# CLARA: Clarification of Language Ambiguity through Result Analysis for Natural-Language Cancer Genomics Queries

arXiv: https://arxiv.org/abs/2608.05195 · HTML: https://mlsanity.com/paper/2608.05195/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 21 references that are in the map.
- First posted on arXiv 3 Aug 2026.

## Builds on (most cited first, 11 of 11)

- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Spider: A Large-Scale Human-Labeled Dataset for Complex and Cross-Domain Semantic Parsing and Text-to-SQL Task](https://mlsanity.com/paper/1809.08887/) (2018)
- [PICARD: Parsing Incrementally for Constrained Auto-Regressive Decoding from Language Models](https://mlsanity.com/paper/2109.05093/) (2021)
- [Spider 2.0: Evaluating Language Models on Real-World Enterprise Text-to-SQL Workflows](https://mlsanity.com/paper/2411.07763/) (2024)
- [CoSQL: A Conversational Text-to-SQL Challenge Towards Cross-Domain Natural Language Interfaces to Databases](https://mlsanity.com/paper/1909.05378/) (2019)
- [SParC: Cross-Domain Semantic Parsing in Context](https://mlsanity.com/paper/1906.02285/) (2019)
- [Semantic Evaluation for Text-to-SQL with Distilled Test Suites](https://mlsanity.com/paper/2010.02840/) (2020)
- [Text-to-SQL Generation for Question Answering on Electronic Medical Records](https://mlsanity.com/paper/1908.01839/) (2019)
- [Robust Text-to-SQL Generation with Execution-Guided Decoding](https://mlsanity.com/paper/1807.03100/) (2018)
- [Error Detection for Text-to-SQL Semantic Parsing](https://mlsanity.com/paper/2305.13683/) (2023)
- ["What Do You Mean by That?" A Parser-Independent Interactive Approach for Enhancing Text-to-SQL](https://mlsanity.com/paper/2011.04151/) (2020)

## Abstract (arXiv)

A natural language interface can be used to make cancer genomics databases easier to use, but even if a question is perfectly fluent, its scientific meaning can be ambiguous. We propose CLARA, a framework that represents a question as a typed scientific query specification, considers a few possible interpretations, executes them, and asks for clarification when the estimates diverge. CLARA was assessed on mutation-prevalence contrasts among eight TCGA PanCancer Atlas cohorts and a 30-gene panel. This benchmark consisted of 330 unique executable contrasts varying in mutation scope, assay denominator, and sample context; 115 contrasts were result-sensitive and 215 were result-stable, per the preregistered definition of relative divergence greater than 0.10 or absolute divergence greater than 5 percentage points. An independently implemented pandas execution engine perfectly replicated all 660 results from the SQLite engine. In a separate 120-question LLM-generated, manually vetted language stress test, CLARA recognized all 60 result-sensitive contrasts and needlessly clarified 13 of 60 stable contrasts (accuracy 89.2%, sensitivity/recall 100%, specificity 78.3%). Standalone machine learning had superior overall accuracy (97.5%) but missed one critical contrast. This demonstrates that downstream execution can distinguish consequential from inconsequential ambiguity and reveal an explicit trade-off between safety and burden.