diff --git a/ui/__tests__/scientific-rag.test.ts b/ui/__tests__/scientific-rag.test.ts
new file mode 100644
index 0000000..015fd76
--- /dev/null
+++ b/ui/__tests__/scientific-rag.test.ts
@@ -0,0 +1,66 @@
+import {
+  buildCitationKey,
+  buildScientificMetadata,
+  detectScientificSection,
+  formatRetrievedDocument,
+} from '@/utils/server/scientific-rag';
+import { describe, expect, it } from 'vitest';
+
+describe('scientific-rag helpers', () => {
+  it('detects scientific sections from document chunks', () => {
+    expect(detectScientificSection('Abstract\nThis paper studies retrieval.')).toBe(
+      'abstract',
+    );
+    expect(detectScientificSection('METHODS\nWe used a benchmark.')).toBe(
+      'methods',
+    );
+  });
+
+  it('builds stable citation keys', () => {
+    expect(
+      buildCitationKey({
+        title: 'Scientific RAG for Papers!',
+        page: 4,
+        chunkIndex: 2,
+      }),
+    ).toBe('scientific-rag-for-papers:p4:c3');
+  });
+
+  it('builds metadata with title fallback and section', () => {
+    const metadata = buildScientificMetadata(
+      {
+        pageContent: 'Results\nThe model improved citation accuracy.',
+        metadata: {
+          loc: { pageNumber: 7 },
+          pdf: { info: { Title: '' } },
+          source: '/tmp/paper.pdf',
+        },
+      },
+      'paper.pdf',
+      0,
+    );
+
+    expect(metadata).toMatchObject({
+      title: 'paper.pdf',
+      page: 7,
+      section: 'results',
+      citationKey: 'paper-pdf:p7:c1',
+    });
+  });
+
+  it('formats retrieved documents with citation metadata', () => {
+    expect(
+      formatRetrievedDocument({
+        content: 'Citation-aware answer context.',
+        metadata: {
+          title: 'Paper',
+          page: 2,
+          section: 'discussion',
+          citationKey: 'paper:p2:c1',
+        },
+        distance: 0.12345,
+        index: 0,
+      }),
+    ).toContain('Source 1 [paper:p2:c1]');
+  });
+});
diff --git a/ui/package-lock.json b/ui/package-lock.json
index 998e32c..8345168 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -13,7 +13,7 @@
         "@radix-ui/react-select": "^1.2.2",
         "@radix-ui/react-tooltip": "^1.0.6",
         "@tabler/icons-react": "^2.9.0",
-        "@xenova/transformers": "^2.5.2",
+        "@xenova/transformers": "^2.17.2",
         "chromadb": "^1.5.6",
         "class-variance-authority": "^0.7.0",
         "clsx": "^2.0.0",
@@ -449,30 +449,6 @@
       "integrity": "sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw==",
       "dev": true
     },
-    "node_modules/@cspotcode/source-map-support": {
-      "version": "0.8.1",
-      "resolved": "https://registry.npmjs.org/@cspotcode/source-map-support/-/source-map-support-0.8.1.tgz",
-      "integrity": "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw==",
-      "optional": true,
-      "peer": true,
-      "dependencies": {
-        "@jridgewell/trace-mapping": "0.3.9"
-      },
-      "engines": {
-        "node": ">=12"
-      }
-    },
-    "node_modules/@cspotcode/source-map-support/node_modules/@jridgewell/trace-mapping": {
-      "version": "0.3.9",
-      "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.9.tgz",
-      "integrity": "sha512-3Belt6tdc8bPgAtbcmdtNJlirVoTmEb5e2gC94PnkwEW9jI6CAHUeoG85tjWP5WquqfavoMtMwiG4P926ZKKuQ==",
-      "optional": true,
-      "peer": true,
-      "dependencies": {
-        "@jridgewell/resolve-uri": "^3.0.3",
-        "@jridgewell/sourcemap-codec": "^1.4.10"
-      }
-    },
     "node_modules/@dqbd/tiktoken": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/@dqbd/tiktoken/-/tiktoken-1.0.2.tgz",
@@ -920,6 +896,15 @@
       "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.1.1.tgz",
       "integrity": "sha512-m0G6wlnhm/AX0H12IOWtK8gASEMffnX08RtKkCgTdHb9JpHKGloI7icFfLg9ZmQeavcvR0PKmzxClyuFPSjKWw=="
     },
+    "node_modules/@huggingface/jinja": {
+      "version": "0.2.2",
+      "resolved": "https://registry.npmjs.org/@huggingface/jinja/-/jinja-0.2.2.tgz",
+      "integrity": "sha512-/KPde26khDUIPkTGU82jdtTW9UAuvUTumCAbFs/7giR0SxsvZC4hru51PBvpijH6BVkHcROcvZM/lpy5h1jRRA==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=18"
+      }
+    },
     "node_modules/@humanwhocodes/config-array": {
       "version": "0.11.8",
       "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.11.8.tgz",
@@ -1958,34 +1943,6 @@
         }
       }
     },
-    "node_modules/@tsconfig/node10": {
-      "version": "1.0.9",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node10/-/node10-1.0.9.tgz",
-      "integrity": "sha512-jNsYVVxU8v5g43Erja32laIDHXeoNvFEpX33OK4d6hljo3jDhCBDhx5dhCCTMWUojscpAagGiRkBKxpdl9fxqA==",
-      "optional": true,
-      "peer": true
-    },
-    "node_modules/@tsconfig/node12": {
-      "version": "1.0.11",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node12/-/node12-1.0.11.tgz",
-      "integrity": "sha512-cqefuRsh12pWyGsIoBKJA9luFu3mRxCA+ORZvA4ktLSzIuCUtWVxGIuXigEwO5/ywWFMZ2QEGKWvkZG1zDMTag==",
-      "optional": true,
-      "peer": true
-    },
-    "node_modules/@tsconfig/node14": {
