fix: improve inline citation parsing bump:patch

libs/kotaemon/kotaemon/indices/qa/citation_qa.py

@@ -342,11 +342,11 @@ def prepare_citations(self, answer, docs) -> tuple[list[Document], list[Document
 
                 span_idx = span.get("idx", None)
                 if span_idx is not None:
-                    to_highlight = f"【{span_idx + 1}】" + to_highlight
+                    to_highlight = f"【{span_idx}】" + to_highlight
 
                 text += Render.highlight(
                     to_highlight,
-                    elem_id=str(span_idx + 1) if span_idx is not None else None,
+                    elem_id=str(span_idx) if span_idx is not None else None,
                 )
                 if idx < len(ss) - 1:
                     text += cur_doc.text[span["end"] : ss[idx + 1]["start"]]

libs/kotaemon/kotaemon/indices/qa/citation_qa_inline.py

@@ -1,14 +1,14 @@
 import re
 import threading
 from collections import defaultdict
+from dataclasses import dataclass
 from typing import Generator
 
 import numpy as np
 
 from kotaemon.base import AIMessage, Document, HumanMessage, SystemMessage
 from kotaemon.llms import PromptTemplate
 
-from .citation import CiteEvidence
 from .citation_qa import CITATION_TIMEOUT, MAX_IMAGES, AnswerWithContextPipeline
 from .format_context import EVIDENCE_MODE_FIGURE
 from .utils import find_start_end_phrase
@@ -61,12 +61,27 @@
 END_PHRASE: this shows good retrieval quality.
 
 FINAL ANSWER
-An alternative to semantic chunking is fixed-size chunking. This traditional method involves splitting documents into chunks of a predetermined or user-specified size, regardless of semantic content, which is computationally efficient【1】. However, it may result in the fragmentation of semantically related content, thereby potentially degrading retrieval performance【2】.
+An alternative to semantic chunking is fixed-size chunking. This traditional method involves splitting documents into chunks of a predetermined or user-specified size, regardless of semantic content, which is computationally efficient【1】. However, it may result in the fragmentation of semantically related content, thereby potentially degrading retrieval performance【1】【2】.
 
 QUESTION: {question}\n
 ANSWER:
 """  # noqa
 
+START_ANSWER = "FINAL ANSWER"
+START_CITATION = "CITATION LIST"
+CITATION_PATTERN = r"citation【(\d+)】"
+START_ANSWER_PATTERN = "start_phrase:"
+END_ANSWER_PATTERN = "end_phrase:"
+
+
+@dataclass
+class InlineEvidence:
+    """List of evidences to support the answer."""
+
+    start_phrase: str | None = None
+    end_phrase: str | None = None
+    idx: int | None = None
+
 
 class AnswerWithInlineCitation(AnswerWithContextPipeline):
     """Answer the question based on the evidence with inline citation"""
@@ -85,15 +100,54 @@ def get_prompt(self, question, evidence, evidence_mode: int):
 
         return prompt, evidence
 
-    def answer_to_citations(self, answer):
-        evidences = []
+    def answer_to_citations(self, answer) -> list[InlineEvidence]:
+        citations: list[InlineEvidence] = []
         lines = answer.split("\n")
-        for line in lines:
-            for keyword in ["START_PHRASE:", "END_PHRASE:"]:
-                if line.startswith(keyword):
-                    evidences.append(line[len(keyword) :].strip())
 
-        return CiteEvidence(evidences=evidences)
+        current_evidence = None
+
+        for line in lines:
+            # check citation idx using regex
+            match = re.match(CITATION_PATTERN, line.lower())
+
+            if match:
+                try:
+                    parsed_citation_idx = int(match.group(1))
+                except ValueError:
+                    parsed_citation_idx = None
+
+                # conclude the current evidence if exists
+                if current_evidence:
+                    citations.append(current_evidence)
+                    current_evidence = None
+
+                current_evidence = InlineEvidence(idx=parsed_citation_idx)
+            else:
+                for keyword in [START_ANSWER_PATTERN, END_ANSWER_PATTERN]:
+                    if line.lower().startswith(keyword):
+                        matched_phrase = line[len(keyword) :].strip()
+                        if not current_evidence:
+                            current_evidence = InlineEvidence(idx=None)
+
+                        if keyword == START_ANSWER_PATTERN:
+                            current_evidence.start_phrase = matched_phrase
+                        else:
+                            current_evidence.end_phrase = matched_phrase
+
+                        break
+
+            if (
+                current_evidence
+                and current_evidence.end_phrase
+                and current_evidence.start_phrase
+            ):
+                citations.append(current_evidence)
+                current_evidence = None
+
+        if current_evidence:
+            citations.append(current_evidence)
+
+        return citations
 
     def replace_citation_with_link(self, answer: str):
         # Define the regex pattern to match 【number】
@@ -114,6 +168,8 @@ def replace_citation_with_link(self, answer: str):
                 ),
             )
 
+        answer = answer.replace(START_CITATION, "")
+
         return answer
 
     def stream(  # type: ignore
@@ -178,21 +234,31 @@ def mindmap_call():
             # append main prompt
             messages.append(HumanMessage(content=prompt))
 
-        START_ANSWER = "FINAL ANSWER"
-        start_of_answer = True
         final_answer = ""
 
         try:
             # try streaming first
             print("Trying LLM streaming")
             for out_msg in self.llm.stream(messages):
                 if START_ANSWER in output:
+                    if not final_answer:
+                        try:
+                            left_over_answer = output.split(START_ANSWER)[1].lstrip()
+                        except IndexError:
+                            left_over_answer = ""
+                        if left_over_answer:
+                            out_msg.text = left_over_answer + out_msg.text
+
                     final_answer += (
-                        out_msg.text.lstrip() if start_of_answer else out_msg.text
+                        out_msg.text.lstrip() if not final_answer else out_msg.text
                     )
-                    start_of_answer = False
                     yield Document(channel="chat", content=out_msg.text)
 
+                    # check for the edge case of citation list is repeated
+                    # with smaller LLMs
+                    if START_CITATION in out_msg.text:
+                        break
+
                 output += out_msg.text
                 logprobs += out_msg.logprobs
         except NotImplementedError:
@@ -235,10 +301,15 @@ def match_evidence_with_context(self, answer, docs) -> dict[str, list[dict]]:
         if not answer.metadata["citation"]:
             return spans
 
-        evidences = answer.metadata["citation"].evidences
+        evidences = answer.metadata["citation"]
+
+        for e_id, evidence in enumerate(evidences):
+            start_phrase, end_phrase = evidence.start_phrase, evidence.end_phrase
+            evidence_idx = evidence.idx
+
+            if evidence_idx is None:
+                evidence_idx = e_id + 1
 
-        for start_idx in range(0, len(evidences), 2):
-            start_phrase, end_phrase = evidences[start_idx : start_idx + 2]
             best_match = None
             best_match_length = 0
             best_match_doc_idx = None
@@ -259,7 +330,7 @@ def match_evidence_with_context(self, answer, docs) -> dict[str, list[dict]]:
                     {
                         "start": best_match[0],
                         "end": best_match[1],
-                        "idx": start_idx // 2,  # implicitly set from the start_idx
+                        "idx": evidence_idx,
                     }
                 )
         return spans