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Analyze aux graphs individually
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@rjawesome
rjawesome committed Apr 19, 2024
1 parent e1ab149 commit 715c1c9
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Showing 2 changed files with 136 additions and 121 deletions.
2 changes: 1 addition & 1 deletion src/inferred_mode/inferred_mode.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -379,7 +379,7 @@ export default class InferredQueryHandler {
};

if (this.pathfinder) {
combinedResponse.original_analyses[auxGraphID] = translatedResult.analyses[0];
combinedResponse.original_analyses[auxGraphID] = result.analyses[0];
}
}

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255 changes: 135 additions & 120 deletions src/inferred_mode/pathfinder.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,12 @@ interface AuxGraphObject {
[id: string]: { edges: Set<string> }
}

interface FullGraph {
[node: string]: { [dst: string]: Set<string> }
}

interface DfsGraph {
[node: string]: { [dst: string]: string[] }
[node: string]: { [dst: string]: boolean };
}

export default class PathfinderQueryHandler {
Expand Down Expand Up @@ -130,20 +134,20 @@ export default class PathfinderQueryHandler {
const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[this.mainEdgeId][0].id;
const kgSrc = creativeResponse.message.results[0].node_bindings[this.mainEdge.subject][0].id;
const kgDst = creativeResponse.message.results[0].node_bindings[this.mainEdge.object][0].id;
const dfsGraph: DfsGraph = {};
const fullGraph: FullGraph = {};
const supportGraphsPerNode: { [node: string]: Set<string> } = {};
const supportGraphs = (creativeResponse.message.knowledge_graph.edges[kgEdge]?.attributes?.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value ?? []) as string[];
for (const supportGraph of supportGraphs) {
const auxGraph = (creativeResponse.message.auxiliary_graphs ?? {})[supportGraph];
for (const subEdge of auxGraph.edges) {
const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge];
if (!dfsGraph[kgSubEdge.subject]) {
dfsGraph[kgSubEdge.subject] = {};
if (!fullGraph[kgSubEdge.subject]) {
fullGraph[kgSubEdge.subject] = {};
}
if (!dfsGraph[kgSubEdge.subject][kgSubEdge.object]) {
dfsGraph[kgSubEdge.subject][kgSubEdge.object] = [];
if (!fullGraph[kgSubEdge.subject][kgSubEdge.object]) {
fullGraph[kgSubEdge.subject][kgSubEdge.object] = new Set();
}
dfsGraph[kgSubEdge.subject][kgSubEdge.object].push(subEdge);
fullGraph[kgSubEdge.subject][kgSubEdge.object].add(subEdge);

if (!supportGraphsPerNode[kgSubEdge.subject]) {
supportGraphsPerNode[kgSubEdge.subject] = new Set();
Expand All @@ -156,7 +160,7 @@ export default class PathfinderQueryHandler {
debug(message1);
this.logs.push(new LogEntry('INFO', null, message1).getLog());

const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsGraph, supportGraphsPerNode, kgSrc, kgDst);
const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, supportGraphsPerNode, kgSrc, kgDst);

creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, this.CREATIVE_LIMIT);
creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.`
Expand All @@ -168,8 +172,8 @@ export default class PathfinderQueryHandler {
const auxGraph = creativeResponse.message.knowledge_graph.edges[edge.id].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value[0];
finalNewAuxGraphs[auxGraph] = { edges: [] };
for (const ed of newAuxGraphs[auxGraph].edges) {
const [st, en] = ed.split('-');
finalNewAuxGraphs[auxGraph].edges.push.apply(finalNewAuxGraphs[auxGraph].edges, dfsGraph[st][en]);
const [st, en] = ed.split('\n');
finalNewAuxGraphs[auxGraph].edges.push.apply(finalNewAuxGraphs[auxGraph].edges, Array.from(fullGraph[st][en]));
}
}
}
Expand All @@ -186,127 +190,138 @@ export default class PathfinderQueryHandler {
return creativeResponse;
}

_searchForIntermediates(creativeResponse: TrapiResponse, dfsGraph: DfsGraph, supportGraphsPerNode: { [node: string]: Set<string> }, kgSrc: string, kgDst: string): ResultAuxObject {
_searchForIntermediates(creativeResponse: TrapiResponse, supportGraphsPerNode: { [node: string]: Set<string> }, kgSrc: string, kgDst: string): ResultAuxObject {
const span = Telemetry.startSpan({ description: 'pathfinderIntermediateSearch' });

// perform dfs
const stack = [{ node: kgSrc, path: [kgSrc] }];
const newResultObject: ResultObject = {};
const newAuxGraphs: AuxGraphObject = {};
let a= 0;
let b=0;
while (stack.length !== 0) {
const { node, path } = stack.pop()!;
a++;