-      "version": "1.0.3",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node14/-/node14-1.0.3.tgz",
-      "integrity": "sha512-ysT8mhdixWK6Hw3i1V2AeRqZ5WfXg1G43mqoYlM2nc6388Fq5jcXyr5mRsqViLx/GJYdoL0bfXD8nmF+Zn/Iow==",
-      "optional": true,
-      "peer": true
-    },
-    "node_modules/@tsconfig/node16": {
-      "version": "1.0.3",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node16/-/node16-1.0.3.tgz",
-      "integrity": "sha512-yOlFc+7UtL/89t2ZhjPvvB/DeAr3r+Dq58IgzsFkOAvVC6NMJXmCGjbptdXdR9qsX7pKcTL+s87FtYREi2dEEQ==",
-      "optional": true,
-      "peer": true
-    },
     "node_modules/@types/chai": {
       "version": "4.3.4",
       "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.3.4.tgz",
@@ -2372,10 +2329,12 @@
       }
     },
     "node_modules/@xenova/transformers": {
-      "version": "2.5.2",
-      "resolved": "https://registry.npmjs.org/@xenova/transformers/-/transformers-2.5.2.tgz",
-      "integrity": "sha512-zmCKv6xMoYPlLlH1f9gWYTsnKfjGDfVcoH0POnqIjT0leB+CljnN+YrPSE5B1/xnXQCGOF03e/SknOCqlLRzRw==",
+      "version": "2.17.2",
+      "resolved": "https://registry.npmjs.org/@xenova/transformers/-/transformers-2.17.2.tgz",
+      "integrity": "sha512-lZmHqzrVIkSvZdKZEx7IYY51TK0WDrC8eR0c5IMnBsO8di8are1zzw8BlLhyO2TklZKLN5UffNGs1IJwT6oOqQ==",
+      "license": "Apache-2.0",
       "dependencies": {
+        "@huggingface/jinja": "^0.2.2",
         "onnxruntime-web": "1.14.0",
         "sharp": "^0.32.0"
       },
@@ -3339,13 +3298,6 @@
         "url": "https://opencollective.com/core-js"
       }
     },
-    "node_modules/create-require": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/create-require/-/create-require-1.1.1.tgz",
-      "integrity": "sha512-dcKFX3jn0MpIaXjisoRvexIJVEKzaq7z2rZKxf+MSr9TkdmHmsU4m2lcLojrj/FHl8mk5VxMmYA+ftRkP/3oKQ==",
-      "optional": true,
-      "peer": true
-    },
     "node_modules/cross-spawn": {
       "version": "7.0.3",
       "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
@@ -6721,13 +6673,6 @@
         "semver": "bin/semver.js"
       }
     },
-    "node_modules/make-error": {
-      "version": "1.3.6",
-      "resolved": "https://registry.npmjs.org/make-error/-/make-error-1.3.6.tgz",
-      "integrity": "sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw==",
-      "optional": true,
-      "peer": true
-    },
     "node_modules/markdown-table": {
       "version": "3.0.3",
       "resolved": "https://registry.npmjs.org/markdown-table/-/markdown-table-3.0.3.tgz",
@@ -10247,77 +10192,6 @@
         "url": "https://github.com/sponsors/wooorm"
       }
     },
-    "node_modules/ts-node": {
-      "version": "10.9.1",
-      "resolved": "https://registry.npmjs.org/ts-node/-/ts-node-10.9.1.tgz",
-      "integrity": "sha512-NtVysVPkxxrwFGUUxGYhfux8k78pQB3JqYBXlLRZgdGUqTO5wU/UyHop5p70iEbGhB7q5KmiZiU0Y3KlJrScEw==",
-      "optional": true,
-      "peer": true,
-      "dependencies": {
-        "@cspotcode/source-map-support": "^0.8.0",
-        "@tsconfig/node10": "^1.0.7",
-        "@tsconfig/node12": "^1.0.7",
-        "@tsconfig/node14": "^1.0.0",
-        "@tsconfig/node16": "^1.0.2",
-        "acorn": "^8.4.1",
-        "acorn-walk": "^8.1.1",
-        "arg": "^4.1.0",
-        "create-require": "^1.1.0",
-        "diff": "^4.0.1",
-        "make-error": "^1.1.1",
-        "v8-compile-cache-lib": "^3.0.1",
-        "yn": "3.1.1"
-      },
-      "bin": {
-        "ts-node": "dist/bin.js",
-        "ts-node-cwd": "dist/bin-cwd.js",
-        "ts-node-esm": "dist/bin-esm.js",
-        "ts-node-script": "dist/bin-script.js",
-        "ts-node-transpile-only": "dist/bin-transpile.js",
-        "ts-script": "dist/bin-script-deprecated.js"
-      },
-      "peerDependencies": {
-        "@swc/core": ">=1.2.50",
-        "@swc/wasm": ">=1.2.50",
-        "@types/node": "*",
-        "typescript": ">=2.7"
-      },
-      "peerDependenciesMeta": {
-        "@swc/core": {
-          "optional": true
-        },
-        "@swc/wasm": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/ts-node/node_modules/acorn-walk": {
-      "version": "8.2.0",
-      "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-8.2.0.tgz",
-      "integrity": "sha512-k+iyHEuPgSw6SbuDpGQM+06HQUa04DZ3o+F6CSzXMvvI5KMvnaEqXe+YVe555R9nn6GPt404fos4wcgpw12SDA==",
-      "optional": true,
-      "peer": true,
-      "engines": {
-        "node": ">=0.4.0"
-      }
-    },
-    "node_modules/ts-node/node_modules/arg": {
-      "version": "4.1.3",
-      "resolved": "https://registry.npmjs.org/arg/-/arg-4.1.3.tgz",
-      "integrity": "sha512-58S9QDqG0Xx27YwPSt9fJxivjYl432YCwfDMfZ+71RAqUrZef7LrKQZ3LHLOwCS4FLNBplP533Zx895SeOCHvA==",
-      "optional": true,
-      "peer": true
-    },
-    "node_modules/ts-node/node_modules/diff": {
-      "version": "4.0.2",
-      "resolved": "https://registry.npmjs.org/diff/-/diff-4.0.2.tgz",
-      "integrity": "sha512-58lmxKSA4BNyLz+HHMUzlOEpg09FV+ev6ZMe3vJihgdxzgcwZ8VoEEPmALCZG9LmqfVoNMMKpttIYTVG6uDY7A==",
-      "optional": true,
-      "peer": true,
-      "engines": {
-        "node": ">=0.3.1"
-      }
-    },
