# The Signal in the Noise: An Auditable Reliability Layer for Biomedical Text Classification

arXiv: https://arxiv.org/abs/2608.28595 · HTML: https://mlsanity.com/paper/2608.28595/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 18 references that are in the map.
- First posted on arXiv 16 Jun 2026.

## Builds on (most cited first, 6 of 6)

- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Snorkel: Rapid Training Data Creation with Weak Supervision](https://mlsanity.com/paper/1711.10160/) (2017)
- [Synthetic and Natural Noise Both Break Neural Machine Translation](https://mlsanity.com/paper/1711.02173/) (2017)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [CORD-19: The COVID-19 Open Research Dataset](https://mlsanity.com/paper/2004.10706/) (2020)
- [Combating Adversarial Misspellings with Robust Word Recognition](https://mlsanity.com/paper/1905.11268/) (2019)

## Abstract (arXiv)

Biomedical NLP pipelines routinely presuppose clean input text, yet large-scale corpora assembled through automated PDF parsing harbour pervasive OCR-like artifacts, token splits and merges, hyphenation remnants, and character-level corruption, that systematically erode lexical evidence and degrade downstream classifiers. We introduce a conservative, fully auditable spell-correction reliability layer conceived as a safety-oriented preprocessing module rather than a maximal-accuracy corrector: under conditions of uncertainty, the system abstains from editing, in accordance with a medical do-no-harm philosophy. The deterministic architecture couples bounded edit-distance candidate generation with corpus-derived n-gram scoring and a suite of biomedical safety gates that protect domain-critical terminology. We evaluate the layer both intrinsically, on a manually curated benchmark of 2,104 token-level cases, and extrinsically, on a tri-class CORD-19 topic classifier (Prevention, Treatment, Epidemiology) spanning 10,000 examples under a principled four-run protocol (Clean, Noisy, Restored, Safety). Intrinsically, the layer attains 94.61% error-fix recall on synthetic errors with zero harmful edits on negative controls. Downstream, it recovers approximately 80.45% of the noise-induced macro-F1 degradation, elevating macro-F1 from 0.7654 (Noisy) to 0.7717 (Restored) while preserving near-clean performance (Safety: 0.7721). A supplementary case study on 103 real-world OCR-extracted abstracts classified with BioBERT confirms that transformer encoders appeared relatively robust to mild noise, motivating a future grey-box architecture that integrates bounded neural signals and UMLS lexicons without compromising auditability. The system is fully deterministic, artifact-driven, and designed with deployment and auditability in mind.