWorkgroups(o,o),A.end();const S=c.createBuffer({label:"result buffer rhos",size:b.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST}),E=c.createBuffer({label:"result buffer sigmas",size:w.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});v.copyBufferToBuffer(b,0,S,0,S.size),v.copyBufferToBuffer(w,0,E,0,E.size);const I=v.finish();return c.queue.submit([I]),yield c.queue.onSubmittedWorkDone(),yield S.mapAsync(GPUMapMode.READ),yield E.mapAsync(GPUMapMode.READ),h.set(new Float32Array(S.getMappedRange())),f.set(new Float32Array(E.getMappedRange())),S.unmap(),E.unmap(),g.destroy(),w.destroy(),b.destroy(),S.destroy(),E.destroy(),{resultRhos:h,resultSigmas:f}},new((o=void 0)||(o=Promise))((function(e,n){function t(e){try{i(u.next(e))}catch(e){n(e)}}function r(e){try{i(u.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof o?i:new o((function(e){e(i)}))).then(t,r)}i((u=u.apply(a,s||[])).next())}));var a,s,o,u}var We=function(e,n,t,r){return new(t||(t=Promise))((function(i,a){function s(e){try{u(r.next(e))}catch(e){a(e)}}function o(e){try{u(r.throw(e))}catch(e){a(e)}}function u(e){var n;e.done?i(e.value):(n=e.value,n instanceof t?n:new t((function(e){e(n)}))).then(s,o)}u((r=r.apply(e,n||[])).next())}))};class He{constructor(){this.nComponents=2,this.gamma=1,this.alpha=1,this.entryLen=0,this.nNeighbours=15,this.spread=1,this.minDist=.1,this.negativeSampleRate=5,this.localConnectivity=1,this.setOpMixRatio=1}}class Ze{constructor(e,n){this.params=new He,this.knnIndexes=null,this.knnDistances=null,this.rhos=null,this.sigmas=null,this.membershipStrengths=null,this.params.entryLen=e,Object.assign(this.params,n)}setPrecomputedKNN(e,n){this.knnIndexes=e,this.knnDistances=n}initializeFit(){return We(this,void 0,void 0,(function*(){yield this.calcSmoothKNNDistances(),yield this.calcMembershipStrengths()}))}fit(){return We(this,void 0,void 0,(function*(){yield this.initializeFit();const e=yield this.initializeSimplicialSetEmbedding();if(!e)throw new Error("failed to compute umap simplistical set embeddings");const{head:n,tail:t,epochsPerSample:r,epochsPerNegativeSample:i,a,b:s,gamma:o,initialAlpha:u,nComponents:l,nEpochs:c,entryLen:f}=e,h=yield function(e,n,t,r,i,a,s,o,u,l,c,f){return h=this,d=void 0,g=function*(){const h=Math.ceil(e.length/100),d=Math.ceil(Math.sqrt(h)),p=10*d,g=yield Ee();if(!g)return;const m=1e7,y=e.length,w=function(e,n,t,r,i,a,s,o,u,l,c,f,h=1e5){return`\n// first define some functions\n\nfn rDist(ar1: array<f32, ${o}>, ar2: array<f32, ${o}>) -> f32 {\n    var res = 0.0;\n    for (var i1 = 0u; i1 < ${o}; i1++) {\n        let diff = ar1[i1] - ar2[i1];\n        res += pow(diff, 2);\n    }\n    return res;\n}\n\nfn clip(x: f32, clipValue: f32) -> f32 {\n    if (x > clipValue) {\n        return clipValue;\n    }\n    else if (x < 0.0 - clipValue) {\n        return 0.0 - clipValue;\n    }\n    return x;\n}\n\nvar<private> randomSeedInt: u32 = 0;\nvar<private> nVertices: u32 = ${l};\nvar<private> initialAlpha: f32 = ${r};\nvar<private> gamma: f32 = ${i};\nvar<private> a: f32 = ${a};\nvar<private> b: f32 = ${s};\nvar<private> dim: u32 = ${o};\nvar<private> nEpochs: f32 = ${u};\nvar<private> moveOther: u32  = 1;\n\nfn random() -> u32 {\n    randomSeedInt = (randomSeedInt ^ 61) ^ (randomSeedInt >> 16);\n    randomSeedInt *= 9;\n    randomSeedInt = randomSeedInt ^ (randomSeedInt >> 4);\n    randomSeedInt *= 0x27d4eb2d;\n    randomSeedInt = randomSeedInt ^ (randomSeedInt >> 15);\n    return randomSeedInt;\n}\n\nfn randInt(maxVal: u32) -> u32 {\n    let nextRandomNum = random();\n    return u32(floor((f32(nextRandomNum) * (f32(maxVal) / 4294967296.0))));\n}\n\nstruct MatrixStorage {\n    head: array<u32, ${e}>,\n    tail: array<u32, ${e}>,\n}\n\nstruct EpochStorage {\n    epochsPerSample: array<f32, ${e}>,\n    epochOfNextSample: array<f32, ${e}>,\n    epochsPerNegativeSample: array<f32, ${e}>,\n    epochOfNextNegativeSample: array<f32, ${e}>\n}\n\nstruct EmbeddingStorage {\n    // embeddings will be in range of -10 to 10, as atomics only can store i32 or u32, we will store them as floor(f32 * 100_000)\n    headEmbeddings: array<array<atomic<i32>, ${o}>, ${n}>,\n    tailEmbeddings: array<array<atomic<i32>, ${o}>, ${n}>\n}\n\nstruct ComputeInfo {\n    n: f32,\n    alpha: f32,\n    randomNumbers: array<u32, ${e}>,\n    //tailOffsets: array<u32, ${n+1}>\n}\n    @group(0) @binding(0) var<storage, read_write> matrixStorage: MatrixStorage;\n    @group(0) @binding(1) var<storage, read_write> epochStorage: EpochStorage;\n    @group(0) @binding(2) var<storage, read_write> embedStorage: EmbeddingStorage;\n    @group(0) @binding(3) var<storage, read_write> computeInfo: ComputeInfo;\n    @compute @workgroup_size(${c}, ${c}) fn optimizeStep(\n        @builtin(global_invocation_id) id: vec3<u32>,\n     ) {\n        let divisionFactor: f32 = ${h};\n        let col: u32 = id.x;\n        let row: u32 = id.y;\n        let threadIndex: u32 = row * ${f} + col;\n        let clipValue: f32 = 4.0;\n\n        if (threadIndex >= ${e}) {\n            return;\n        }\n\n        let workingIndex = threadIndex;\n        //let startAtOffset = computeInfo.tailOffsets[threadIndex];\n        //let endAtOffset = computeInfo.tailOffsets[threadIndex + 1];\n        //for (var workingIndex = startAtOffset; workingIndex < endAtOffset; workingIndex++) {\n            randomSeedInt = computeInfo.randomNumbers[workingIndex] * u32(computeInfo.n);\n\n            let epochOfNextSample = epochStorage.epochOfNextSample[workingIndex];\n            if (epochOfNextSample > computeInfo.n) {\n                return;\n            }\n\n            let j = matrixStorage.head[workingIndex];\n            let k = matrixStorage.tail[workingIndex];\n\n            // as said before, we will store embeddings as floor(f32 * 100_000)\n            var current: array<f32, ${o}>;\n            var other: array<f32, ${o}>;\n            for (var i = 0u; i < ${o}u; i++) {\n                current[i] = f32(atomicLoad(&embedStorage.headEmbeddings[j][i])) / divisionFactor;\n                other[i] = f32(atomicLoad(&embedStorage.tailEmbeddings[k][i])) / divisionFactor;\n            }\n\n            let distSquared = rDist(current, other);\n            \n            var gradCoeff: f32 = 0.0;\n            if (distSquared > 0.0) {\n                gradCoeff = (0.0 - 2.0) * ${a} * ${s} * pow(distSquared, b - 1.0);\n                gradCoeff /= (a * pow(distSquared, b) + 1.0);\n            }\n\n            var gradBuff: array<i32, ${o}>;\n            for (var d = 0u; d < ${o}u; d++) {\n                let gradD = clip((gradCoeff * (current[d] - other[d])), clipValue);\n                let toAdd = gradD * computeInfo.alpha;\n                gradBuff[d] = i32(floor(toAdd * divisionFactor));\n                current[d] += toAdd;\n                other[d] -= toAdd;\n            }\n\n            for (var d = 0u; d < ${o}u; d++) {\n                atomicAdd(&embedStorage.headEmbeddings[j][d], gradBuff[d]);\n                atomicSub(&embedStorage.tailEmbeddings[k][d], gradBuff[d]);\n            }\n\n            epochStorage.epochOfNextSample[workingIndex] += epochStorage.epochsPerSample[workingIndex];\n            var nNegSamples: i32 = i32(floor((computeInfo.n - epochStorage.epochOfNextNegativeSample[workingIndex]) / epochStorage.epochsPerNegativeSample[workingIndex]));\n\n            for (var p = 0i; p < nNegSamples; p++) {\n                let k1 = randInt(nVertices);\n                var other1: array<f32, ${o}>;\n                for (var i = 0u; i < ${o}u; i++) {\n                    other1[i] = f32(atomicLoad(&embedStorage.tailEmbeddings[k1][i])) / divisionFactor;\n                }\n\n                let distSquared1 = rDist(current, other1);\n\n                var gradCoeff1: f32 = 0.0;\n                if (distSquared1 > 0.0) {\n                    gradCoeff1 = 2.0 * gamma * b;\n                    gradCoeff1 /= (0.001 + distSquared1) * (a * pow(distSquared1, b) + 1);\n                }\n                else if (j == k1) {\n                    continue;\n                }\n\n                var gradDBuff: array<i32, ${o}>;\n                for (var d = 0u; d < ${o}u; d++) {\n                    var gradD: f32 = 4.0;\n                    if (gradCoeff1 > 0.0) {\n                        gradD = clip(gradCoeff1 * (current[d] - other1[d]), clipValue);\n                    }\n\n                    gradDBuff[d] = i32(floor(gradD * computeInfo.alpha * divisionFactor));\n                    \n                }\n                for (var d = 0u; d < ${o}u; d++) {\n                    atomicAdd(&embedStorage.headEmbeddings[j][d], gradDBuff[d]);\n                }\n            }\n            epochStorage.epochOfNextNegativeSample[workingIndex] += f32(nNegSamples) * epochStorage.epochsPerNegativeSample[workingIndex];\n    //}\n    }\n`}(y,t,0,a,s,o,u,l,c,f,10,p,m);let b=2*y*4;const x=15&b;0!==x&&(b+=16-x);let v=4*y*4;const A=15&v;0!==A&&(v+=16-A);let S=2*t*2*4;const E=15&S;0!==E&&(S+=16-E);let I=4*(2+y);const M=15&I;0!==M&&(I+=16-M);const N=g.createShaderModule({label:"optimizeShader",code:w}),P=g.createComputePipeline({label:"optimizePipeline",layout:"auto",compute:{module:N,entryPoint:"optimizeStep"}}),D=g.createBuffer({label:"matrix storage buffer",size:b,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),C=D.getMappedRange();new Uint32Array(C,0,y).set(e),new Uint32Array(C,4*y,y).set(n),D.unmap();const k=g.createBuffer({label:"epoch storage buffer",size:v,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),R=k.getMappedRange(),U=new Float32Array(R);U.set(r,0),U.set(r,y),U.set(i,2*y),U.set(i,3*y),k.unmap();const T=new Int32Array(t*l).map((()=>Math.floor((2*Math.random()-1)*m)));new Int32Array(t*l).set(T);const B=g.createBuffer({label:"embedding storage buffer",size:S,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),O=B.getMappedRange(),z=new Int32Array(O);z.set(T,0),z.set(T,T.length),B.unmap();const _=g.createBuffer({label:"compute info buffer",size:I,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),L=new Uint32Array(y).map((()=>Math.floor(Math.random()*m))),G=_.getMappedRange();new Float32Array(G,0,2).set([0,a]),new Uint32Array(G,8,y).set(L),_.unmap();const $=g.createBindGroup({label:"bindGroup for optimize",layout:P.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:D}},{binding:1,resource:{buffer:k}},{binding:2,resource:{buffer:B}},{binding:3,resource:{buffer:_}}]});let F=a;const j=g.createBuffer({label:"result buffer",size:B.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});for(let e=0;e<c;e++){g.queue.writeBuffer(_,0,new Float32Array([e,F]),0);const n=g.createCommandEncoder({label:"matrix ops encoder"}),t=n.beginComputePass({label:"matrix ops compute pass"});t.setPipeline(P),t.setBindGroup(0,$),t.dispatchWorkgroups(d,d),t.end(),e===c-1&&n.copyBufferToBuffer(B,0,j,0,j.size);const r=n.finish();g.queue.submit([r]),yield g.queue.onSubmittedWorkDone(),F=a*(1-e/c)}yield j.mapAsync(GPUMapMode.READ);const Y=j.getMappedRange(),V=new Int32Array(Y,0,T.length);T.set(V),j.unmap();const K=new Array(l).fill(null).map((e=>new Float32Array(t)));for(let e=0;e<t;e++)for(let n=0;n<l;n++)K[n][e]=T[e*l+n]/m;return D.destroy(),k.destroy(),B.destroy(),_.destroy(),j.destroy(),K},new((p=void 0)||(p=Promise))((function(e,n){function t(e){try{i(g.next(e))}catch(e){n(e)}}function r(e){try{i(g.