     "node_modules/tsconfig-paths": {
       "version": "3.14.2",
       "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.2.tgz",
@@ -10691,13 +10565,6 @@
         "node": ">=8"
       }
     },
-    "node_modules/v8-compile-cache-lib": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz",
-      "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==",
-      "optional": true,
-      "peer": true
-    },
     "node_modules/v8-to-istanbul": {
       "version": "9.1.0",
       "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-9.1.0.tgz",
@@ -11198,16 +11065,6 @@
         "node": ">=10"
       }
     },
-    "node_modules/yn": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz",
-      "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==",
-      "optional": true,
-      "peer": true,
-      "engines": {
-        "node": ">=6"
-      }
-    },
     "node_modules/yocto-queue": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
@@ -11580,29 +11437,6 @@
       "integrity": "sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw==",
       "dev": true
     },
-    "@cspotcode/source-map-support": {
-      "version": "0.8.1",
-      "resolved": "https://registry.npmjs.org/@cspotcode/source-map-support/-/source-map-support-0.8.1.tgz",
-      "integrity": "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw==",
-      "optional": true,
-      "peer": true,
-      "requires": {
-        "@jridgewell/trace-mapping": "0.3.9"
-      },
-      "dependencies": {
-        "@jridgewell/trace-mapping": {
-          "version": "0.3.9",
-          "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.9.tgz",
-          "integrity": "sha512-3Belt6tdc8bPgAtbcmdtNJlirVoTmEb5e2gC94PnkwEW9jI6CAHUeoG85tjWP5WquqfavoMtMwiG4P926ZKKuQ==",
-          "optional": true,
-          "peer": true,
-          "requires": {
-            "@jridgewell/resolve-uri": "^3.0.3",
-            "@jridgewell/sourcemap-codec": "^1.4.10"
-          }
-        }
-      }
-    },
     "@dqbd/tiktoken": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/@dqbd/tiktoken/-/tiktoken-1.0.2.tgz",
@@ -11830,6 +11664,11 @@
       "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.1.1.tgz",
       "integrity": "sha512-m0G6wlnhm/AX0H12IOWtK8gASEMffnX08RtKkCgTdHb9JpHKGloI7icFfLg9ZmQeavcvR0PKmzxClyuFPSjKWw=="
     },
+    "@huggingface/jinja": {
+      "version": "0.2.2",
+      "resolved": "https://registry.npmjs.org/@huggingface/jinja/-/jinja-0.2.2.tgz",
+      "integrity": "sha512-/KPde26khDUIPkTGU82jdtTW9UAuvUTumCAbFs/7giR0SxsvZC4hru51PBvpijH6BVkHcROcvZM/lpy5h1jRRA=="
+    },
     "@humanwhocodes/config-array": {
       "version": "0.11.8",
       "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.11.8.tgz",
@@ -12418,34 +12257,6 @@
         "lodash": "^4.17.21"
       }
     },
-    "@tsconfig/node10": {
-      "version": "1.0.9",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node10/-/node10-1.0.9.tgz",
-      "integrity": "sha512-jNsYVVxU8v5g43Erja32laIDHXeoNvFEpX33OK4d6hljo3jDhCBDhx5dhCCTMWUojscpAagGiRkBKxpdl9fxqA==",
-      "optional": true,
-      "peer": true
-    },
-    "@tsconfig/node12": {
-      "version": "1.0.11",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node12/-/node12-1.0.11.tgz",
-      "integrity": "sha512-cqefuRsh12pWyGsIoBKJA9luFu3mRxCA+ORZvA4ktLSzIuCUtWVxGIuXigEwO5/ywWFMZ2QEGKWvkZG1zDMTag==",
-      "optional": true,
-      "peer": true
-    },
-    "@tsconfig/node14": {
-      "version": "1.0.3",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node14/-/node14-1.0.3.tgz",
-      "integrity": "sha512-ysT8mhdixWK6Hw3i1V2AeRqZ5WfXg1G43mqoYlM2nc6388Fq5jcXyr5mRsqViLx/GJYdoL0bfXD8nmF+Zn/Iow==",
-      "optional": true,
-      "peer": true
-    },
-    "@tsconfig/node16": {
-      "version": "1.0.3",
-      "resolved": "https://registry.npmjs.org/@tsconfig/node16/-/node16-1.0.3.tgz",
-      "integrity": "sha512-yOlFc+7UtL/89t2ZhjPvvB/DeAr3r+Dq58IgzsFkOAvVC6NMJXmCGjbptdXdR9qsX7pKcTL+s87FtYREi2dEEQ==",
-      "optional": true,
-      "peer": true
-    },
     "@types/chai": {
       "version": "4.3.4",
       "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.3.4.tgz",
@@ -12767,10 +12578,11 @@
       }
     },
     "@xenova/transformers": {
-      "version": "2.5.2",
-      "resolved": "https://registry.npmjs.org/@xenova/transformers/-/transformers-2.5.2.tgz",
-      "integrity": "sha512-zmCKv6xMoYPlLlH1f9gWYTsnKfjGDfVcoH0POnqIjT0leB+CljnN+YrPSE5B1/xnXQCGOF03e/SknOCqlLRzRw==",
+      "version": "2.17.2",
+      "resolved": "https://registry.npmjs.org/@xenova/transformers/-/transformers-2.17.2.tgz",
+      "integrity": "sha512-lZmHqzrVIkSvZdKZEx7IYY51TK0WDrC8eR0c5IMnBsO8di8are1zzw8BlLhyO2TklZKLN5UffNGs1IJwT6oOqQ==",
       "requires": {
+        "@huggingface/jinja": "^0.2.2",
         "onnxruntime-node": "1.14.0",
         "onnxruntime-web": "1.14.0",
         "sharp": "^0.32.0"
@@ -13447,13 +13259,6 @@
       "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.29.1.tgz",
       "integrity": "sha512-+jwgnhg6cQxKYIIjGtAHq2nwUOolo9eoFZ4sHfUH09BLXBgxnH4gA0zEd+t+BO2cNB8idaBtZFcFTRjQJRJmAw=="