// continue creating path if we haven't reached end yet
if (node !== kgDst) {
for (const neighbor in dfsGraph[node]) {
if (!path.includes(neighbor)) {
stack.push({ node: neighbor, path: [...path, neighbor] });
}
for (let analysis of Object.values(this.originalAnalyses)) {
const dfsGraph: DfsGraph = {};
for (const subEdge of Object.values(analysis.edge_bindings).map(eb => eb[0].id)) {
const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge];
if (!dfsGraph[kgSubEdge.subject]) {
dfsGraph[kgSubEdge.subject] = {};
}
if (!dfsGraph[kgSubEdge.subject][kgSubEdge.object]) {
dfsGraph[kgSubEdge.subject][kgSubEdge.object] = true;
}
continue;
}

// path to dest too short
if (path.length <= 2) {
continue;
}
b++;
// loop through all intermediate nodes in path to dest
for (let i = 1; i < path.length - 1; i++) {
const intermediateNode = path[i];

if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) {
newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set() };
newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set() };
newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set() };
}
// perform dfs
const stack = [{ node: kgSrc, path: [kgSrc] }];

// add "edges" to aux graphs (kg edges will be added later)
for (let j = 0; j < i; j++) {
newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`);
newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`);
while (stack.length !== 0) {
const { node, path } = stack.pop()!;

// continue creating path if we haven't reached end yet
if (node !== kgDst) {
for (const neighbor in dfsGraph[node]) {
if (!path.includes(neighbor)) {
stack.push({ node: neighbor, path: [...path, neighbor] });
}
}
continue;
}
for (let j = i; j < path.length - 1; j++) {
newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`);
newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`);
}

// code below is only for new results
if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) continue;

// create new edges & aux graph
newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = {
node_bindings: {
[this.mainEdge.subject]: [{ id: kgSrc }],
[this.mainEdge.object]: [{ id: kgDst }],
[this.unpinnedNodeId]: [{ id: intermediateNode }]
},
analyses: [{
resource_id: "infores:biothings-explorer",
edge_bindings: {
[this.mainEdgeId]: [{ id: `pathfinder-${intermediateNode}` }],
[this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }],
[this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }],
},
score: undefined
}],
};
creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = {
predicate: 'biolink:related_to',
subject: kgSrc,
object: intermediateNode,
sources: [
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
],
attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }],
};
creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = {
predicate: 'biolink:related_to',
subject: intermediateNode,
object: kgDst,
sources: [
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
],
attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }],
};
creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}`] = {
predicate: 'biolink:related_to',
subject: kgSrc,
object: kgDst,
sources: [
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',

// path to dest too short
if (path.length <= 2) {
continue;
}

// loop through all intermediate nodes in path to dest
for (let i = 1; i < path.length - 1; i++) {
const intermediateNode = path[i];

if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) {
newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set() };
newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set() };
newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set() };
}

// add "edges" to aux graphs (kg edges will be added later)
for (let j = 0; j < i; j++) {
newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(`${path[j]}\n${path[j+1]}`);
newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${path[j]}\n${path[j+1]}`);
}
for (let j = i; j < path.length - 1; j++) {
newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(`${path[j]}\n${path[j+1]}`);
newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${path[j]}\n${path[j+1]}`);
}

// code below is only for new results
if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) continue;

// create new edges & aux graph
newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = {
node_bindings: {
[this.mainEdge.subject]: [{ id: kgSrc }],
[this.mainEdge.object]: [{ id: kgDst }],
[this.unpinnedNodeId]: [{ id: intermediateNode }]
},
],
attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-support`] }],
};

// calculate score
if (supportGraphsPerNode[intermediateNode]?.size > 0) {
let score: number | undefined = undefined;
for (const supportGraph of supportGraphsPerNode[intermediateNode]) {
score = scaled_sigmoid(
inverse_scaled_sigmoid(score ?? 0) +
inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score),
);
analyses: [{
resource_id: "infores:biothings-explorer",
edge_bindings: {
[this.mainEdgeId]: [{ id: `pathfinder-${intermediateNode}` }],
[this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }],
[this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }],
},
score: undefined
}],
};
creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = {
predicate: 'biolink:related_to',
subject: kgSrc,
object: intermediateNode,
sources: [
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
],
attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }],
};
creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = {
predicate: 'biolink:related_to',
subject: intermediateNode,
object: kgDst,
sources: [
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
],
attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }],
};
creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}`] = {
predicate: 'biolink:related_to',
subject: kgSrc,
object: kgDst,
sources: [
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
],
attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-support`] }],
};

// calculate score
if (supportGraphsPerNode[intermediateNode]?.size > 0) {
let score: number | undefined = undefined;
for (const supportGraph of supportGraphsPerNode[intermediateNode]) {
score = scaled_sigmoid(
inverse_scaled_sigmoid(score ?? 0) +
inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score),
);
}
newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score;
}
newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score;
}
}
}
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