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof p?i:new p((function(e){e(i)}))).then(t,r)}i((g=g.apply(h,d||[])).next())}));var h,d,p,g}(n,t,f,r,i,u,o,a,s,l,c,f);return h}))}calcSmoothKNNDistances(){return We(this,void 0,void 0,(function*(){if(!this.knnIndexes||!this.knnDistances)throw new Error("knn indexes and distances must be set before calling fit");const e=yield qe(this.knnDistances,this.params.nNeighbours,this.params.localConnectivity,64);if(!e)throw new Error("failed to compute smooth knn distances");this.rhos=e.resultRhos,this.sigmas=e.resultSigmas}))}calcMembershipStrengths(){return We(this,void 0,void 0,(function*(){if(!(this.knnIndexes&&this.knnDistances&&this.rhos&&this.sigmas))throw new Error("knn indexes, distances, rhos, and sigmas must be set before calling fit");const e=yield function(e,n,t){return r=this,i=void 0,s=function*(){const r=e.length,i=Math.ceil(r/100),a=Math.ceil(Math.sqrt(i)),s=function(e=10,n,t,r,i){const a=t.length,s=r.length,o=i.length;return`\n           struct MembershipStrengthsInfo {\n               knnDistances: array<array<f32, ${t[0].length}>, ${a}>,\n               sigmas: array<f32, ${s}>,\n               rhos: array<f32, ${o}>\n           };\n           var<private> nNeighbors: u32 = ${t[0].length};\n           @group(0) @binding(0) var<storage, read> membershipStrengthsInfo: MembershipStrengthsInfo;\n           @group(0) @binding(1) var<storage, read_write> resultKnnDistances: array<array<f32, ${t[0].length}>, ${a}>;\n           @compute @workgroup_size(${e}, ${e}) fn computeMembershipStrengths(\n               @builtin(global_invocation_id) id: vec3<u32>,\n           ) {\n               let col: u32 = id.x;\n               let row: u32 = id.y;\n               let workingIndex: u32 = row * ${n} + col;\n\n               if (workingIndex >= ${a}) {\n                   return;\n               }\n\n               let workingResKnnDistances = &resultKnnDistances[workingIndex];\n               let knnDistances = &membershipStrengthsInfo.knnDistances[workingIndex];\n               for (var j = 0u; j < nNeighbors; j = j + 1u) {\n                   var val: f32 = 0.0;\n\n                   if ((*knnDistances)[j] - membershipStrengthsInfo.rhos[workingIndex] <= 0.0) {\n                       val = 1.0;\n                   } else {\n                       val = exp(0.0 - ((knnDistances[j] - membershipStrengthsInfo.rhos[workingIndex]) / membershipStrengthsInfo.sigmas[workingIndex]));   \n                   }\n\n                   (*workingResKnnDistances)[j] = val;\n               }\n           }\n   `}(10,10*a,e,n,t),o=r*e[0].length,u=yield Ee();if(null==u)return;const l=u.createShaderModule({label:"rowsColsValsCalulation",code:s}),c=u.createComputePipeline({label:"rowsColsValsPipeline",layout:"auto",compute:{module:l,entryPoint:"computeMembershipStrengths"}});let f=4*(t.length+n.length+o);const h=15&f;0!=h&&(f+=16-h);const d=u.createBuffer({label:"info buffer",size:f,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),p=d.getMappedRange(),g=new Float32Array(p);for(let n=0;n<e.length;n++)g.set(e[n],n*e[n].length);let m=e[0].length*e.length;g.set(n,m),m+=n.length,g.set(t,m),d.unmap();const y=u.createBuffer({label:"knn distance buffer",size:e[0].length*e.length*Float32Array.BYTES_PER_ELEMENT,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST}),w=u.createBindGroup({label:"bindGroup for membership strhegths buffers",layout:c.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:d}},{binding:1,resource:{buffer:y}}]}),b=u.createCommandEncoder({label:"membership strengths encoder"}),x=b.beginComputePass({label:"membership strengths compute pass"});x.setPipeline(c),x.setBindGroup(0,w),x.dispatchWorkgroups(a,a),x.end();const v=u.createBuffer({label:"result buffer distances",size:y.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});b.copyBufferToBuffer(y,0,v,0,v.size);const A=b.finish();u.queue.submit([A]),yield u.queue.onSubmittedWorkDone(),yield v.mapAsync(GPUMapMode.READ);const S=v.getMappedRange(),E=e[0].length*Float32Array.BYTES_PER_ELEMENT,I=new Array(e.length).fill(null).map(((n,t)=>{const r=new Float32Array(S,E*t,e[0].length),i=new Float32Array(e[0].length);return i.set(r),i}));return v.unmap(),v.destroy(),y.destroy(),d.destroy(),I},new((a=void 0)||(a=Promise))((function(e,n){function t(e){try{u(s.next(e))}catch(e){n(e)}}function o(e){try{u(s.throw(e))}catch(e){n(e)}}function u(n){var r;n.done?e(n.value):(r=n.value,r instanceof a?r:new a((function(e){e(r)}))).then(t,o)}u((s=s.apply(r,i||[])).next())}));var r,i,a,s}(this.knnDistances,this.sigmas,this.rhos);if(!e)throw new Error("failed to compute membership strengths");this.membershipStrengths=e}))}fuzzySimplicialSet(){return We(this,void 0,void 0,(function*(){if(!(this.knnIndexes&&this.knnDistances&&this.rhos&&this.sigmas&&this.membershipStrengths))throw new Error("knn indexes, distances, rhos, sigmas, and membership strengths must be set before calling fit");const e=yield Ke(this.knnIndexes,this.membershipStrengths,this.params.setOpMixRatio);if(!e)throw new Error("failed to compute pairwise multiply with transpose");return e}))}initializeSimplicialSetEmbedding(){return We(this,void 0,void 0,(function*(){const e=yield this.fuzzySimplicialSet();if(!(e&&e.res&&e.unionMatrixOffsets&&e.unionSizes))throw new Error("failed to compute fuzzy simplicial set");const n=yield function(e,n,t,r,i=5){return a=this,s=void 0,u=function*(){if(!e.unionSizes)return;const a=function(e){return e<=2500?1e3:e<=5e3?800:e<=7500?650:400}(n),s=e.res.resultKnnDistances.reduce(((e,n)=>Math.max(e,n))),o=s/a,u=new Uint32Array(e.unionSizes.length);u.set(e.unionSizes);let l=0;for(let n=0;n<e.unionSizes.length;n++){for(let t=0;t<e.unionSizes[n];t++){const r=l+t;e.res.resultKnnDistances[r]<o&&(e.res.resultKnnDistances[r]=0,u[n]--)}l+=e.unionSizes[n]}const c=Ye(u),f=c[c.length-1],h=new Float32Array(f),d=new Uint32Array(f),p=new Uint32Array(f);l=0;for(let n=0;n<e.unionSizes.length;n++)for(let t=0;t<e.unionSizes[n];t++){const r=e.unionMatrixOffsets[n]+t;0!=e.res.resultKnnDistances[r]&&(h[l]=e.res.resultKnnDistances[r],d[l]=e.res.resultKnnIndexes[r],p[l]=n,l+=1)}const g=new Float32Array(h.length).fill(-1),m=h.map((e=>e/s*a));m.forEach(((e,n)=>{e>0&&(g[n]=a/m[n])}));const{a:y,b:w}=je(t,r),b=g.map((e=>e/i));return{epochsPerSample:g,epochsPerNegativeSample:b,a:y,b:w,head:d,tail:p,entryLen:n,nEpochs:a,nComponents:2,initialAlpha:1,gamma:1}},new((o=void 0)||(o=Promise))((function(e,n){function 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this.optimizeLayoutAsync(n),this.embedding}setSupervisedProjection(e,n={}){this.Y=e,this.targetMetric=n.targetMetric||this.targetMetric,this.targetWeight=n.targetWeight||this.targetWeight,this.targetNNeighbors=n.targetNNeighbors||this.targetNNeighbors}setPrecomputedKNN(e,n){this.knnIndices=e,this.knnDistances=n}initializeFit(e){if(e.length<=this.nNeighbors)throw new Error(`Not enough data points (${e.length}) to create nNeighbors: ${this.nNeighbors}.  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s=0;s<r.length;s++){const o=te(r[s],e,a);for(let e=0;e<o.length;e++){if(o[e]<0)return;R(i,s,t(n[o[e]],r[s]),o[e],1)}}}});var t;this.initFromTree=e,this.initFromRandom=n,this.search=function(e){return function(n,t,r,i){const{indices:a,indptr:s}=W(t);for(let t=0;t<i.length;t++){const o=new Set(r[0][t]);for(;;){const u=_(r,t);if(-1===u)break;const l=a.slice(s[u],s[u+1]);for(const a of l)a===u||-1===a||o.has(a)||(U(r,t,e(n[a],i[t]),a,1),o.add(a))}}return r}}(this.distanceFn)}makeSearchGraph(e){const n=this.knnIndices,t=this.knnDistances,r=[e.length,e.length],i=new z([],[],[],r);for(let e=0;e<n.length;e++){const r=n[e],a=t[e];for(let n=0;n<r.length;n++){const t=r[n],s=a[n];s>0&&i.set(e,t,s)}}return K(i,L(i),((e,n)=>e>n?e:n))}transform(e){const n=this.X;if(void 0===n||0===n.length)throw new Error("No data has been fit.");let t=Math.floor(this.nNeighbors*this.transformQueueSize);t=Math.min(n.length,t);const r=function(e,n,t,r,i,a,s){const o=D(t.length,r);if(i(r,n,t,o,s),e)for(const r of e)a(r,n,t,o,s);return o}(this.rpForest,n,e,t,this.initFromRandom,this.initFromTree,this.random),i=this.search(n,this.searchGraph,r,e);let{indices:a,weights:s}=T(i);a=a.map((e=>e.slice(0,this.nNeighbors))),s=s.map((e=>e.slice(0,this.nNeighbors)));const o=Math.max(0,this.localConnectivity-1),{sigmas:u,rhos:l}=this.smoothKNNDistance(s,this.nNeighbors,o),{rows:c,cols:f,vals:h}=this.computeMembershipStrengths(a,s,u,l),d=[e.length,n.length];let p=new z(c,f,h,d);const m=W(q(p,"l1")),g=e.length,y=function(e,n,t){const r=I(e.length).map((e=>I(t[0].length)));for(let i=0;i<e.length;i++)for(let a=0;a<e[0].length;a++)for(let s=0;s<t[0].length;s++){const o=e[i][a];r[i][s]+=n[i][a]*t[o][s]}return r}(C(m.indices,g,this.nNeighbors),C(m.values,g,this.nNeighbors),this.embedding),w=this.nEpochs?this.nEpochs/3:p.nRows<=1e4?100:30,b=p.getValues().reduce(((e,n)=>n>e?n:e),0);p=p.map((e=>e<b/w?0:e)),p=Y(p);const x=this.makeEpochsPerSample(p.getValues(),w),v=p.getRows(),A=p.getCols();return this.assignOptimizationStateParameters({headEmbedding:y,tailEmbedding:this.embedding,head:v,tail:A,currentEpoch:0,nEpochs:w,nVertices:p.getDims()[1],epochsPerSample:x}),this.prepareForOptimizationLoop(),this.optimizeLayout()}processGraphForSupervisedProjection(){const{Y:e,X:n}=this;if(e){if(e.length!==n.length)throw new Error("Length of X and y must be equal");if("categorical"===this.targetMetric){const n=this.targetWeight<1?1/(1-this.targetWeight)*2.5:1e12;this.graph=this.categoricalSimplicialSetIntersection(this.graph,e,n)}}}step(){const{currentEpoch:e}=this.optimizationState;return e<this.getNEpochs()&&this.optimizeLayoutStep(e),this.optimizationState.currentEpoch}getEmbedding(){return this.embedding}nearestNeighbors(e){const{distanceFn:n,nNeighbors:t}=this,r=function(e,n){return function(t,r,i,a=10,s=50,o=.001,u=.5,l=!0){const c=t.length,f=D(t.length,i);for(let r=0;r<t.length;r++){const a=k(i,t.length,n);for(let n=0;n<a.length;n++){const i=e(t[r],t[a[n]]);R(f,r,i,a[n],1),R(f,a[n],i,r,1)}}if(l)for(let n=0;n<r.length;n++)for(let i=0;i<r[n].length&&!(r[n][i]<0);i++)for(let a=i+1;a<r[n].length&&!(r[n][a]<0);a++){const s=e(t[r[n][i]],t[r[n][a]]);R(f,r[n][i],s,r[n][a],1),R(f,r[n][a],s,r[n][i],1)}for(let r=0;r<a;r++){const r=O(f,c,i,s,n);let a=0;for(let i=0;i<c;i++)for(let o=0;o<s;o++){const l=Math.floor(r[0][i][o]);if(!(l<0||v(n)<u))for(let n=0;n<s;n++){const s=Math.floor(r[0][i][n]),u=r[2][i][o],c=r[2][i][n];if(s<0||!u&&!c)continue;const h=e(t[l],t[s]);a+=R(f,l,h,s,1),a+=R(f,s,h,l,1)}}if(a<=o*i*t.length)break}return T(f)}}(n,this.random),i=5+Math.floor(.5==(a=e.length**.5/20)?0:Math.round(a));var a;const s=Math.max(5,Math.floor(Math.round((e=>Math.log(e)/Math.log(2))(e.length))));this.rpForest=Z(e,t,i,this.random);const o=function(e){if(e.length>0){const n=[];for(const t of e)n.push(...t.indices);return n}return[[-1]]}(this.rpForest),{indices:u,weights:l}=r(e,o,t,s);return{knnIndices:u,knnDistances:l}}fuzzySimplicialSet(e,n,t=1){const{knnIndices:r=[],knnDistances:i=[],localConnectivity:a}=this,{sigmas:s,rhos:o}=this.smoothKNNDistance(i,n,a),{rows:u,cols:l,vals:c}=this.computeMembershipStrengths(r,i,s,o),f=[e.length,e.length],h=new z(u,l,c,f),d=L(h),p=G(h,d),m=F($(h,d),p);return $(j(m,t),j(p,1-t))}categoricalSimplicialSetIntersection(e,n,t,r=1){let i=function(e,n,t=1,r=5){return e.map(((e,i,a)=>-1===n[i]||-1===n[a]?e*Math.exp(-t):n[i]!