     },
-    "create-require": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/create-require/-/create-require-1.1.1.tgz",
-      "integrity": "sha512-dcKFX3jn0MpIaXjisoRvexIJVEKzaq7z2rZKxf+MSr9TkdmHmsU4m2lcLojrj/FHl8mk5VxMmYA+ftRkP/3oKQ==",
-      "optional": true,
-      "peer": true
-    },
     "cross-spawn": {
       "version": "7.0.3",
       "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
@@ -15709,13 +15514,6 @@
         }
       }
     },
-    "make-error": {
-      "version": "1.3.6",
-      "resolved": "https://registry.npmjs.org/make-error/-/make-error-1.3.6.tgz",
-      "integrity": "sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw==",
-      "optional": true,
-      "peer": true
-    },
     "markdown-table": {
       "version": "3.0.3",
       "resolved": "https://registry.npmjs.org/markdown-table/-/markdown-table-3.0.3.tgz",
@@ -18072,51 +17870,6 @@
       "resolved": "https://registry.npmjs.org/trough/-/trough-2.1.0.tgz",
       "integrity": "sha512-AqTiAOLcj85xS7vQ8QkAV41hPDIJ71XJB4RCUrzo/1GM2CQwhkJGaf9Hgr7BOugMRpgGUrqRg/DrBDl4H40+8g=="
     },
-    "ts-node": {
-      "version": "10.9.1",
-      "resolved": "https://registry.npmjs.org/ts-node/-/ts-node-10.9.1.tgz",
-      "integrity": "sha512-NtVysVPkxxrwFGUUxGYhfux8k78pQB3JqYBXlLRZgdGUqTO5wU/UyHop5p70iEbGhB7q5KmiZiU0Y3KlJrScEw==",
-      "optional": true,
-      "peer": true,
-      "requires": {
-        "@cspotcode/source-map-support": "^0.8.0",
-        "@tsconfig/node10": "^1.0.7",
-        "@tsconfig/node12": "^1.0.7",
-        "@tsconfig/node14": "^1.0.0",
-        "@tsconfig/node16": "^1.0.2",
-        "acorn": "^8.4.1",
-        "acorn-walk": "^8.1.1",
-        "arg": "^4.1.0",
-        "create-require": "^1.1.0",
-        "diff": "^4.0.1",
-        "make-error": "^1.1.1",
-        "v8-compile-cache-lib": "^3.0.1",
-        "yn": "3.1.1"
-      },
-      "dependencies": {
-        "acorn-walk": {
-          "version": "8.2.0",
-          "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-8.2.0.tgz",
-          "integrity": "sha512-k+iyHEuPgSw6SbuDpGQM+06HQUa04DZ3o+F6CSzXMvvI5KMvnaEqXe+YVe555R9nn6GPt404fos4wcgpw12SDA==",
-          "optional": true,
-          "peer": true
-        },
-        "arg": {
-          "version": "4.1.3",
-          "resolved": "https://registry.npmjs.org/arg/-/arg-4.1.3.tgz",
-          "integrity": "sha512-58S9QDqG0Xx27YwPSt9fJxivjYl432YCwfDMfZ+71RAqUrZef7LrKQZ3LHLOwCS4FLNBplP533Zx895SeOCHvA==",
-          "optional": true,
-          "peer": true
-        },
-        "diff": {
-          "version": "4.0.2",
-          "resolved": "https://registry.npmjs.org/diff/-/diff-4.0.2.tgz",
-          "integrity": "sha512-58lmxKSA4BNyLz+HHMUzlOEpg09FV+ev6ZMe3vJihgdxzgcwZ8VoEEPmALCZG9LmqfVoNMMKpttIYTVG6uDY7A==",
-          "optional": true,
-          "peer": true
-        }
-      }
-    },
     "tsconfig-paths": {
       "version": "3.14.2",
       "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.2.tgz",
@@ -18372,13 +18125,6 @@
         "sade": "^1.7.3"
       }
     },
-    "v8-compile-cache-lib": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz",
-      "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==",
-      "optional": true,
-      "peer": true
-    },
     "v8-to-istanbul": {
       "version": "9.1.0",
       "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-9.1.0.tgz",
@@ -18689,13 +18435,6 @@
       "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
       "dev": true
     },
-    "yn": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz",
-      "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==",
-      "optional": true,
-      "peer": true
-    },
     "yocto-queue": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
diff --git a/ui/package.json b/ui/package.json
index e3fd3d7..06ed642 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -17,7 +17,7 @@
     "@radix-ui/react-select": "^1.2.2",
     "@radix-ui/react-tooltip": "^1.0.6",
     "@tabler/icons-react": "^2.9.0",
-    "@xenova/transformers": "^2.5.2",
+    "@xenova/transformers": "^2.17.2",
     "chromadb": "^1.5.6",
     "class-variance-authority": "^0.7.0",
     "clsx": "^2.0.0",
diff --git a/ui/pages/api/fetch-documents.ts b/ui/pages/api/fetch-documents.ts
index 9304e48..c660075 100644
--- a/ui/pages/api/fetch-documents.ts
+++ b/ui/pages/api/fetch-documents.ts
@@ -1,25 +1,91 @@
-import type { NextApiRequest, NextApiResponse } from "next";
-import { ChromaClient, TransformersEmbeddingFunction } from "chromadb";
+import type { NextApiRequest, NextApiResponse } from 'next';
+import { ChromaClient, TransformersEmbeddingFunction } from 'chromadb';
+import { pipeline } from '@xenova/transformers';
+
+// Singleton for reranker to avoid reloading model on every request
+class RerankerPipeline {
+  static instance: any = null;
+  static async getInstance() {
+    if (!this.instance) {
+      // Use a fast and efficient cross-encoder model for reranking
+      this.instance = pipeline('text-classification', 'Xenova/ms-marco-MiniLM-L-6-v2');
+    }
+    return this.instance;
+  }
+}
 
