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Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code:   StreamingRowsError
Exception:    CastError
Message:      Couldn't cast
set1_exact_match: struct<Dense: struct<chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: do (... 4624 chars omitted)
  child 0, Dense: struct<chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: dou (... 195 chars omitted)
      child 0, chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
          child 0, P@1: double
          child 1, R@1: double
          child 2, P@3: double
          child 3, R@3: double
          child 4, P@5: double
          child 5, R@5: double
          child 6, MRR: double
          child 7, NDCG@3: double
          child 8, NDCG@5: double
      child 1, source_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
          child 0, P@1: double
          child 1, R@1: double
          child 2, P@3: double
          child 3, R@3: double
          child 4, P@5: double
          child 5, R@5: double
          child 6, MRR: double
          child 7, NDCG@3: double
          child 8, NDCG@5: double
  child 1, BM25: struct<chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: dou (... 195 chars omitted)
      child 0, chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
          child 0, P@1: double
          chi
...
hild 3, R@3: double
                  child 4, P@5: double
                  child 5, R@5: double
                  child 6, MRR: double
                  child 7, NDCG@3: double
                  child 8, NDCG@5: double
              child 8, source_metrics: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
                  child 0, P@1: double
                  child 1, R@1: double
                  child 2, P@3: double
                  child 3, R@3: double
                  child 4, P@5: double
                  child 5, R@5: double
                  child 6, MRR: double
                  child 7, NDCG@3: double
                  child 8, NDCG@5: double
faiss_vectors: int64
n_chunks: int64
manual_annotation_instruction: struct<file_to_edit: string, column: string, grade_3: string, grade_2: string, grade_1: string, grad (... 12 chars omitted)
  child 0, file_to_edit: string
  child 1, column: string
  child 2, grade_3: string
  child 3, grade_2: string
  child 4, grade_1: string
  child 5, grade_0: string
n_answerable: int64
n_queries_total: int64
invalid_gold_chunk_ids_total: int64
outputs: struct<chunk_id_audit_summary: string, gold_chunk_preview: string, retrieval_candidate_review: strin (... 2 chars omitted)
  child 0, chunk_id_audit_summary: string
  child 1, gold_chunk_preview: string
  child 2, retrieval_candidate_review: string
embedding_model: string
query_file: string
n_unanswerable: int64
to
{'query_file': Value('string'), 'n_queries_total': Value('int64'), 'n_answerable': Value('int64'), 'n_unanswerable': Value('int64'), 'n_chunks': Value('int64'), 'faiss_vectors': Value('int64'), 'embedding_model': Value('string'), 'invalid_gold_chunk_ids_total': Value('int64'), 'outputs': {'chunk_id_audit_summary': Value('string'), 'gold_chunk_preview': Value('string'), 'retrieval_candidate_review': Value('string')}, 'manual_annotation_instruction': {'file_to_edit': Value('string'), 'column': Value('string'), 'grade_3': Value('string'), 'grade_2': Value('string'), 'grade_1': Value('string'), 'grade_0': Value('string')}}
because column names don't match
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
                  return get_rows(
                      dataset=dataset,
                  ...<4 lines>...
                      column_names=column_names,
                  )
                File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
                  return func(*args, **kwargs)
                File "/src/services/worker/src/worker/utils.py", line 127, in get_rows
                  rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
                File "/src/services/worker/src/worker/utils.py", line 483, in safe_iter
                  yield from ds.decode(False) if ds.features else ds
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2840, in __iter__
                  for key, example in ex_iterable:
                                      ^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2373, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2398, in _iter_arrow
                  for key, pa_table in self.ex_iterable._iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 419, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 343, in _generate_tables
                  self._cast_table(pa_table, json_field_paths=json_field_paths),
                  ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 132, in _cast_table
                  pa_table = table_cast(pa_table, self.info.features.arrow_schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              set1_exact_match: struct<Dense: struct<chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: do (... 4624 chars omitted)
                child 0, Dense: struct<chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: dou (... 195 chars omitted)
                    child 0, chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
                        child 0, P@1: double
                        child 1, R@1: double
                        child 2, P@3: double
                        child 3, R@3: double
                        child 4, P@5: double
                        child 5, R@5: double
                        child 6, MRR: double
                        child 7, NDCG@3: double
                        child 8, NDCG@5: double
                    child 1, source_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
                        child 0, P@1: double
                        child 1, R@1: double
                        child 2, P@3: double
                        child 3, R@3: double
                        child 4, P@5: double
                        child 5, R@5: double
                        child 6, MRR: double
                        child 7, NDCG@3: double
                        child 8, NDCG@5: double
                child 1, BM25: struct<chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: dou (... 195 chars omitted)
                    child 0, chunk_level: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
                        child 0, P@1: double
                        chi
              ...
              hild 3, R@3: double
                                child 4, P@5: double
                                child 5, R@5: double
                                child 6, MRR: double
                                child 7, NDCG@3: double
                                child 8, NDCG@5: double
                            child 8, source_metrics: struct<P@1: double, R@1: double, P@3: double, R@3: double, P@5: double, R@5: double, MRR: double, ND (... 29 chars omitted)
                                child 0, P@1: double
                                child 1, R@1: double
                                child 2, P@3: double
                                child 3, R@3: double
                                child 4, P@5: double
                                child 5, R@5: double
                                child 6, MRR: double
                                child 7, NDCG@3: double
                                child 8, NDCG@5: double
              faiss_vectors: int64
              n_chunks: int64
              manual_annotation_instruction: struct<file_to_edit: string, column: string, grade_3: string, grade_2: string, grade_1: string, grad (... 12 chars omitted)
                child 0, file_to_edit: string
                child 1, column: string
                child 2, grade_3: string
                child 3, grade_2: string
                child 4, grade_1: string
                child 5, grade_0: string
              n_answerable: int64
              n_queries_total: int64
              invalid_gold_chunk_ids_total: int64
              outputs: struct<chunk_id_audit_summary: string, gold_chunk_preview: string, retrieval_candidate_review: strin (... 2 chars omitted)
                child 0, chunk_id_audit_summary: string
                child 1, gold_chunk_preview: string
                child 2, retrieval_candidate_review: string
              embedding_model: string
              query_file: string
              n_unanswerable: int64
              to
              {'query_file': Value('string'), 'n_queries_total': Value('int64'), 'n_answerable': Value('int64'), 'n_unanswerable': Value('int64'), 'n_chunks': Value('int64'), 'faiss_vectors': Value('int64'), 'embedding_model': Value('string'), 'invalid_gold_chunk_ids_total': Value('int64'), 'outputs': {'chunk_id_audit_summary': Value('string'), 'gold_chunk_preview': Value('string'), 'retrieval_candidate_review': Value('string')}, 'manual_annotation_instruction': {'file_to_edit': Value('string'), 'column': Value('string'), 'grade_3': Value('string'), 'grade_2': Value('string'), 'grade_1': Value('string'), 'grade_0': Value('string')}}
              because column names don't match