==n[a]?e*Math.exp(-r):e))}(e,n,r,t);return i=Y(i),function(e){const n=L(e=q(e,"max"));return Y(e=$(e,F(n,G(n,e))))}(i)}smoothKNNDistance(e,n,t=1,r=64,i=1){const a=Math.log(n)/Math.log(2)*i,s=I(e.length),o=I(e.length);for(let n=0;n<e.length;n++){let i=0,u=1/0,l=1;const c=e[n],f=c.filter((e=>e>0));if(f.length>=t){const e=Math.floor(t),r=t-e;e>0?(s[n]=f[e-1],r>ue&&(s[n]+=r*(f[e]-f[e-1]))):s[n]=r*f[0]}else f.length>0&&(s[n]=N(f));for(let t=0;t<r;t++){let t=0;for(let r=1;r<e[n].length;r++){const i=e[n][r]-s[n];t+=i>0?Math.exp(-i/l):1}if(Math.abs(t-a)<ue)break;t>a?(u=l,l=(i+u)/2):(i=l,u===1/0?l*=2:l=(i+u)/2)}if(o[n]=l,s[n]>0){const e=M(c);o[n]<le*e&&(o[n]=le*e)}else{const t=M(e.map(M));o[n]<le*t&&(o[n]=le*t)}}return{sigmas:o,rhos:s}}computeMembershipStrengths(e,n,t,r){const i=e.length,a=e[0].length,s=I(i*a),o=I(i*a),u=I(i*a);for(let l=0;l<i;l++)for(let i=0;i<a;i++){let c=0;-1!==e[l][i]&&(c=e[l][i]===l?0:n[l][i]-r[l]<=0?1:Math.exp(-(n[l][i]-r[l])/t[l]),s[l*a+i]=l,o[l*a+i]=e[l][i],u[l*a+i]=c)}return{rows:s,cols:o,vals:u}}initializeSimplicialSetEmbedding(){const e=this.getNEpochs(),{nComponents:n}=this,t=this.graph.getValues();let r=0;for(let e=0;e<t.length;e++){const n=t[e];r<t[e]&&(r=n)}const i=this.graph.map((n=>n<r/e?0:n));this.embedding=I(i.nRows).map((()=>I(n).map((()=>20*v(this.random)-10))));const a=[],s=[],o=[],u=i.getAll();for(let e=0;e<u.length;e++){const 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A(300).map(((e,t)=>0+t*((n-0)/299)))}(0,3*e).map((e=>e<n?1:e)),r=I(t.length).map(((r,i)=>t[i]>=n?Math.exp(-(t[i]-n)/e):r)),i={x:t,y:r},{parameterValues:a}=function(e,n,t={}){let{maxIterations:r=100,gradientDifference:i=.1,damping:a=0,errorTolerance:s=.01,minValues:o,maxValues:u,initialValues:l}=t;if(a<=0)throw new Error("The damping option must be a positive number");if(!e.x||!e.y)throw new Error("The data parameter must have x and y elements");if(!ie(e.x)||e.x.length<2||!ie(e.y)||e.y.length<2)throw new Error("The data parameter elements must be an array with more than 2 points");if(e.x.length!==e.y.length)throw new Error("The data parameter elements must have the same size");let c=l||new Array(n.length).fill(1),f=c.length;if(u=u||new Array(f).fill(Number.MAX_SAFE_INTEGER),o=o||new Array(f).fill(Number.MIN_SAFE_INTEGER),u.length!==o.length)throw new Error("minValues and maxValues must be the same size");if(!ie(c))throw new Error("initialValues must be an array");let 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You must have some data!"),console.time("distances to matrix"),this.P=this.d2p(e,this.perplexity,1e-4,n),console.timeEnd("distances to matrix"),this.N=n,this.initSolution()}initSolution(){this.Y=this.randn2d(this.N,this.dim),this.gains=this.randn2d(this.N,this.dim,1),this.ystep=this.randn2d(this.N,this.dim,0),this.iter=0}getSolution(){return this.Y}step(){this.iter+=1;const e=this.N,n=this.costGrad(this.Y),t=n.cost,r=n.grad,i=this.zeros(this.dim);for(let n=0;n<e;n++)for(let e=0;e<this.dim;e++){const t=r[n][e],a=this.ystep[n][e],s=this.gains[n][e];let o=this.sign(t)===this.sign(a)?.8*s:s+.2;o<.01&&(o=.01),this.gains[n][e]=o;const u=(this.iter<250?.5:.8)*a-this.epsilon*o*r[n][e];this.ystep[n][e]=u,this.Y[n][e]+=u,i[e]+=this.Y[n][e]}for(let n=0;n<e;n++)for(let t=0;t<this.dim;t++)this.Y[n][t]-=i[t]/e;return t}debugGrad(){const e=this.N,n=this.costGrad(this.Y).grad,t=1e-5;for(let r=0;r<e;r++)for(let e=0;e<this.dim;e++){const i=this.Y[r][e];this.Y[r][e]=i+t;const a=this.costGrad(this.Y);this.Y[r][e]=i-t;const s=this.costGrad(this.Y),o=n[r][e],u=(a.cost-s.cost)/(2*t);console.log(r+","+e+": gradcheck analytic: "+o+" vs. numerical: "+u),this.Y[r][e]=i}}costGrad(e){const n=this.N,t=this.dim,r=this.P,i=this.iter<100?4:1;this.quArr??(this.quArr=this.zeros(n*n));let a=0;for(let r=0;r<n;r++)for(let i=r+1;i<n;i++){const s=1/(1+new Array(t).reduce(((n,t,a)=>n+Math.pow(e[r][a]-e[i][a],2)),0));this.quArr[r*n+i]=s,this.quArr[i*n+r]=s,a+=2*s}let s=0;const o=new Array(n).fill(null).map((()=>new Float32Array(t).fill(0)));for(let u=0;u<n;u++)for(let l=u+1;l<n;l++){const c=Math.max(this.quArr[u*n+l]/a,1e-100);s+=-r[u*n+l]*Math.log(c)*2;const f=4*(i*r[u*n+l]-c)*this.quArr[u*n+l];for(let n=0;n<t;n++)o[u][n]+=f*(e[u][n]-e[l][n]),o[l][n]+=f*(e[l][n]-e[u][n])}return{cost:s,grad:o}}}t(5540);let ve=null,Ae=null;function Se(){return e=this,n=void 0,r=function*(){if(!navigator.gpu)return console.error("WebGPU is not supported in this browser"),null;if(!ve&&(ve=yield navigator.gpu.requestAdapter({powerPreference:"high-performance"}),null==ve))return null;let e=!1;if(Ae&&(Ae.lost.then((()=>{e=!0})),yield new Promise((e=>setTimeout(e,10)))),!Ae||e){const e=1e9,n=ve.limits,t=n.maxBufferSize,r=n.maxStorageBufferBindingSize;try{return Ae=yield ve.requestDevice({requiredLimits:{maxBufferSize:Math.min(t,e),maxStorageBufferBindingSize:Math.min(r,e)}}),Ae}catch(e){return console.error("Failed to create device with required limits",e),Ae=yield ve.requestDevice(),Ae}}return Ae},new((t=void 0)||(t=Promise))((function(i,a){function s(e){try{u(r.next(e))}catch(e){a(e)}}function o(e){try{u(r.throw(e))}catch(e){a(e)}}function u(e){var n;e.done?i(e.value):(n=e.value,n instanceof t?n:new t((function(e){e(n)}))).then(s,o)}u((r=r.apply(e,n||[])).next())}));var e,n,t,r}var Ee,Ie;(Ie=Ee||(Ee={})).EUCLIDEAN="EUCLIDEAN",Ie.MANHATTAN="MANHATTAN";const Me={[Ee.EUCLIDEAN]:function(e){return`\n        var sum = 0.0;\n        for (var i = 0u; i < ${e}; i = i + 1u) {\n            sum = sum + distances[i] * distances[i] * computeInfo.weights[i] * computeInfo.weights[i];\n        }\n        return sqrt(sum);\n    `},[Ee.MANHATTAN]:function(e){return`\n        var sum = 0.0;\n        for (var i = 0u; i < ${e}; i = i + 1u) {\n            sum = sum + abs(distances[i]) * computeInfo.weights[i];\n        }\n        return sum;\n    `}};var Ne,Pe;(Pe=Ne||(Ne={})).HAMMING="Hamming",Pe.EUCLIDEAN="Euclidean",Pe.VECTOR_COSINE="Vector Cosine",Pe.MANHATTAN="Manhattan",Pe.TANIMOTO="Tanimoto",Pe.LEVENSTEIN="Levenshtein",Pe.NEEDLEMAN_WUNSCH="Needlemann-Wunsch",Pe.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",Pe.SOKAL="Sokal",Pe.COSINE="Cosine",Pe.ASYMMETRIC="Asymmetric",Pe.Difference="Difference",Pe.OneHot="One-Hot";const Ce={[Ne.HAMMING]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n  let sizeDiff: u32 = maxLength - minLength;\n  \n  let maxIntDistance = ceil(maxDistance * f32(maxLength)) - f32(sizeDiff);\n\n  var diff: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n      diff = diff + f32(a[i] != b[i]);\n      if (diff > maxIntDistance) {\n            return 1.0;\n        }\n  }\n  diff += f32(sizeDiff);\n  return diff / ${e};\n  `},[Ne.EUCLIDEAN]:function(e,n){return`\n  var dist: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n    dist = dist + f32(a[i] - b[i]) * f32(a[i] - b[i]);\n  }\n  return sqrt(dist);\n  `},[Ne.MANHATTAN]:function(e,n){return`\n  var dist: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n    dist = dist + abs(f32(a[i] - b[i]));\n  }\n  return dist;\n  `},[Ne.VECTOR_COSINE]:function(e,n){return`\n  var dist: f32 = 0.0;\n  var productSum: f32 = 0.0;\n  var aSquareSum: f32 = 0.0;\n  var bSquareSum: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n    productSum = productSum + f32(a[i] * b[i]);\n    aSquareSum = aSquareSum + f32(a[i] * a[i]);\n    bSquareSum = bSquareSum + f32(b[i] * b[i]);\n  }\n  var sim = productSum / (sqrt(aSquareSum) * sqrt(bSquareSum));\n  return (1.0 - sim) / 2.0;\n  `},[Ne.TANIMOTO]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n\n  if (onBitsa == 0u && onBitsb == 0u) {\n      return 0.0;\n  }\n\n  let totalOnBits = onBitsa + onBitsb;\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n\n  return 1.0 - f32(commonBits) / f32(totalOnBits - commonBits);\n  `},[Ne.LEVENSTEIN]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n\n  let maxIntDistance = ceil(maxDistance * f32(maxLength));\n\n  // we will store two arrays as matrix and swap the working indices per pass.\n  // this way we can reduce memory usage per computation to just O(aLength)\n  // the grid will have aLength + 1 columns and bLength + 1 rows\n  // this will be guaranteed by iteration, but the array sizes must be known at compile time, so we will use a fixed size of maxArraySize\n  var dynamicPassMat: array<array<f32, ${e+1}u>, 2>; // initialize to 0\n  \n  var prevIndex: u32 = 0;\n  var curIndex: u32 = 1; // we will swap these indices per pass\n\n  // initialize the first row\n  for (var i = 0u; i <= aLength; i = i + 1u) {\n      dynamicPassMat[prevIndex][i] = f32(i);\n  }\n\n  // iterate over the rows\n  for (var i = 1u; i <= bLength; i = i + 1u) {\n      dynamicPassMat[curIndex][0] = f32(i);\n      var minEntry: f32 = f32(maxLength);\n      let prevRow = &dynamicPassMat[prevIndex];\n      let curRow = &dynamicPassMat[curIndex];\n      let bMon = u32(b[i - 1]);\n      for (var j = 1u; j <= aLength; j = j + 1u) {\n          var cost: f32 = f32(a[j - 1] != bMon);\n          var res: f32 = min(\n              min(\n                (*prevRow)[j] + 1.0, // deletion\n                (*curRow)[j - 1] + 1.0, // insertion\n              ),\n              (*prevRow)[j - 1] + cost // substitution\n              );\n              (*curRow)[j] = res;\n          if (res < minEntry) {\n              minEntry = res;\n          }\n      }\n      // swap the indices\n      let temp: u32 = prevIndex;\n      prevIndex = curIndex;\n      curIndex = temp;\n      if (minEntry > maxIntDistance) {\n          return 1.0;\n      }\n  }\n\n  return dynamicPassMat[prevIndex][aLength] / f32(maxLength);\n  `},[Ne.NEEDLEMAN_WUNSCH]:function(e,n){return`\n      let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n      let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n      let maxLength: u32 = max(aLength, bLength);\n      let minLength: u32 = min(aLength, bLength);\n  \n      let maxIntDistance = ceil(maxDistance * f32(maxLength));\n      // we will store two arrays as matrix and swap the working indices per pass.