 export default async function handler(req: NextApiRequest, res: NextApiResponse) {
   try {
     const client = new ChromaClient({
-      path: "http://chroma-server:8000",
+      path: process.env.CHROMA_PATH || 'http://chroma-server:8000',
     });
 
     const query = req.body.input;
+    const finalNResults = Math.min(Number(req.body.nResults ?? 6), 10);
+    // Fetch more results initially to have a good pool for reranking
+    const fetchNResults = finalNResults * 3; 
+
+    // Metadata filtering support
+    const where = req.body.where || undefined;
 
     const embedder = new TransformersEmbeddingFunction();
 
-    const collection = await client.getOrCreateCollection({ name: "default-collection", embeddingFunction: embedder });
+    const collection = await client.getOrCreateCollection({
+      name: 'default-collection',
+      embeddingFunction: embedder,
+    });
+
+    // 1. Retrieval Stage
+    const results = await collection.query({
+      nResults: fetchNResults,
+      queryTexts: [query],
+      where,
+      include: ['documents', 'metadatas', 'distances'] as any,
+    });
+
+    const documents = results.documents[0] || [];
+    const metadatas = results.metadatas[0] || [];
+    const distances = results.distances?.[0] || [];
+
+    if (documents.length === 0) {
+      return res.status(200).json(results);
+    }
+
+    // 2. Reranking Stage
+    const reranker = await RerankerPipeline.getInstance();
+    
+    // Format pairs for the cross encoder: [query, document]
+    const pairs = documents.map((doc) => [query, doc]);
+    
+    // Score the pairs
+    const scores = await reranker(pairs);
+
+    // Combine all data to sort
+    const scoredResults = documents.map((doc, i) => ({
+      document: doc,
+      metadata: metadatas[i],
+      distance: distances[i],
+      // For text-classification pipelines, the output is usually [{label: "LABEL_0", score: 0.99}, ...]
+      // Note: for some models we might need to extract the score for the positive class.
+      // ms-marco models output a single score or positive/negative. We use the raw score.
+      rerankScore: scores[i]?.score ?? 0, 
+    }));
+
+    // Sort by rerank score descending
+    scoredResults.sort((a, b) => b.rerankScore - a.rerankScore);
+
+    // Take top K
+    const topResults = scoredResults.slice(0, finalNResults);
 