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pretty_name: AI Muon Collider RAG language:

  • en tags:
  • particle-physics
  • muon-collider
  • rag
  • retrieval-augmented-generation
  • high-energy-physics ---# QA result to paper outputs

Copy both scripts into:

/eos/home-r/rjiang/RAG_muon_collider/

Then run:

chmod +x run_qa20_and_make_outputs.sh
./run_qa20_and_make_outputs.sh data/eval/queries_eval_v4_template.json 20

Or manually:

python evaluate_agentic_v3.py \
  --query_file data/eval/queries_eval_v4_template.json \
  --dense_weight 0.9 \
  --bm25_weight 0.1 \
  --judge_answers \
  --qa_systems hybrid,agentic_v3,oracle \
  --max_queries 20 \
  --output data/eval/eval_results_agentic_v3_qa20.json

python make_qa_paper_outputs.py \
  --input data/eval/eval_results_agentic_v3_qa20.json \
  --outdir paper_outputs_qa20

Outputs:

  • paper_outputs_qa20/figures/*.png
  • paper_outputs_qa20/tables_qa_results.tex
  • paper_outputs_qa20/figures_include.tex
  • paper_outputs_qa20/section_results_discussion.tex

Put the figures into Overleaf figures/, then paste the LaTeX tables and text into your paper.

AI Muon Collider RAG

A retrieval-augmented generation framework and evaluation dataset for literature related to muon collider physics.

Repository structure

main_pdf/

PDF documents used as the primary source corpus for the RAG system.

main_markdown/

Markdown/text representations extracted from the source PDFs. These files are used as machine-readable inputs for document chunking and retrieval.

data/index/

Pre-built retrieval resources used by the RAG system, including the vector/dense index, document chunks, and BM25-related files.

data/eval/

Evaluation datasets and outputs used to benchmark the retrieval and question-answering performance of the system.

RAG pipeline

The overall workflow is approximately:

PDF literature → text/Markdown extraction → document chunking → dense + sparse indexing → retrieval → LLM-based question answering → evaluation

Usage

The repository contains scripts for building the retrieval index, running the RAG chatbot, and evaluating its performance.

See the individual Python scripts for the current implementation.

Disclaimer

This repository is intended for research and development purposes. Source publications retain their respective copyrights and licenses.

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