\n      // this way we can reduce memory usage per computation to just O(aLength)\n      // the grid will have aLength + 1 columns and bLength + 1 rows\n      // this will be guaranteed by iteration, but the array sizes must be known at compile time, so we will use a fixed size of maxArraySize\n      var dynamicPassMat: array<array<f32, ${e+1}u>, 2>; // initialize to 0\n      \n      // we need to keep track of which operation led to the current cell\n      // i.e. whether we came from the left, top or diagonal to assign gap open/gap extend penalty\n      var verticalGaps: array<u32, ${e+1}u>;\n      var horizontalGaps: array<u32, ${e+1}u>;\n\n      let gapOpenPenalty: f32 = suppInfo.gapOpenPenalty${n};\n      let gapExtensionPenalty: f32 = suppInfo.gapExtensionPenalty${n};\n      var prevIndex: u32 = 0;\n      var curIndex: u32 = 1; // we will swap these indices per pass\n      // initialize the first row\n      for (var i = 0u; i <= aLength; i = i + 1u) {\n          dynamicPassMat[prevIndex][i] = gapExtensionPenalty + f32(i - 1) * gapExtensionPenalty; // accounting for the fact that left and right gaps are less costly\n          dynamicPassMat[curIndex][i] = 0.0;\n      }\n      dynamicPassMat[0][0] = 0.0;\n\n      let simMatrix = &suppInfo.similarityMatrix${n}; // using pointers make things faster\n      // iterate over the rows\n      for (var i = 1u; i <= bLength; i = i + 1u) {\n          let prevRow = &dynamicPassMat[prevIndex];\n          let curRow = &dynamicPassMat[curIndex];\n          (*curRow)[0] = gapExtensionPenalty + f32(i - 1) * gapExtensionPenalty;\n          var minEntry: f32 = f32(maxLength);\n          let monB = u32(b[i - 1]);\n          for (var j = 1u; j <= aLength; j = j + 1u) {\n              let monA = u32(a[j - 1]);\n              \n              let cost: f32 = (*prevRow)[j - 1] + 1f - (*simMatrix)[monA][monB];\n              var top = (*prevRow)[j]; // deletion\n              if (verticalGaps[j] > 0 || i == 1 || i == bLength) {\n                  top = top + gapExtensionPenalty;\n              } else {\n                  top = top + gapOpenPenalty;\n              }\n              var left = (*curRow)[j - 1]; // insertion\n              if (horizontalGaps[j - 1] > 0 || j == 1 || j == aLength) {\n                  left = left + gapExtensionPenalty;\n              } else {\n                  left = left + gapOpenPenalty;\n              }\n              var res: f32 = min(\n                  min(\n                      top, // deletion\n                      left, // insertion\n                  ),\n                  cost // substitution\n                  );\n                  (*curRow)[j] = res;\n              if (res < minEntry) {\n                  minEntry = res;\n              }\n              // update the horizontal and vertical gaps\n              if (res == cost) {\n                  verticalGaps[j] = 0;\n                  horizontalGaps[j] = 0;\n              } else if (res == left) {\n                  verticalGaps[j] = 0;\n                  horizontalGaps[j] = 1;\n              } else {\n                  verticalGaps[j] = 1;\n                  horizontalGaps[j] = 0;\n              }\n          }\n          // swap the indices\n          let temp: u32 = prevIndex;\n          prevIndex = curIndex;\n          curIndex = temp;\n          if (minEntry > maxIntDistance) {\n              return 1.0;\n          }\n      }\n      return dynamicPassMat[prevIndex][aLength] / f32(minLength);\n\n  `},[Ne.MONOMER_CHEMICAL_DISTANCE]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  let maxLength: u32 = max(aLength, bLength);\n  let minLength: u32 = min(aLength, bLength);\n  let sizeDiff: u32 = maxLength - minLength;\n  \n  let maxIntDistance = ceil(maxDistance * f32(maxLength)) - f32(sizeDiff);\n\n  let simMatrix = &(suppInfo.similarityMatrix${n}); // using pointers make things faster\n  var diff: f32 = 0.0;\n  for (var i = 0u; i < ${e}; i = i + 1u) {\n      diff = diff + 1.0 - (*simMatrix)[u32(a[i])][u32(b[i])];\n      if (diff > maxIntDistance) {\n            return 1.0;\n        }\n  }\n  diff += f32(sizeDiff);\n  return diff / ${e};\n  `},[Ne.SOKAL]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let total = onBitsa + onBitsb;\n  if (total == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / f32(total * 2 - commonBits * 3);\n  `},[Ne.COSINE]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let total = onBitsa * onBitsb; // p.s. here total is taken by multiplying\n  if (total == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / sqrt(f32(total));\n  `},[Ne.ASYMMETRIC]:function(e,n){return`\n  var onBitsa: u32 = 0u;\n  var onBitsb: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      onBitsa = onBitsa + countOneBits(a[i]);\n      onBitsb = onBitsb + countOneBits(b[i]);\n  }\n  let min = min(onBitsa, onBitsb);\n  if (min == 0u) {\n    return 1.0;\n  }\n  var commonBits: u32 = 0u;\n  for (var i = 0u; i < ${e}u; i = i + 1u) {\n      commonBits = commonBits + countOneBits(a[i] & b[i]);\n  }\n  return 1.0 - f32(commonBits) / f32(min);\n  `},[Ne.Difference]:function(e,n){return`\n    let range = suppInfo.range${n};\n    return f32(abs(f32(a[0]) - f32(b[0])) / range);\n  `},[Ne.OneHot]:function(e,n){return`\n  let aLength: u32 = computeInfo.entrySizes[${n}][aIndex];\n  let bLength: u32 = computeInfo.entrySizes[${n}][bIndex];\n  if (aLength != bLength) {\n    return 1.0;\n  }\n  for (var i = 0u; i < aLength; i = i + 1u) {\n    if(a[i] != b[i]) {\n      return 1.0;\n    }\n  }\n  return 0.0;\n  `}},De={[Ne.HAMMING]:e=>Math.ceil(e/30),[Ne.EUCLIDEAN]:e=>Math.ceil(e/30),[Ne.MANHATTAN]:e=>Math.ceil(e/30),[Ne.TANIMOTO]:e=>Math.ceil(e/30),[Ne.SOKAL]:e=>Math.ceil(e/30),[Ne.COSINE]:e=>Math.ceil(e/30),[Ne.ASYMMETRIC]:e=>Math.ceil(e/30),[Ne.LEVENSTEIN]:e=>Math.ceil(e*e/60),[Ne.NEEDLEMAN_WUNSCH]:e=>Math.ceil(e*e/60),[Ne.MONOMER_CHEMICAL_DISTANCE]:e=>Math.ceil(e/25),[Ne.Difference]:e=>1,[Ne.OneHot]:e=>Math.ceil(e/40),[Ne.VECTOR_COSINE]:e=>Math.ceil(e/30)},ke={STRING:new Set([Ne.HAMMING,Ne.LEVENSTEIN,Ne.NEEDLEMAN_WUNSCH,Ne.MONOMER_CHEMICAL_DISTANCE,Ne.OneHot]),UINT32ARRAY:new Set([Ne.HAMMING,Ne.EUCLIDEAN,Ne.MANHATTAN,Ne.MONOMER_CHEMICAL_DISTANCE,Ne.LEVENSTEIN,Ne.NEEDLEMAN_WUNSCH,Ne.TANIMOTO,Ne.COSINE,Ne.VECTOR_COSINE,Ne.SOKAL,Ne.ASYMMETRIC,Ne.OneHot,Ne.Difference]),INT32ARRAY:new Set([Ne.EUCLIDEAN,Ne.MANHATTAN,Ne.OneHot,Ne.Difference,Ne.VECTOR_COSINE]),FLOAT32ARRAY:new Set([Ne.EUCLIDEAN,Ne.MANHATTAN,Ne.Difference,Ne.VECTOR_COSINE]),NUMBER:new Set([Ne.EUCLIDEAN,Ne.MANHATTAN,Ne.Difference]),BITARRAY:new Set([Ne.TANIMOTO,Ne.COSINE,Ne.SOKAL,Ne.ASYMMETRIC])};var Re,Ue,Oe;function Te(e,n=15,t,r,i,a){return s=this,o=void 0,l=function*(){if(a.length!==e.length||a.length!==t.length||a.length!==i.length)throw new Error("Options, weigths and distance functions must be provided for each column");if(e.some((n=>n.length!==e[0].length)))throw new Error("All entry lists must be the same length");const s=Object.values(Ne);if(t.some((e=>!s.includes(e))))throw new Error("Invalid distance metrics provided: "+t.join(", "));if(!Object.values(Ee).includes(r))throw new Error("Invalid aggregation function provided: "+r);const o=e.length;if(0===o)throw new Error("No columns provided. Please provide at least one column of data.");const u=yield Se();if(!u)return null;let l=!1;u.lost.then((()=>{l=!0}));const c=e[0].length,f=e.map(((e,n)=>function(e,n=Ne.HAMMING,t,r={gapOpenPenalty:1,gapExtensionPenalty:.6}){var i,a;let s=null;const o=e.some((e=>"string"==typeof e))?(s="STRING",e.map((e=>new Uint32Array(e.split("").map((e=>e.charCodeAt(0))))))):e.some((e=>"number"==typeof e))?(s="NUMBER",e.map((e=>new Float32Array([e])))):"object"==typeof e[0]&&e.some((e=>"_data"in e&&"_length"in e))?(s="BITARRAY",e.map((e=>e._data))):e.some((e=>e instanceof Float32Array))?(s="FLOAT32ARRAY",e):e.some((e=>e instanceof Uint32Array))?(s="UINT32ARRAY",e):e.some((e=>e instanceof Int32Array))?(s="INT32ARRAY",e):void 0;if(!o||!s)throw new Error("Invalid entry type, could not determine entry type from input list");const u=o[0]instanceof Int32Array?"INT32ARRAY":o[0]instanceof Float32Array?"FLOAT32ARRAY":"UINT32ARRAY",l=new Uint32Array(o.map((e=>e.length)));if(!ke[s]||!ke[s].has(n))throw new Error(`Distance metric '${n}' not supported for entry type '${s}'`);const c=l.reduce(((e,n)=>Math.max(e,n)),0),f=De[n](c),h="INT32ARRAY"===u?Int32Array:"FLOAT32ARRAY"===u?Float32Array:Uint32Array,d=new h(o.length*c);o.forEach(((e,n)=>{d.set(e,n*c)}));let p="",m=0,g="FLOAT32ARRAY",y=null;if(n===Ne.NEEDLEMAN_WUNSCH||n===Ne.MONOMER_CHEMICAL_DISTANCE){let e=r.scoringMatrix&&r.alphabetIndexes?Object.keys(r.alphabetIndexes).reduce(((e,n)=>Math.max(e,n.charCodeAt(0))),0):-1;if(!r.alphabetIndexes||!r.scoringMatrix){for(let n=0;n<d.length;n++)d[n]>e&&(e=d[n]);r.scoringMatrix=new Array(e+1).fill(null).map((()=>new Array(e+1).fill(0))),r.alphabetIndexes={};for(let e=0;e<r.scoringMatrix.length;e++)r.scoringMatrix[e][e]=1,r.alphabetIndexes[String.fromCharCode(e)]=e}const n=(e+1)*(e+1),s=new Array(e+1).fill(null).map((()=>new Float32Array(e+1)));for(let n=0;n<e+1;n++)s[n][n]=1;const o=r.alphabetIndexes;for(const e of Object.keys(o))for(const n of Object.keys(o))e!==n&&(s[e.charCodeAt(0)][n.charCodeAt(0)]=r.scoringMatrix[o[e]][o[n]]);m=2+n,g="FLOAT32ARRAY",y=new Float32Array(m),y[0]=null!==(i=r.gapOpenPenalty)&&void 0!==i?i:1,y[1]=null!==(a=r.gapExtensionPenalty)&&void 0!==a?a:.6;let u=2;for(let e=0;e<s.length;e++)y.set(s[e],u),u+=s[e].length;p=`\n            gapOpenPenalty${t}: f32,\n            gapExtensionPenalty${t}: f32,\n            similarityMatrix${t}: array<array<f32, ${e+1}>, ${e+1}>`}else if(n===Ne.Difference){if(!r.range||"number"!=typeof r.range||r.range<=0){const e=d.reduce(((e,n)=>Math.min(e,n)),d[0]),n=d.reduce(((e,n)=>Math.max(e,n)),d[0]);r.range=n-e}r.range<=0&&(r.range=1),m=1,g="FLOAT32ARRAY",y=new Float32Array([r.range]),p=`\n            range${t}: f32`}const w=d instanceof Int32Array?"i32":d instanceof Float32Array?"f32":"u32",b=`data${t}: array<array<${w}, ${c}>, ${o.length}>`;return{flatSourceArray:d,sourceArraySize:d.length,maxEntryLen:c,arraySizes:l,complexity:f,suppInfoBuffer:y,suppInfoSize:m,suppInfoType:g,suppInfoStructWgsl:p,entryType:s,dataTypeWGSL:w,dataStructWgsl:b,EncodedArrayConstructor:h}}(e,t[n],n,a[n])));1===o&&(r=Ee.MANHATTAN);let h=f.map((e=>e.suppInfoStructWgsl)).filter((e=>!!e&&""!=e)).join(",\n"),d=!1;h&&""!=h.trim()||(d=!0,h="\ndummy: f32\n");const p=f.reduce(((e,n)=>e+n.complexity),0),m=f.map((e=>e.dataStructWgsl)).filter((e=>!!e&&""!=e)).join(",\n"),g=new Uint32Array(o*c);f.forEach(((e,n)=>{g.set(e.arraySizes,n*c)}));const y=1e4,w=Math.ceil(1e4/p),b=Math.ceil(Math.sqrt(Math.ceil(100))),x=10*b,v=new Array(c).fill(null).map((()=>new Uint32Array(n))),A=new Array(c).fill(null).map((()=>new Float32Array(n))),S=u.createShaderModule({label:"KNN compute shader",code:`\n          // this struct will contain all the info about the computation, startAtEndAt will contain the start and end of the knnDistances and knnIndexes.\n          // array of sizes for each entries, and the main data as arrays of arrays called data0, data1 and so on. good thing is that because the first entry is vec4<u32>,\n          // there will be no paddings, so no need to worry about padding data. also, arrays and matrices get stucked together, so no padding there as well.\n          // what we need to worry about is the padding of overall struct. the size of overall struct will be factor of 16 bytes, so keep that in mind.\n          struct ComputeInfo {\n            // the x coordinate will contain the start index of the knnDistances and knnIndexes, while y will contain the end index   \n            // the z coordinate will contain the start of the pair comparisons, while w will contain the end of the pair comparisons\n            // just keep in mind that this vec4 will be in first 16 bytes of corresponding buffer.\n            startAtEndAt: vec4<u32>,\n            // the ACTUALLY sizes of each entry\n            entrySizes: array<array<u32, ${c}>, ${o}>,\n            // the weights for each entry\n            weights: array<f32, ${o}>,\n            // the data for each entry\n            ${m} // an example of the dataWgsl would be:\n            //data0: array<array<u32,20>,100>,\n            //data1: array<array<u32,20>,100>\n          };\n\n          struct SuppInfo {\n            // struct containing all the supplementary info, like scoring matrix, alphabet indexes, range, etc.