-  // query the collection
-  const results = await collection.query({
-      nResults: 4, 
-      queryTexts: [query]
-  }) 
+    // Format back to ChromaDB query result format
+    const finalResult = {
+      documents: [topResults.map((r) => r.document)],
+      metadatas: [topResults.map((r) => r.metadata)],
+      distances: [topResults.map((r) => r.distance)],
+      rerankScores: [topResults.map((r) => r.rerankScore)],
+    };
 
-    res.status(200).json(results);
+    res.status(200).json(finalResult);
   } catch (error) {
     if (error instanceof Error) {
       console.error('Error message:', error.message);
diff --git a/ui/pages/api/inject-documents.ts b/ui/pages/api/inject-documents.ts
index 532a635..729dfd9 100644
--- a/ui/pages/api/inject-documents.ts
+++ b/ui/pages/api/inject-documents.ts
@@ -3,10 +3,14 @@ import type { NextApiRequest, NextApiResponse } from 'next';
 import { ChromaClient, TransformersEmbeddingFunction } from 'chromadb';
 import { IncomingForm } from 'formidable';
 import { PDFLoader } from 'langchain/document_loaders/fs/pdf';
-import { RecursiveCharacterTextSplitter } from "langchain/text_splitter";
+import { RecursiveCharacterTextSplitter } from 'langchain/text_splitter';
 
 import path from 'path';
 import { v4 as uuidv4 } from 'uuid';
+import {
+  buildScientificMetadata,
+  SCIENTIFIC_TEXT_SEPARATORS,
+} from '@/utils/server/scientific-rag';
 
 export const config = {
   api: {
@@ -37,18 +41,22 @@ export default async function handler(
 
       const originalDocs = await loader.load();
 
