Datasets:

Milad96
/

Kluyveromyces-marxianus-chunks

Error code:   FeaturesError
Exception:    ArrowInvalid
Message:      Schema at index 1 was different: 
text: string
token_count: int64
char_count: int64
word_count: int64
semantic_coherence: int64
information_density: double
quality_score: double
entities: struct<genes: list<item: string>, proteins: list<item: null>, pathways: list<item: null>, organisms: list<item: null>, conditions: list<item: string>>
biobert_ready: bool
timestamp: string
source: struct<split: string, doc_id: int64>
chunk_id: string
global_id: int64
vs
text: string
token_count: int64
char_count: int64
word_count: int64
semantic_coherence: int64
information_density: double
quality_score: double
entities: struct<conditions: list<item: string>, genes: list<item: string>, organisms: list<item: null>, pathways: list<item: null>, proteins: list<item: null>>
biobert_ready: bool
timestamp: timestamp[ns]
source: struct<doc_id: int64, split: string>
chunk_id: string
global_id: int64
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 228, in compute_first_rows_from_streaming_response
                  iterable_dataset = iterable_dataset._resolve_features()
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 3496, in _resolve_features
                  features = _infer_features_from_batch(self.with_format(None)._head())
                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2257, in _head
                  return next(iter(self.iter(batch_size=n)))
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2461, in iter
                  for key, example in iterator:
                                      ^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 1952, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 1974, in _iter_arrow
                  yield from self.ex_iterable._iter_arrow()
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 547, in _iter_arrow
                  yield new_key, pa.Table.from_batches(chunks_buffer)
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "pyarrow/table.pxi", line 5039, in pyarrow.lib.Table.from_batches
                File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
                File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
              pyarrow.lib.ArrowInvalid: Schema at index 1 was different: 
              text: string
              token_count: int64
              char_count: int64
              word_count: int64
              semantic_coherence: int64
              information_density: double
              quality_score: double
              entities: struct<genes: list<item: string>, proteins: list<item: null>, pathways: list<item: null>, organisms: list<item: null>, conditions: list<item: string>>
              biobert_ready: bool
              timestamp: string
              source: struct<split: string, doc_id: int64>
              chunk_id: string
              global_id: int64
              vs
              text: string
              token_count: int64
              char_count: int64
              word_count: int64
              semantic_coherence: int64
              information_density: double
              quality_score: double
              entities: struct<conditions: list<item: string>, genes: list<item: string>, organisms: list<item: null>, pathways: list<item: null>, proteins: list<item: null>>
              biobert_ready: bool
              timestamp: timestamp[ns]
              source: struct<doc_id: int64, split: string>
              chunk_id: string
              global_id: int64

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🧬 Kluyveromyces marxianus - BioBERT-Optimized Chunks

PhD Research Dataset: Functional Genomics of Robust Linear Yeasts

Overview

Semantically-optimized 512-token chunks for BioBERT fine-tuning, processed with BiOMistral-7B.

Dataset Info

Processing Date: 2025-11-01
Target Model: BioBERT-Large v1.1
Chunk Size: 512 tokens (optimal)
Source: Milad96/Kluyveromyces-marxianus

Features

Deep semantic coherence analysis
Automatic genomic entity extraction
Quality scoring and filtering
BioBERT-ready format

Usage

from datasets import load_dataset
import json

# Load high-quality chunks
with open('chunks_high_quality.json', 'r') as f:
    chunks = json.load(f)

# Each chunk has:
# - text: optimized content
# - token_count: ~512
# - semantic_coherence: 0-1
# - quality_score: 0-1
# - entities: {genes, proteins, pathways}

Citation

@dataset{kmx_chunks_2024,
  author = {Milad96},
  title = {Kluyveromyces marxianus BioBERT Chunks},
  year = {2024},
  publisher = {HuggingFace},
  url = {https://huggingface.co/datasets/Milad96/Kluyveromyces-marxianus-chunks}
}

License

Apache 2.0

Downloads last month: 187

Total file size:

4.8 MB