\n            ${h}\n          };\n    \n          @group(0) @binding(0) var<storage, read_write> knnIndexes: array<array<u32, ${n}>, 10000>;\n          @group(0) @binding(1) var<storage, read_write> knnDistances: array<array<f32, ${n}>, 10000>; // each time just compute for a subset of the list\n          @group(0) @binding(2) var<storage, read_write> computeInfo: ComputeInfo;\n          @group(0) @binding(3) var<storage, read_write> suppInfo: SuppInfo;\n          \n          @compute @workgroup_size(10, 10) fn calcKNN(\n            @builtin(global_invocation_id) id: vec3<u32>\n          ) {\n            ${d?"let otherDummy = suppInfo.dummy * 2;":""} // just to make sure that the suppInfo is not optimized out\n            let col = id.x; //* 10 + localId.x;\n            let row = id.y; //* 10 + localId.y;\n            let graphIndex = row * ${x} + col;\n            let index = graphIndex + computeInfo.startAtEndAt.x; // add the starting index of the knnDistances and knnIndexes\n    \n            if (index >= min(${c}u, computeInfo.startAtEndAt.y)) {return;}\n    \n            let pairComparisonStartAt = computeInfo.startAtEndAt.z;\n            let pairComparisonEndAt = min(computeInfo.startAtEndAt.w, ${c}u);\n    \n    \n            // only clear the knnDistances and knnIndexes if we are at the start of the pair comparison\n            if (pairComparisonStartAt == 0u) {\n              for (var i = 0u; i < ${n}; i = i + 1u) {\n                knnDistances[graphIndex][i] = 99999.0;\n                knnIndexes[graphIndex][i] = 0u;\n              }\n            }\n    \n            for (var i: u32 = pairComparisonStartAt; i < pairComparisonEndAt; i = i + 1u) {\n              if (i == index) {continue;}\n              let dist = combinedDistance(index, i);\n              insertKnn(graphIndex, dist, i);\n            }\n            \n          }\n          // this will generate the distance script for each distance metric and then combine them into one\n          ${Be(t,f.map((e=>e.maxEntryLen)),n,r)}\n    \n          fn insertKnn(knnIndex: u32, dist: f32, index: u32) {\n            // small optimization, if the distance is larger than the last element in the knnDistances, we can skip\n            if (dist >= knnDistances[knnIndex][${n} - 1u]) {return;}\n            for (var i = 0u; i < ${n}; i = i + 1u) {\n              if (dist < knnDistances[knnIndex][i]) {\n                for (var j = ${n} - 1u; j > i; j = j - 1u) {\n                  knnDistances[knnIndex][j] = knnDistances[knnIndex][j - 1u];\n                  knnIndexes[knnIndex][j] = knnIndexes[knnIndex][j - 1u];\n                }\n                knnDistances[knnIndex][i] = dist;\n                knnIndexes[knnIndex][i] = index;\n                return;\n              }\n            }\n          }\n        `}),E=u.createComputePipeline({label:"hamming compute pipeline",layout:"auto",compute:{module:S,entryPoint:"calcKNN"}}),I=4+o*c+o+f.reduce(((e,n)=>e+n.sourceArraySize),0),M=f.reduce(((e,n)=>e+n.suppInfoSize),0),N=I*Uint32Array.BYTES_PER_ELEMENT;let P=N;const C=15&N;0!==C&&(P+=16-C);const D=u.createBuffer({label:"compute info buffer",size:P,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),k=D.getMappedRange();let R=0,U=y,O=0,T=w,B=0;new Uint32Array(k,B,4).set([R,U,O,T]),B+=4*Uint32Array.BYTES_PER_ELEMENT,new Uint32Array(k,B,g.length).set(g),B+=g.byteLength,new Float32Array(k,B,o).set(i),B+=o*Float32Array.BYTES_PER_ELEMENT;for(const e of f){const n=e.EncodedArrayConstructor,t=e.sourceArraySize;new n(k,B,t).set(e.flatSourceArray),B+=t*n.BYTES_PER_ELEMENT}D.unmap();const _=M*Uint32Array.BYTES_PER_ELEMENT;let z=_;const L=15&_;0!==L&&(z+=16-L),z=Math.max(z,16);const G=u.createBuffer({label:"supp info buffer",size:z,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),$=G.getMappedRange();let F=0;for(const e of f)e.suppInfoBuffer&&e.suppInfoBuffer.byteLength>0&&e.suppInfoSize>0&&(new("UINT32ARRAY"===e.suppInfoType?Uint32Array:Float32Array)($,F,e.suppInfoBuffer.length).set(e.suppInfoBuffer),F+=e.suppInfoBuffer.byteLength);0===F&&new Uint32Array($,0,4).set([1,1,1,1]),G.unmap();const j=n*Uint32Array.BYTES_PER_ELEMENT*y,Y=u.createBuffer({label:"buffer distances",size:j,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),q=u.createBuffer({label:"buffer indexes",size:j,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),V=n*Uint32Array.BYTES_PER_ELEMENT,K=u.createBindGroup({label:"bindGroup for knn buffer",layout:E.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:q}},{binding:1,resource:{buffer:Y}},{binding:2,resource:{buffer:D}},{binding:3,resource:{buffer:G}}]}),W=u.createBuffer({label:"result buffer distances",size:Y.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST}),H=u.createBuffer({label:"result buffer indexes",size:q.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});for(let e=0;e<Math.ceil(c/y);e++){R=e*y,U=Math.min((e+1)*y,c);const t=Math.ceil(c/w);for(let e=0;e<t;e++){O=e*w,T=Math.min((e+1)*w,c),u.queue.writeBuffer(D,0,new Uint32Array([R,U,O,T]));const r=u.createCommandEncoder({label:"distance encoder"}),i=r.beginComputePass({label:"distance compute pass"});if(i.setPipeline(E),i.setBindGroup(0,K),i.dispatchWorkgroups(b,Math.ceil(y/b/100)),i.end(),e===t-1){r.copyBufferToBuffer(Y,0,W,0,W.size),r.copyBufferToBuffer(q,0,H,0,H.size);const e=r.finish();u.queue.submit([e]),yield u.queue.onSubmittedWorkDone(),yield W.mapAsync(GPUMapMode.READ),yield H.mapAsync(GPUMapMode.READ);const t=H.getMappedRange(),i=W.getMappedRange();for(let e=0;e<U-R;e++){const r=new Uint32Array(t,e*V,n),a=new Float32Array(i,e*V,n);v[R+e].set(r),A[R+e].set(a)}H.unmap(),W.unmap()}else{const e=r.finish();u.queue.submit([e]),yield u.queue.onSubmittedWorkDone()}if(l)return null}}return Y.destroy(),q.destroy(),D.destroy(),G.destroy(),W.destroy(),H.destroy(),l?null:{knnIndexes:v,knnDistances:A}},new((u=void 0)||(u=Promise))((function(e,n){function t(e){try{i(l.next(e))}catch(e){n(e)}}function r(e){try{i(l.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof u?i:new u((function(e){e(i)}))).then(t,r)}i((l=l.apply(s,o||[])).next())}));var s,o,u,l}function Be(e,n,t,r){return e.map(((e,r)=>`\n        fn distanceScript${r}(aIndex: u32, bIndex: u32) -> f32 {\n          let a = computeInfo.data${r}[aIndex];\n          let b = computeInfo.data${r}[bIndex];\n          let maxDistance: f32 = knnDistances[aIndex - computeInfo.startAtEndAt.x][${t} - 1u];\n          ${Ce[e](n[r],r)}\n        }\n      `)).join("\n")+"\n"+`\n      fn combinedDistance(aIndex: u32, bIndex: u32) -> f32 {\n        var distances: array<f32, ${e.length}>;\n        ${e.map(((e,n)=>`distances[${n}] = distanceScript${n}(aIndex, bIndex);`)).join("\n")}\n        ${Me[r](e.length)}\n      }\n    \n    `}!function(e){e.ADD="ADD",e.SUB="SUB",e.MULT="MULT"}(Re||(Re={})),function(e){e.SQUARE="SQUARE",e.INVERSE="INVERSE",e.TRANSPOSE="TRANSPOSE",e.NORM="NORM",e.COLUMN_NORM="COLUMN_NORM"}(Ue||(Ue={})),function(e){e.SCALARMULT="SCALARMULT",e.SCALARADD="SCALARADD",e.SCALARPOW="SCALARPOW"}(Oe||(Oe={}));function _e(e,n,t,r,i,a,s,o,u){return l=this,c=void 0,h=function*(){const l=Math.ceil(s/100),c=Math.ceil(Math.sqrt(l)),f=10*c,h=t[t.length-1],d=a[a.length-1],p=o[o.length-1],m=`\n        struct SparseKNNStorage1 {\n            indexes:array<i32, ${h}>,\n            knnDistances: array<f32, ${h}>,\n            offsets: array<u32, ${s+1}>\n        }\n\n        struct SparseKNNStorage2 {\n            indexes:array<i32, ${d}>,\n            knnDistances: array<f32, ${d}>,\n            offsets: array<u32, ${s+1}>\n        }\n\n        struct ResKnn {\n            knnIndexes: array<i32, ${p}>,\n            knnDistances: array<f32, ${p}>\n        }\n\n        @group(0) @binding(0) var<storage, read_write> source1: SparseKNNStorage1;\n        @group(0) @binding(1) var<storage, read_write> source2: SparseKNNStorage2;\n        @group(0) @binding(2) var<storage, read_write> result: ResKnn;\n        @group(0) @binding(3) var<storage, read_write> unionMatrixOffsets: array<u32, ${s+1}>;\n        @compute @workgroup_size(10, 10) fn pairwiseOp(\n            @builtin(global_invocation_id) id: vec3<u32>,\n        ) {\n\n            let col: u32 = id.x;\n            let row: u32 = id.y;\n            let workingIndex: u32 = row * ${f} + col;\n\n            if (workingIndex >= ${s}) {\n                return;\n            }\n            var curUnionOffset: u32 = unionMatrixOffsets[workingIndex]; // offset at which to start writing in union matrix\n\n            let start1 = source1.offsets[workingIndex];\n            let end1 = source1.offsets[workingIndex + 1];\n            let start2 = source2.offsets[workingIndex];\n            let end2 = source2.offsets[workingIndex + 1];\n            // TODO: sort a copy of these arrays, will make operation faster\n            for (var i: u32 = start1; i < end1; i++) {\n                let val1: f32 = source1.knnDistances[i];\n                var val2: f32 = 0.0;\n                let curIndex: i32 = source1.indexes[i];\n                for (var j: u32 = start2; j < end2; j++) {\n                    if (source2.indexes[j] == curIndex) {\n                        val2 = source2.knnDistances[j];\n                        break;\n                    }\n                }\n                \n                result.knnIndexes[curUnionOffset] = curIndex;\n                result.knnDistances[curUnionOffset] = val1 ${u} val2;\n                curUnionOffset += 1;\n            }\n\n            if (curUnionOffset >= unionMatrixOffsets[workingIndex + 1]) {\n                // small optimization applicable only to our case, but saves a good amount of time\n                return;\n            }\n\n            // do the same for source2 but skip the indexes where they are already present in source1\n            for (var i: u32 = start2; i < end2; i++) {\n                let val1: f32 = source2.knnDistances[i];\n                let curIndex: i32 = source2.indexes[i];\n                var found = false;\n                for (var j: u32 = start1; j < end1; j++) {\n                    if (source1.indexes[j] == curIndex) {\n                        found = true;\n                        break;\n                    }\n                }\n                if (!found) {\n                    result.knnIndexes[curUnionOffset] = curIndex;\n                    result.knnDistances[curUnionOffset] = val1 ${u} 0.0;\n                    curUnionOffset += 1;\n                }\n            }\n        }\n`;let g=4*(2*h+s+1);const y=15&g;0!==y&&(g+=16-y);let w=4*(2*d+s+1);const b=15&w;0!==b&&(w+=16-b);let x=2*p*4;const v=15&x;0!==v&&(x+=16-v);const A=yield Se();if(null==A)return;const S=A.createShaderModule({label:"pairwiseOpShader",code:m}),E=A.createComputePipeline({label:"pairwiseOpPipeline",layout:"auto",compute:{module:S,entryPoint:"pairwiseOp"}}),I=A.createBuffer({label:"source 1 buffer",size:g,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),M=I.getMappedRange();new Int32Array(M,0,h).set(e),new Float32Array(M,4*h,h).set(n),new Uint32Array(M,8*h,s+1).set(t),I.unmap();const N=A.createBuffer({label:"source 2 buffer",size:w,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),P=N.getMappedRange();new Int32Array(P,0,d).set(r),new Float32Array(P,4*d,d).set(i),new Uint32Array(P,8*d,s+1).set(a),N.unmap();const C=A.createBuffer({label:"res buffer",size:x,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST}),D=A.createBuffer({label:"union matrix offsets buffer",size:4*(s+1),usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),k=D.getMappedRange();new Uint32Array(k).set(o),D.unmap();const R=A.createBindGroup({label:"bindGroup for pairwise ops",layout:E.