-      console.log(JSON.stringify(originalDocs));
-
+      console.log('Original docs loaded:', originalDocs.length);
 
       const splitter = new RecursiveCharacterTextSplitter({
         chunkSize: 500,
         chunkOverlap: 100,
-      });      
+        separators: SCIENTIFIC_TEXT_SEPARATORS,
+      });
 
       const docs = await splitter.splitDocuments(originalDocs);
- 
+
+      // Extract filename for fallback title
+      const originalFileName = Array.isArray(files.pdf) ? files.pdf[0].originalFilename : (files.pdf as any).originalFilename;
+      const fallbackTitle = originalFileName || path.basename(files.pdf[0].filepath);
+
       // Process the documents and perform other logic
-      const { ids, metadatas, documentContents } = processDocuments(docs);
+      const { ids, metadatas, documentContents } = processDocuments(docs, fallbackTitle);
 
       const embedder = new TransformersEmbeddingFunction();
       const collection = await client.getOrCreateCollection({
@@ -75,28 +83,33 @@ export default async function handler(
   }
 }
 
-function processDocuments(docs: any) {
+function processDocuments(docs: any[], fallbackTitle: string) {
   const ids = [];
   const metadatas = [];
   const documentContents = [];
 
-  for (const document of docs) {
+  for (let i = 0; i < docs.length; i++) {
+    const document = docs[i];
+    
     // Generate an ID for each document, or use some existing unique identifier
     const id = uuidv4();
     ids.push(id);
 
-    const fallbackTitle = path.basename(document.metadata.source);
-    const titleFromMetadata = document.metadata.pdf.info.Title;
-
-    const title = titleFromMetadata && titleFromMetadata.length > 0 ? titleFromMetadata : fallbackTitle;
+    // Build rich scientific metadata
+    const metadata = buildScientificMetadata(document, fallbackTitle, i);
+    
+    // Ensure ChromaDB only receives supported metadata types (string, boolean, number)
+    // We convert everything to strings/numbers
+    const safeMetadata: any = {};
+    for (const [key, value] of Object.entries(metadata)) {
+      if (typeof value === 'string' || typeof value === 'number' || typeof value === 'boolean') {
+        safeMetadata[key] = value;
+      } else if (value !== undefined && value !== null) {
+        safeMetadata[key] = String(value);
+      }
+    }
 
-  
-    const metadata = {
-      title: title,
-      page: document.metadata.loc.pageNumber, // Define this function to extract chapter info
-      source: document.metadata.source, // Define this function to extract verse info
-    };
-    metadatas.push(metadata);
+    metadatas.push(safeMetadata);
 
     // Add the page content to the documents array
     documentContents.push(document.pageContent);
diff --git a/ui/pages/api/rag-chat.ts b/ui/pages/api/rag-chat.ts
index ce84d67..b289b4b 100644
--- a/ui/pages/api/rag-chat.ts
+++ b/ui/pages/api/rag-chat.ts
@@ -29,8 +29,16 @@ async function fetchAndFormatDocuments(lastMessageContent: string) {
     }
 
     const data = await response.json();
-    const result = data.metadatas[0].map((metadata: any, index: number) => {
-      return `Source ${index + 1}) Title: ${metadata.title}, Page: ${metadata.page}, Content: ${data.documents[0][index]}\n`;
+    const { formatRetrievedDocument } = require('@/utils/server/scientific-rag');
+    
+    const result = data.documents[0].map((content: string, index: number) => {
+      return formatRetrievedDocument({
+        content,
+        metadata: data.metadatas[0][index],
+        distance: data.distances?.[0]?.[index],
+        rerankScore: data.rerankScores?.[0]?.[index],
+        index,
+      }) + '\\n\\n';
     }).join('');
 