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:I}},{binding:1,resource:{buffer:N}},{binding:2,resource:{buffer:C}},{binding:3,resource:{buffer:D}}]}),U=A.createCommandEncoder({label:"matrix ops encoder"}),O=U.beginComputePass({label:"matrix ops 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r=0;r<e.length;r++)n[r]=t,t+=e[r];return n[e.length]=t,n}function je(e,n){for(let t=0;t<e.length;t++)e[t]=e[t]*n}function Ye(e,n,t=1){return r=this,i=void 0,s=function*(){const r=new Int32Array(e.length*e[0].length),i=new Float32Array(n.length*n[0].length);for(let t=0;t<e.length;t++)r.set(e[t],t*e[t].length),i.set(n[t],t*n[t].length);const a=yield function(e){return n=this,t=void 0,i=function*(){const n=e.length,t=Math.ceil(n/100),r=Math.ceil(Math.sqrt(t)),i=e[0].length,a=function(e,n,t,r=15){return`\n\n        @group(0) @binding(0) var<storage, read_write> knnIndexes: array<array<i32, ${r}>, ${t}>;\n        @group(0) @binding(1) var<storage, read_write> resTransposedSizes: array<atomic<u32>, ${t}>;\n        // this array will store the union of knn and its transpose sizes per index. should be initialized to knnSize each.\n        @group(0) @binding(2) var<storage, read_write> resUnionMatrixSizes: array<atomic<u32>, ${t}>;\n\n        @compute @workgroup_size(${e}, ${e}) fn countTransposedCols(\n            @builtin(global_invocation_id) id: vec3<u32>,\n         ) {\n            let col: u32 = id.x;\n            let row: u32 = id.y;\n            let workingIndex: u32 = row * ${n} + col;\n\n            if (workingIndex >= ${t}) {\n                return;\n            }\n            \n            for (var i = 0u; i < ${r}u; i++) {\n                let otherIndex: i32 = knnIndexes[workingIndex][i];\n                if (otherIndex != -1 && otherIndex < ${t}) {\n                    atomicAdd(&resTransposedSizes[otherIndex], 1u);\n                    atomicAdd(&resUnionMatrixSizes[otherIndex], 1u);\n                    let otherIndexes = &knnIndexes[otherIndex];\n                    for(var j = 0u; j < ${r}; j++) {\n                        if ((*otherIndexes)[j] == i32(workingIndex)) {\n                            atomicSub(&resUnionMatrixSizes[workingIndex], 1u);\n                            // if same is found in other array, decrement by one;\n                            break;\n                        }\n                    }\n                }\n\n            }\n         }\n    `}(10,10*r,n,i),s=n*e[0].length,o=yield Se();if(null==o)return;const u=o.createShaderModule({label:"transposedSizesCalulation",code:a}),l=o.createComputePipeline({label:"transposedSizesPipeline",layout:"auto",compute:{module:u,entryPoint:"countTransposedCols"}}),c=o.createBuffer({label:"indexes buffer",size:4*s,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),f=c.getMappedRange(),h=new Int32Array(f);for(let n=0;n<e.length;n++)h.set(e[n],n*e[n].length);c.unmap();const d=o.createBuffer({label:"transpose sizes buffer",size:4*e.length,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST}),p=o.createBuffer({label:"union sizes buffer",size:4*e.length,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),m=p.getMappedRange();new Uint32Array(m).fill(i),p.unmap();const g=o.createBindGroup({label:"bindGroup for count ops",layout:l.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:c}},{binding:1,resource:{buffer:d}},{binding:2,resource:{buffer:p}}]}),y=o.createCommandEncoder({label:"matrix ops encoder"}),w=y.beginComputePass({label:"matrix ops compute pass"});w.setPipeline(l),w.setBindGroup(0,g),w.dispatchWorkgroups(r,r),w.end();const b=o.createBuffer({label:"result transpose sizes",size:d.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST}),x=o.createBuffer({label:"result union sizes",size:p.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});y.copyBufferToBuffer(d,0,b,0,b.size),y.copyBufferToBuffer(p,0,x,0,x.size);const v=y.finish();o.queue.submit([v]),yield o.queue.onSubmittedWorkDone(),yield b.mapAsync(GPUMapMode.READ),yield x.mapAsync(GPUMapMode.READ);const A=b.getMappedRange(),S=x.getMappedRange(),E=new Uint32Array(e.length);E.set(new Uint32Array(A,0,e.length)),b.unmap();const I=new Uint32Array(e.length);I.set(new Uint32Array(S,0,e.length)),x.unmap();const M=I.reduce(((e,n)=>e+n),0);return x.destroy(),b.destroy(),d.destroy(),c.destroy(),p.destroy(),{resultTransposeSizesArray:E,resultUnionSizesArray:I,unionMatrixSize:M}},new((r=void 0)||(r=Promise))((function(e,a){function s(e){try{u(i.next(e))}catch(e){a(e)}}function o(e){try{u(i.throw(e))}catch(e){a(e)}}function u(n){var t;n.done?e(n.value):(t=n.value,t instanceof r?t:new r((function(e){e(t)}))).then(s,o)}u((i=i.apply(n,t||[])).next())}));var n,t,r,i}(e),s=e.length,o=yield function(e,n,t,r=15){return i=this,a=void 0,o=function*(){const i=e.length,a=r*i,s=Fe(t.resultTransposeSizesArray),o=new Uint32Array(s.length);o.set(s);const u=new Int32Array(a).fill(0),l=new Float32Array(a).fill(0);for(let t=0;t<i;t++)for(let i=0;i<r;i++){const r=e[t][i],a=o[r];u[a]=t,l[a]=n[t][i],o[r]+=1}return{transposeKNNIndexes:u,transposeKNNDistances:l,transposeOffsets:s}},new((s=void 0)||(s=Promise))((function(e,n){function t(e){try{u(o.next(e))}catch(e){n(e)}}function r(e){try{u(o.throw(e))}catch(e){n(e)}}function u(n){var i;n.done?e(n.value):(i=n.value,i instanceof s?i:new s((function(e){e(i)}))).then(t,r)}u((o=o.apply(i,a||[])).next())}));var i,a,s,o}(e,n,a,n[0].length),u=Fe(new Uint32Array(s).fill(e[0].length)),l=Fe(a.resultUnionSizesArray),c=yield _e(r,i,u,o.transposeKNNIndexes,o.transposeKNNDistances,o.transposeOffsets,s,l,"*"),f=yield _e(r,i,u,o.transposeKNNIndexes,o.transposeKNNDistances,o.transposeOffsets,s,l,"+"),h=yield _e(f.resultKnnIndexes,f.resultKnnDistances,l,c.resultKnnIndexes,c.resultKnnDistances,l,s,l,"-");return 1!==t?(je(h.resultKnnDistances,t),je(c.resultKnnDistances,1-t),{res:yield _e(h.resultKnnIndexes,h.resultKnnDistances,l,c.resultKnnIndexes,c.resultKnnDistances,l,s,l,"+"),unionMatrixOffsets:l}):{res:h,unionMatrixOffsets:l,unionSizes:a.resultUnionSizesArray}},new((a=void 0)||(a=Promise))((function(e,n){function t(e){try{u(s.next(e))}catch(e){n(e)}}function o(e){try{u(s.throw(e))}catch(e){n(e)}}function u(n){var r;n.done?e(n.value):(r=n.value,r instanceof a?r:new a((function(e){e(r)}))).then(t,o)}u((s=s.apply(r,i||[])).next())}));var r,i,a,s}function qe(e,n=15,t=1,r=64,i=1){return a=this,s=void 0,u=function*(){const a=e.length,s=Math.ceil(a/100),o=Math.ceil(Math.sqrt(s)),u=function(e=10,n,t,r=15,i=1,a=64,s=1){const o=t.length;let u=0;for(let e=0;e<o;e++){let n=0;for(let i=0;i<r;i++)n+=t[e][i];u+=n/r}return`  \n        var<private> SMOOTH_K_TOLERANCE: f32 = 1e-5;\n        var<private> MIN_K_DIST_SCALE: f32 = 1e-3;\n        var<private> nNeighbors: u32 = ${r};\n        var<private> localConnectivity: f32 = ${i}; \n        var<private> nIter: u32 = ${a};\n        var<private> bandwidth: u32 = ${s};\n        var<private> meanDistances: f32 = ${u/o};\n        var<private> targetValue: f32 = ${Math.log(r)/Math.log(2)*s};\n        @group(0) @binding(0) var<storage, read_write> sigmas: array<f32, ${o}>;\n        @group(0) @binding(1) var<storage, read_write> rhos: array<f32, ${o}>;\n        @group(0) @binding(2) var<storage, read> distances: array<array<f32, ${r}>, ${o}>;\n        @compute @workgroup_size(${e}, ${e}) fn smoothKNNDistance(\n            @builtin(global_invocation_id) id: vec3<u32>,\n        ) {\n            let col: u32 = id.x;\n            let row: u32 = id.y;\n            let workingIndex: u32 = row * ${n} + col;\n\n            if (workingIndex >= ${o}) {\n                return;\n            }\n\n            var lo: f32 = 0.0;\n            var hi: f32 = 1.0e+30; // treated as Infinity\n            var mid: f32 = 1.0;\n\n            var nonZeroDists: array<f32, ${r}>;\n            var nonZeroDistsSize: u32 = 0;\n            for (var j = 0u; j < nNeighbors; j = j + 1u) {\n                if (distances[workingIndex][j] > 0.0) {\n                    nonZeroDists[nonZeroDistsSize] = distances[workingIndex][j];\n                    nonZeroDistsSize = nonZeroDistsSize + 1u;\n                }\n            }\n\n            if (f32(nonZeroDistsSize) >= localConnectivity) {\n                let index: u32 = u32(floor(localConnectivity));\n                let interpolation: f32 = localConnectivity - f32(index);\n                if (index > 0) {\n                    rhos[workingIndex] = nonZeroDists[index - 1];\n                    if (interpolation > SMOOTH_K_TOLERANCE) {\n                        rhos[workingIndex] += interpolation * (nonZeroDists[index] - nonZeroDists[index - 1]);\n                    }\n                }\n                else {\n                    rhos[workingIndex] = interpolation * nonZeroDists[0];\n                }\n            }\n            else if (nonZeroDistsSize > 0u) {\n                var maxDist: f32 = 0.0;\n                for (var j = 0u; j < nonZeroDistsSize; j = j + 1u) {\n                    maxDist = max(nonZeroDists[j], maxDist);\n                }\n                rhos[workingIndex] = maxDist;\n            }\n\n            for (var n = 0u; n < nIter; n = n + 1u) {\n                var psum: f32 = 0.0;\n                for (var j = 1u; j < ${r}; j = j + 1u) {\n                    let d: f32 = distances[workingIndex][j] - rhos[workingIndex];\n                    if (d > 0.0) {\n                        psum += exp(0.0 - (d / mid));\n                    }\n                    else {\n                        psum += 1.0;\n                    }\n                }\n\n                if (abs(psum - targetValue) < SMOOTH_K_TOLERANCE) {\n                    break;\n                }\n\n                if (psum > targetValue) {\n                    hi = mid;\n                    mid = (lo + hi) / 2.0;\n                }\n                else {\n                    lo = mid;\n                    if (hi == 1.0e+30) {\n                        mid *= 2.0;\n                    }\n                    else {\n                        mid = (lo + hi) / 2.0;\n                    }\n                }\n            }\n\n            sigmas[workingIndex] = mid;\n\n            if (rhos[workingIndex] > 0.0) {\n                var sum: f32 = 0.0;\n                for (var j = 0u; j < ${r}; j = j + 1u) {\n                    sum += distances[workingIndex][j];\n                }\n                let meanIthDistances: f32 = sum / ${r}.0;\n                if (sigmas[workingIndex] < MIN_K_DIST_SCALE * meanIthDistances) {\n                    sigmas[workingIndex] = MIN_K_DIST_SCALE * meanIthDistances;\n                }\n            }\n            else {\n                if (sigmas[workingIndex] < MIN_K_DIST_SCALE * meanDistances) {\n                    sigmas[workingIndex] = MIN_K_DIST_SCALE * meanDistances;\n                }\n            }\n        }\n    `}(10,10*o,e,n,t,r,i),l=a*e[0].length,c=yield Se();if(null==c)return;const f=new Float32Array(a),h=new Float32Array(a),d=c.createShaderModule({label:"sigmaRhoCalulation",code:u}),p=c.createComputePipeline({label:"sigmaRhoPipeline",layout:"auto",compute:{module:d,entryPoint:"smoothKNNDistance"}}),m=c.createBuffer({label:"distance buffer",size:4*l,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),g=m.getMappedRange(),y=new Float32Array(g);for(let n=0;n<e.length;n++)y.set(e[n],n*e[n].length);m.unmap();const w=c.createBuffer({label:"buffer sigmas",size:4*a,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),b=c.createBuffer({label:"buffer Rhos",size:4*a,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC}),x=c.createBindGroup({label:"bindGroup for sigmarho buffers",layout:p.