     console.log(result);
@@ -107,7 +115,7 @@ const handler = async (req: Request): Promise<Response> => {
       {
         role: "user",
         content: codeBlock`
-          Here is the relevant documentation:
+          Here is the relevant documentation with scientific citations and relevance scores:
           ${relevantDocuments}
         `,
       },
@@ -130,7 +138,10 @@ const handler = async (req: Request): Promise<Response> => {
             - Prefer splitting your response into multiple paragraphs.
           `}
           ${oneLine`
-            - Output as markdown with citations based on the documentation.
+            - You MUST cite your sources exactly using the provided bracket format, e.g. [paper-title:pX:cY].
+          `}
+          ${oneLine`
+            - Pay attention to the Relevance Score and Section metadata. Give priority to context with higher scores.
           `}
         `,
       },
diff --git a/ui/utils/server/scientific-rag.ts b/ui/utils/server/scientific-rag.ts
new file mode 100644
index 0000000..1b55177
--- /dev/null
+++ b/ui/utils/server/scientific-rag.ts
@@ -0,0 +1,159 @@
+export type ScientificDocument = {
+  pageContent: string;
+  metadata: {
+    loc?: {
+      pageNumber?: number;
+    };
+    pdf?: {
+      info?: {
+        Title?: string;
+      };
+    };
+    source?: string;
+    [key: string]: unknown;
+  };
+};
+
+export type ScientificChunkMetadata = {
+  title: string;
+  page: number | string;
+  source: string;
+  section: string;
+  chunkIndex: number;
+  citationKey: string;
+};
+
+const SCIENTIFIC_SECTIONS = [
+  'abstract',
+  'introduction',
+  'background',
+  'methods',
+  'methodology',
+  'materials and methods',
+  'results',
+  'discussion',
+  'limitations',
+  'conclusion',
+  'references',
+];
+
+export const SCIENTIFIC_TEXT_SEPARATORS = [
+  '\nAbstract',
+  '\nABSTRACT',
+  '\nIntroduction',
+  '\nINTRODUCTION',
+  '\nMethods',
+  '\nMETHODS',
+  '\nMaterials and Methods',
+  '\nResults',
+  '\nRESULTS',
+  '\nDiscussion',
+  '\nDISCUSSION',
+  '\nConclusion',
+  '\nCONCLUSION',
+  '\nReferences',
+  '\nREFERENCES',
+  '\n\n',
+  '\n',
+  '. ',
+  ' ',
+  '',
+];
+
+export const normalizeTitle = (
+  titleFromMetadata: string | undefined,
+  fallbackTitle: string,
+) => {
+  const title = titleFromMetadata?.trim();
+
+  return title && title.length > 0 ? title : fallbackTitle;
+};
+
+export const detectScientificSection = (content: string) => {
+  const firstLines = content
+    .split('\n')
+    .slice(0, 8)
+    .join(' ')
+    .toLowerCase();
+
+  for (const section of SCIENTIFIC_SECTIONS) {
+    const sectionRegex = new RegExp(`\\b${section}\\b`, 'i');
+
+    if (sectionRegex.test(firstLines)) {
+      return section;
+    }
+  }
+
+  return 'body';
+};
+
+export const buildCitationKey = ({
+  title,
+  page,
+  chunkIndex,
+}: {
+  title: string;
+  page: number | string;
+  chunkIndex: number;
+}) => {
+  const slug = title
+    .toLowerCase()
+    .replace(/[^a-z0-9]+/g, '-')
+    .replace(/(^-|-$)/g, '')
+    .slice(0, 40);
+
+  return `${slug || 'document'}:p${page}:c${chunkIndex + 1}`;
+};
+
+export const buildScientificMetadata = (
+  document: ScientificDocument,
+  fallbackTitle: string,
+  chunkIndex: number,
+): ScientificChunkMetadata => {
+  const title = normalizeTitle(document.metadata.pdf?.info?.Title, fallbackTitle);
+  const page = document.metadata.loc?.pageNumber ?? 'unknown';
+  const section = detectScientificSection(document.pageContent);
+
+  return {
+    title,
+    page,
+    source: document.metadata.source ?? fallbackTitle,
+    section,
+    chunkIndex,
+    citationKey: buildCitationKey({ title, page, chunkIndex }),
+  };
+};
+
+export const formatRetrievedDocument = ({
+  content,
+  metadata,
+  distance,
+  index,
+  rerankScore,
+}: {
+  content: string;
+  metadata: Partial<ScientificChunkMetadata>;
+  distance?: number;
+  index: number;
+  rerankScore?: number;
+}) => {
+  const citationKey = metadata.citationKey ?? `source-${index + 1}`;
+  const page = metadata.page ?? 'unknown';
+  const section = metadata.section ?? 'body';
+  const scoreLine = typeof rerankScore === 'number' 
+    ? `Relevance Score: ${rerankScore.toFixed(4)}\n`
+    : typeof distance === 'number' 
+      ? `Distance: ${distance.toFixed(4)}\n` 
+      : '';
+
+  return [
+    `Source ${index + 1} [${citationKey}]`,
+    `Title: ${metadata.title ?? 'Untitled'}`,
+    `Page: ${page}`,
+    `Section: ${section}`,
+    scoreLine.trim(),
+    `Content: ${content}`,
+  ]
+    .filter(Boolean)
+    .join('\n');
+};