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:w}},{binding:1,resource:{buffer:b}},{binding:2,resource:{buffer:m}}]}),v=c.createCommandEncoder({label:"sigmarho encoder"}),A=v.beginComputePass({label:"sigmarho compute pass"});A.setPipeline(p),A.setBindGroup(0,x),A.dispatchWorkgroups(o,o),A.end();const S=c.createBuffer({label:"result buffer rhos",size:b.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST}),E=c.createBuffer({label:"result buffer sigmas",size:w.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});v.copyBufferToBuffer(b,0,S,0,S.size),v.copyBufferToBuffer(w,0,E,0,E.size);const I=v.finish();return c.queue.submit([I]),yield c.queue.onSubmittedWorkDone(),yield S.mapAsync(GPUMapMode.READ),yield E.mapAsync(GPUMapMode.READ),h.set(new Float32Array(S.getMappedRange())),f.set(new Float32Array(E.getMappedRange())),S.unmap(),E.unmap(),m.destroy(),w.destroy(),b.destroy(),S.destroy(),E.destroy(),{resultRhos:h,resultSigmas:f}},new((o=void 0)||(o=Promise))((function(e,n){function t(e){try{i(u.next(e))}catch(e){n(e)}}function r(e){try{i(u.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof o?i:new o((function(e){e(i)}))).then(t,r)}i((u=u.apply(a,s||[])).next())}));var a,s,o,u}var Ve=function(e,n,t,r){return new(t||(t=Promise))((function(i,a){function s(e){try{u(r.next(e))}catch(e){a(e)}}function o(e){try{u(r.throw(e))}catch(e){a(e)}}function u(e){var n;e.done?i(e.value):(n=e.value,n instanceof t?n:new t((function(e){e(n)}))).then(s,o)}u((r=r.apply(e,n||[])).next())}))};class Ke{constructor(){this.nComponents=2,this.gamma=1,this.alpha=1,this.entryLen=0,this.nNeighbours=15,this.spread=1,this.minDist=.1,this.negativeSampleRate=5,this.localConnectivity=1,this.setOpMixRatio=1}}class We{constructor(e,n){this.params=new Ke,this.knnIndexes=null,this.knnDistances=null,this.rhos=null,this.sigmas=null,this.membershipStrengths=null,this.params.entryLen=e,Object.assign(this.params,n)}setPrecomputedKNN(e,n){this.knnIndexes=e,this.knnDistances=n}initializeFit(){return Ve(this,void 0,void 0,(function*(){yield this.calcSmoothKNNDistances(),yield this.calcMembershipStrengths()}))}fit(){return Ve(this,void 0,void 0,(function*(){yield this.initializeFit();const e=yield this.initializeSimplicialSetEmbedding();if(!e)throw new Error("failed to compute umap simplistical set embeddings");const{head:n,tail:t,epochsPerSample:r,epochsPerNegativeSample:i,a,b:s,gamma:o,initialAlpha:u,nComponents:l,nEpochs:c,entryLen:f}=e,h=yield function(e,n,t,r,i,a,s,o,u,l,c,f){return h=this,d=void 0,m=function*(){const h=Math.ceil(e.length/100),d=Math.ceil(Math.sqrt(h)),p=10*d,m=yield Se();if(!m)return;const g=1e7,y=e.length,w=function(e,n,t,r,i,a,s,o,u,l,c,f,h=1e5){return`\n// first define some functions\n\nfn rDist(ar1: array<f32, ${o}>, ar2: array<f32, ${o}>) -> f32 {\n    var res = 0.0;\n    for (var i1 = 0u; i1 < ${o}; i1++) {\n        let diff = ar1[i1] - ar2[i1];\n        res += pow(diff, 2);\n    }\n    return res;\n}\n\nfn clip(x: f32, clipValue: f32) -> f32 {\n    if (x > clipValue) {\n        return clipValue;\n    }\n    else if (x < 0.0 - clipValue) {\n        return 0.0 - clipValue;\n    }\n    return x;\n}\n\nvar<private> randomSeedInt: u32 = 0;\nvar<private> nVertices: u32 = ${l};\nvar<private> initialAlpha: f32 = ${r};\nvar<private> gamma: f32 = ${i};\nvar<private> a: f32 = ${a};\nvar<private> b: f32 = ${s};\nvar<private> dim: u32 = ${o};\nvar<private> nEpochs: f32 = ${u};\nvar<private> moveOther: u32  = 1;\n\nfn random() -> u32 {\n    randomSeedInt = (randomSeedInt ^ 61) ^ (randomSeedInt >> 16);\n    randomSeedInt *= 9;\n    randomSeedInt = randomSeedInt ^ (randomSeedInt >> 4);\n    randomSeedInt *= 0x27d4eb2d;\n    randomSeedInt = randomSeedInt ^ (randomSeedInt >> 15);\n    return randomSeedInt;\n}\n\nfn randInt(maxVal: u32) -> u32 {\n    let nextRandomNum = random();\n    return u32(floor((f32(nextRandomNum) * (f32(maxVal) / 4294967296.0))));\n}\n\nstruct MatrixStorage {\n    head: array<u32, ${e}>,\n    tail: array<u32, ${e}>,\n}\n\nstruct EpochStorage {\n    epochsPerSample: array<f32, ${e}>,\n    epochOfNextSample: array<f32, ${e}>,\n    epochsPerNegativeSample: array<f32, ${e}>,\n    epochOfNextNegativeSample: array<f32, ${e}>\n}\n\nstruct EmbeddingStorage {\n    // embeddings will be in range of -10 to 10, as atomics only can store i32 or u32, we will store them as floor(f32 * 100_000)\n    headEmbeddings: array<array<atomic<i32>, ${o}>, ${n}>,\n    tailEmbeddings: array<array<atomic<i32>, ${o}>, ${n}>\n}\n\nstruct ComputeInfo {\n    n: f32,\n    alpha: f32,\n    randomNumbers: array<u32, ${e}>,\n    //tailOffsets: array<u32, ${n+1}>\n}\n    @group(0) @binding(0) var<storage, read_write> matrixStorage: MatrixStorage;\n    @group(0) @binding(1) var<storage, read_write> epochStorage: EpochStorage;\n    @group(0) @binding(2) var<storage, read_write> embedStorage: EmbeddingStorage;\n    @group(0) @binding(3) var<storage, read_write> computeInfo: ComputeInfo;\n    @compute @workgroup_size(${c}, ${c}) fn optimizeStep(\n        @builtin(global_invocation_id) id: vec3<u32>,\n     ) {\n        let divisionFactor: f32 = ${h};\n        let col: u32 = id.x;\n        let row: u32 = id.y;\n        let threadIndex: u32 = row * ${f} + col;\n        let clipValue: f32 = 4.0;\n\n        if (threadIndex >= ${e}) {\n            return;\n        }\n\n        let workingIndex = threadIndex;\n        //let startAtOffset = computeInfo.tailOffsets[threadIndex];\n        //let endAtOffset = computeInfo.tailOffsets[threadIndex + 1];\n        //for (var workingIndex = startAtOffset; workingIndex < endAtOffset; workingIndex++) {\n            randomSeedInt = computeInfo.randomNumbers[workingIndex] * u32(computeInfo.n);\n\n            let epochOfNextSample = epochStorage.epochOfNextSample[workingIndex];\n            if (epochOfNextSample > computeInfo.n) {\n                return;\n            }\n\n            let j = matrixStorage.head[workingIndex];\n            let k = matrixStorage.tail[workingIndex];\n\n            // as said before, we will store embeddings as floor(f32 * 100_000)\n            var current: array<f32, ${o}>;\n            var other: array<f32, ${o}>;\n            for (var i = 0u; i < ${o}u; i++) {\n                current[i] = f32(atomicLoad(&embedStorage.headEmbeddings[j][i])) / divisionFactor;\n                other[i] = f32(atomicLoad(&embedStorage.tailEmbeddings[k][i])) / divisionFactor;\n            }\n\n            let distSquared = rDist(current, other);\n            \n            var gradCoeff: f32 = 0.0;\n            if (distSquared > 0.0) {\n                gradCoeff = (0.0 - 2.0) * ${a} * ${s} * pow(distSquared, b - 1.0);\n                gradCoeff /= (a * pow(distSquared, b) + 1.0);\n            }\n\n            var gradBuff: array<i32, ${o}>;\n            for (var d = 0u; d < ${o}u; d++) {\n                let gradD = clip((gradCoeff * (current[d] - other[d])), clipValue);\n                let toAdd = gradD * computeInfo.alpha;\n                gradBuff[d] = i32(floor(toAdd * divisionFactor));\n                current[d] += toAdd;\n                other[d] -= toAdd;\n            }\n\n            for (var d = 0u; d < ${o}u; d++) {\n                atomicAdd(&embedStorage.headEmbeddings[j][d], gradBuff[d]);\n                atomicSub(&embedStorage.tailEmbeddings[k][d], gradBuff[d]);\n            }\n\n            epochStorage.epochOfNextSample[workingIndex] += epochStorage.epochsPerSample[workingIndex];\n            var nNegSamples: i32 = i32(floor((computeInfo.n - epochStorage.epochOfNextNegativeSample[workingIndex]) / epochStorage.epochsPerNegativeSample[workingIndex]));\n\n            for (var p = 0i; p < nNegSamples; p++) {\n                let k1 = randInt(nVertices);\n                var other1: array<f32, ${o}>;\n                for (var i = 0u; i < ${o}u; i++) {\n                    other1[i] = f32(atomicLoad(&embedStorage.tailEmbeddings[k1][i])) / divisionFactor;\n                }\n\n                let distSquared1 = rDist(current, other1);\n\n                var gradCoeff1: f32 = 0.0;\n                if (distSquared1 > 0.0) {\n                    gradCoeff1 = 2.0 * gamma * b;\n                    gradCoeff1 /= (0.001 + distSquared1) * (a * pow(distSquared1, b) + 1);\n                }\n                else if (j == k1) {\n                    continue;\n                }\n\n                var gradDBuff: array<i32, ${o}>;\n                for (var d = 0u; d < ${o}u; d++) {\n                    var gradD: f32 = 4.0;\n                    if (gradCoeff1 > 0.0) {\n                        gradD = clip(gradCoeff1 * (current[d] - other1[d]), clipValue);\n                    }\n\n                    gradDBuff[d] = i32(floor(gradD * computeInfo.alpha * divisionFactor));\n                    \n                }\n                for (var d = 0u; d < ${o}u; d++) {\n                    atomicAdd(&embedStorage.headEmbeddings[j][d], gradDBuff[d]);\n                }\n            }\n            epochStorage.epochOfNextNegativeSample[workingIndex] += f32(nNegSamples) * epochStorage.epochsPerNegativeSample[workingIndex];\n    //}\n    }\n`}(y,t,0,a,s,o,u,l,c,f,10,p,g);let b=2*y*4;const x=15&b;0!==x&&(b+=16-x);let v=4*y*4;const A=15&v;0!==A&&(v+=16-A);let S=2*t*2*4;const E=15&S;0!==E&&(S+=16-E);let I=4*(2+y);const M=15&I;0!==M&&(I+=16-M);const N=m.createShaderModule({label:"optimizeShader",code:w}),P=m.createComputePipeline({label:"optimizePipeline",layout:"auto",compute:{module:N,entryPoint:"optimizeStep"}}),C=m.createBuffer({label:"matrix storage buffer",size:b,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),D=C.getMappedRange();new Uint32Array(D,0,y).set(e),new Uint32Array(D,4*y,y).set(n),C.unmap();const k=m.createBuffer({label:"epoch storage buffer",size:v,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),R=k.getMappedRange(),U=new Float32Array(R);U.set(r,0),U.set(r,y),U.set(i,2*y),U.set(i,3*y),k.unmap();const O=new Int32Array(t*l).map((()=>Math.floor((2*Math.random()-1)*g)));new Int32Array(t*l).set(O);const T=m.createBuffer({label:"embedding storage buffer",size:S,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),B=T.getMappedRange(),_=new Int32Array(B);_.set(O,0),_.set(O,O.length),T.unmap();const z=m.createBuffer({label:"compute info buffer",size:I,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),L=new Uint32Array(y).map((()=>Math.floor(Math.random()*g))),G=z.getMappedRange();new Float32Array(G,0,2).set([0,a]),new Uint32Array(G,8,y).set(L),z.unmap();const $=m.createBindGroup({label:"bindGroup for optimize",layout:P.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:C}},{binding:1,resource:{buffer:k}},{binding:2,resource:{buffer:T}},{binding:3,resource:{buffer:z}}]});let F=a;const j=m.createBuffer({label:"result buffer",size:T.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});for(let e=0;e<c;e++){m.queue.writeBuffer(z,0,new Float32Array([e,F]),0);const n=m.createCommandEncoder({label:"matrix ops encoder"}),t=n.beginComputePass({label:"matrix ops compute pass"});t.setPipeline(P),t.setBindGroup(0,$),t.dispatchWorkgroups(d,d),t.end(),e===c-1&&n.copyBufferToBuffer(T,0,j,0,j.size);const r=n.finish();m.queue.submit([r]),yield m.queue.onSubmittedWorkDone(),F=a*(1-e/c)}yield j.mapAsync(GPUMapMode.READ);const Y=j.getMappedRange(),q=new Int32Array(Y,0,O.length);O.set(q),j.unmap();const V=new Array(l).fill(null).map((e=>new Float32Array(t)));for(let e=0;e<t;e++)for(let n=0;n<l;n++)V[n][e]=O[e*l+n]/g;return C.destroy(),k.destroy(),T.destroy(),z.destroy(),j.destroy(),V},new((p=void 0)||(p=Promise))((function(e,n){function t(e){try{i(m.next(e))}catch(e){n(e)}}function r(e){try{i(m.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof p?i:new p((function(e){e(i)}))).then(t,r)}i((m=m.apply(h,d||[])).next())}));var h,d,p,m}(n,t,f,r,i,u,o,a,s,l,c,f);return h}))}calcSmoothKNNDistances(){return Ve(this,void 0,void 0,(function*(){if(!this.knnIndexes||!this.knnDistances)throw new Error("knn indexes and distances must be set before calling fit");const e=yield qe(this.knnDistances,this.params.nNeighbours,this.params.localConnectivity,64);if(!e)throw new Error("failed to compute smooth knn distances");this.rhos=e.resultRhos,this.sigmas=e.resultSigmas}))}calcMembershipStrengths(){return Ve(this,void 0,void 0,(function*(){if(!(this.knnIndexes&&this.knnDistances&&this.rhos&&this.sigmas))throw new Error("knn indexes, distances, rhos, and sigmas must be set before calling fit");const e=yield function(e,n,t){return r=this,i=void 0,s=function*(){const r=e.length,i=Math.ceil(r/100),a=Math.ceil(Math.sqrt(i)),s=function(e=10,n,t,r,i){const a=t.length,s=r.length,o=i.length;return`\n           struct MembershipStrengthsInfo {\n               knnDistances: array<array<f32, ${t[0].length}>, ${a}>,\n               sigmas: array<f32, ${s}>,\n               rhos: array<f32, ${o}>\n           };\n           var<private> nNeighbors: u32 = ${t[0].length};\n           @group(0) @binding(0) var<storage, read> membershipStrengthsInfo: MembershipStrengthsInfo;\n           @group(0) @binding(1) var<storage, read_write> resultKnnDistances: array<array<f32, ${t[0].length}>, ${a}>;\n           @compute @workgroup_size(${e}, ${e}) fn computeMembershipStrengths(\n               @builtin(global_invocation_id) id: vec3<u32>,\n           ) {\n               let col: u32 = id.x;\n               let row: u32 = id.y;\n               let workingIndex: u32 = row * ${n} + col;\n\n               if (workingIndex >= ${a}) {\n                   return;\n               }\n\n               let workingResKnnDistances = &resultKnnDistances[workingIndex];\n               let knnDistances = &membershipStrengthsInfo.knnDistances[workingIndex];\n               for (var j = 0u; j < nNeighbors; j = j + 1u) {\n                   var val: f32 = 0.0;\n\n                   if ((*knnDistances)[j] - membershipStrengthsInfo.rhos[workingIndex] <= 0.0) {\n                       val = 1.0;\n                   } else {\n                       val = exp(0.0 - ((knnDistances[j] - membershipStrengthsInfo.rhos[workingIndex]) / membershipStrengthsInfo.sigmas[workingIndex]));   \n                   }\n\n                   (*workingResKnnDistances)[j] = val;\n               }\n           }\n   `}(10,10*a,e,n,t),o=r*e[0].length,u=yield Se();if(null==u)return;const l=u.createShaderModule({label:"rowsColsValsCalulation",code:s}),c=u.createComputePipeline({label:"rowsColsValsPipeline",layout:"auto",compute:{module:l,entryPoint:"computeMembershipStrengths"}});let f=4*(t.length+n.length+o);const h=15&f;0!=h&&(f+=16-h);const d=u.createBuffer({label:"info buffer",size:f,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST,mappedAtCreation:!0}),p=d.getMappedRange(),m=new Float32Array(p);for(let n=0;n<e.length;n++)m.set(e[n],n*e[n].length);let g=e[0].length*e.length;m.set(n,g),g+=n.length,m.set(t,g),d.unmap();const y=u.createBuffer({label:"knn distance buffer",size:e[0].length*e.length*Float32Array.BYTES_PER_ELEMENT,usage:GPUBufferUsage.STORAGE|GPUBufferUsage.COPY_SRC|GPUBufferUsage.COPY_DST}),w=u.createBindGroup({label:"bindGroup for membership strhegths buffers",layout:c.getBindGroupLayout(0),entries:[{binding:0,resource:{buffer:d}},{binding:1,resource:{buffer:y}}]}),b=u.createCommandEncoder({label:"membership strengths encoder"}),x=b.beginComputePass({label:"membership strengths compute pass"});x.setPipeline(c),x.setBindGroup(0,w),x.dispatchWorkgroups(a,a),x.end();const v=u.createBuffer({label:"result buffer distances",size:y.size,usage:GPUBufferUsage.MAP_READ|GPUBufferUsage.COPY_DST});b.copyBufferToBuffer(y,0,v,0,v.size);const A=b.finish();u.queue.submit([A]),yield u.queue.onSubmittedWorkDone(),yield v.mapAsync(GPUMapMode.READ);const S=v.getMappedRange(),E=e[0].length*Float32Array.BYTES_PER_ELEMENT,I=new Array(e.length).fill(null).map(((n,t)=>{const r=new Float32Array(S,E*t,e[0].length),i=new Float32Array(e[0].length);return i.set(r),i}));return v.unmap(),v.destroy(),y.destroy(),d.destroy(),I},new((a=void 0)||(a=Promise))((function(e,n){function t(e){try{u(s.next(e))}catch(e){n(e)}}function o(e){try{u(s.throw(e))}catch(e){n(e)}}function u(n){var r;n.done?e(n.value):(r=n.value,r instanceof a?r:new a((function(e){e(r)}))).then(t,o)}u((s=s.apply(r,i||[])).next())}));var r,i,a,s}(this.knnDistances,this.sigmas,this.rhos);if(!e)throw new Error("failed to compute membership strengths");this.membershipStrengths=e}))}fuzzySimplicialSet(){return Ve(this,void 0,void 0,(function*(){if(!(this.knnIndexes&&this.knnDistances&&this.rhos&&this.sigmas&&this.membershipStrengths))throw new Error("knn indexes, distances, rhos, sigmas, and membership strengths must be set before calling fit");const e=yield Ye(this.knnIndexes,this.membershipStrengths,this.params.setOpMixRatio);if(!e)throw new Error("failed to compute pairwise multiply with transpose");return e}))}initializeSimplicialSetEmbedding(){return Ve(this,void 0,void 0,(function*(){const e=yield this.fuzzySimplicialSet();if(!(e&&e.res&&e.unionMatrixOffsets&&e.unionSizes))throw new Error("failed to compute fuzzy simplicial set");const n=yield function(e,n,t,r,i=5){return a=this,s=void 0,u=function*(){if(!e.unionSizes)return;const a=function(e){return e<=2500?1e3:e<=5e3?800:e<=7500?650:400}(n),s=e.res.resultKnnDistances.reduce(((e,n)=>Math.max(e,n))),o=s/a,u=new Uint32Array(e.unionSizes.length);u.set(e.unionSizes);let l=0;for(let n=0;n<e.unionSizes.length;n++){for(let t=0;t<e.unionSizes[n];t++){const r=l+t;e.res.resultKnnDistances[r]<o&&(e.res.resultKnnDistances[r]=0,u[n]--)}l+=e.unionSizes[n]}const c=Fe(u),f=c[c.length-1],h=new Float32Array(f),d=new Uint32Array(f),p=new Uint32Array(f);l=0;for(let n=0;n<e.unionSizes.length;n++)for(let t=0;t<e.unionSizes[n];t++){const r=e.unionMatrixOffsets[n]+t;0!=e.res.resultKnnDistances[r]&&(h[l]=e.res.resultKnnDistances[r],d[l]=e.res.resultKnnIndexes[r],p[l]=n,l+=1)}const m=new Float32Array(h.length).fill(-1),g=h.map((e=>e/s*a));g.forEach(((e,n)=>{e>0&&(m[n]=a/g[n])}));const{a:y,b:w}=$e(t,r),b=m.map((e=>e/i));return{epochsPerSample:m,epochsPerNegativeSample:b,a:y,b:w,head:d,tail:p,entryLen:n,nEpochs:a,nComponents:2,initialAlpha:1,gamma:1}},new((o=void 0)||(o=Promise))((function(e,n){function t(e){try{i(u.next(e))}catch(e){n(e)}}function r(e){try{i(u.throw(e))}catch(e){n(e)}}function i(n){var i;n.done?e(n.value):(i=n.value,i instanceof o?i:new o((function(e){e(i)}))).then(t,r)}i((u=u.apply(a,s||[])).next())}));var a,s,o,u}(e,this.params.entryLen,this.params.spread,this.params.minDist,this.params.negativeSampleRate);if(!n)throw new Error("failed to compute umap simplistical set embeddings");return n}))}}class He{constructor(e){this.data=e.data,this.weights=e.weights,this.aggregationMethod=e.aggregationMethod}}class Ze extends He{constructor(e){super(e);const n=e.randomSeed??Date(),t=be()(n);e.dim=2,e.random=t,this.reducer=new xe(e),this.iterations=e?.iterations??this.reducer.getIterSize(this.data[0].length),this.distanceFnames=e.distanceFnames,this.distanceFns=e.distanceFns,this.distanceFnArgs=e.distanceFnArgs,this.progressFunc=e.progressFunc}async transform(){if(this.data[0].length>1e4)throw new Error("Maximum number of samples for T-SNE is 10000");const e=new b(!0,!1);try{const n=await e.calcMulti(this.data,this.distanceFnames,!1,this.distanceFnArgs,this.weights,this.aggregationMethod);e.terminate(),this.reducer.initDataDist(n,this.data[0].length);for(let e=0;e<this.iterations;++e)this.reducer.step(),this.progressFunc&&this.progressFunc(e,this.iterations,[]);return this.reducer.getSolution()}catch(n){throw e.terminate(),n}}}class Xe extends He{constructor(e){const n=e.randomSeed??Date(),t=be()(n);super(e),this.useWebGPU=!1,me("distanceFnames"in e),me("distanceFns"in e),this.distanceFnArgs=e.distanceFnArgs,this.distanceFns=e.distanceFns,this.progressFunc=e.progressFunc,this.useWebGPU=e.useWebGPU??!1,this.distanceFnames=e.distanceFnames,e.nComponents=2,this.vectors=new Array(this.data[0].length).fill(0).map(((e,n)=>n)),this.data[0].length<=(e.nNeighbors??15)&&(e.nNeighbors=this.data[0].length-1),e.random=t,this.reducer=new ce(e)}async transform(e){let n;if(console.time("knn graph"),this.useWebGPU)try{n=await Te(this.data,this.reducer.neighbors,this.distanceFnames,this.aggregationMethod,this.weights,this.distanceFnArgs)}catch(e){console.error(e)}if(n||(this.useWebGPU&&console.error("WEBGPU KNN failed, falling back to multithreaded CPU implementation"),n=await(new ge.p).multiColumnKNN(this.data,this.distanceFnames,this.reducer.neighbors,this.distanceFnArgs,this.weights,this.aggregationMethod)),console.timeEnd("knn graph"),!n)throw new Error("Failed to compute KNN graph");const t=this.data[0].length;for(let e=0;e<n.knnIndexes.length;++e)for(let r=0;r<n.knnIndexes[e].length;++r)n.knnDistances[e][r]<0&&(n.knnDistances[e][r]=0),(n.knnIndexes[e][r]<0||n.knnIndexes[e][r]>=t||n.knnDistances[e][r]>10)&&(n.knnIndexes[e][r]=e==r?r+1:r,n.knnDistances[e][r]=10);this.useWebGPU?(this.webGPUReducer=new We(this.vectors.length,{nComponents:this.reducer.nComponents,gamma:this.reducer.repulsionStrength,alpha:this.reducer.learningRate,nNeighbours:this.reducer.neighbors,spread:this.reducer.spread,minDist:this.reducer.minDist,negativeSampleRate:this.reducer.negativeSampleRate,localConnectivity:this.reducer.localConnectivity,setOpMixRatio:this.reducer.setOpMixRatio}),this.webGPUReducer.setPrecomputedKNN(n.knnIndexes,n.knnDistances)):this.reducer.setPrecomputedKNN(n.knnIndexes,n.knnDistances),await new Promise((e=>{setTimeout((()=>{e()}),300)}));let i=null;console.time("fit");try{if(this.useWebGPU&&this.webGPUReducer){if(i=await this.webGPUReducer.fit(),!i)throw new Error("Failed to compute embedding");i=new Array(i[0].length).fill(null).map(((e,n)=>new Float32Array(i.map((e=>e[n])))))}}catch(e){console.error(e)}return i||(this.useWebGPU&&(console.error("WEBGPU UMAP failed, falling back to CPU implementation"),this.reducer.setPrecomputedKNN(n.knnIndexes,n.knnDistances)),i=await this.reducer.fitAsync(this.vectors,(e=>{this.progressFunc&&this.progressFunc(e,this.reducer.getNEpochs(),this.reducer.getEmbedding())}))),console.timeEnd("fit"),a=i,new Array(a.length).fill(0).map(((e,n)=>r.from(a[n])));var a}}const Qe={UMAP:Xe,"t-SNE":Ze};class Je{constructor(e,n,t,r,i,a){const s=[];for(let n=0;n<t.length;++n){const r=new y(t[n]).getMeasure(a.distanceFnArgs[n]);s.push(r);let i=2048;for(let t=0;t<e[n].length;++t)if(e[n][t]&&e[n][t]._length){i=e[n][t]._length;break}if(o=t[n],"BitArray"==g[o])for(let t=0;t<e[n].length;++t)e[n][t]&&e[n][t]._data?e[n][t]=new ye.A(e[n][t]._data,e[n][t]._length):e[n][t]=new ye.A(i)}var 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