cs.AIApr 13, 2026
SaveSanity Checks for Agentic Data Science
Organizations: Dept. of Statistics, UC Berkeley · Dept. of EECS, UC Berkeley · Microsoft Research · Dept. of Statistics, Dept. of EECS, Center for Computational Biology, UC Berkeley
Abstract
Agentic data science (ADS) pipelines have grown rapidly in both capability and adoption, with systems such as OpenAI Codex now able to directly analyze datasets and produce answers to statistical questions. However, these systems can reach falsely optimistic conclusions that are difficult for users to detect. To address this, we propose a pair of lightweight sanity checks grounded in the Predictability-Computability-Stability (PCS) framework for veridical data science. These checks use reasonable perturbations to screen whether an agent can reliably distinguish signal from noise, acting as a falsifiability constraint that can expose affirmative conclusions as unsupported. Together, the two checks characterize the trustworthiness of an ADS output, e.g. whether it has found stable signal, is responding to noise, or is sensitive to incidental aspects of the input. We validate the approach on synthetic data with controlled signal-to-noise ratios, confirming that the sanity checks track ground-truth signal strength. We then demonstrate the checks on 11 real-world datasets using OpenAI Codex, characterizing the trustworthiness of each conclusion and finding that in 6 of the datasets an affirmative conclusion is not well-supported, even though a single ADS run may support one. We further analyze failure modes of ADS systems and find that ADS self-reported confidence is poorly calibrated to the empirical stability of its conclusions.
Figures & tables
Figure 1: Pipeline for computing the PCS sanity checks. The user supplies a dataset and question. The pipeline then generates perturbed variants of these under both null-defining and PCS perturbations. The coding agent analyzes each independently, producing null and alternative response distributions. A bootstrap test & overlap coefficient then inform whether the agent found a data-grounded, stable positive conclusion.
| Perturbation | Type | Description | Failure Mode Tested |
| Shuffle Feature Values | Null-Defining | Shuffles each column independently to break associations in the data. | Incorrect data analysis conclusions. |
| Add Non-Signal Features | PCS | Appends features irrelevant to & uncorrelated with the task of interest. | Distraction by irrelevant covariates. |
| Anonymize Feature Names | PCS | Replaces all column names with generic identifiers (e.g., feature1 , feature2 ). | Reliance on semantic variable names from pre-training data. |
| Shuffle Feature Names | PCS | Applies a random permutation of existing column names while leaving data values and feature descriptions in metadata unchanged. | Robustness to misleading variable names. |
| Positive Leading Statement | PCS | Prepends the question with a strong prior belief that the answer is “Yes.” | Sycophancy toward user-stated beliefs. |
| Negative Leading Statement | PCS | Prepends the question with a strong prior belief that the answer is “No.” | Sycophancy toward user-stated beliefs. |
Table 1: Perturbations used in the PCS sanity checks. The null-defining distribution breaks associations between the features and the outcome. The PCS perturbations should not affect an experienced data scientist or agentic data science system, although some perturbations (e.g. positive leading statement ) may mislead human data scientists due to confirmation bias.
| Overlap check passed ✓ | Overlap check failed ✗ | |
| Yes check passed ✓ | The positive conclusion is stable. | The positive conclusion may not be grounded in the data. |
| Yes check failed ✗ | There is some positive signal, but not enough for a “Yes”. | No evidence supporting a positive conclusion. |
Table 2: Interpretations of the four PCS sanity-check regimes.
Figure 2: The PCS sanity checks behave as expected. As more signal is introduced to the data, the agent’s responses become more positive, leading to less similarity with the null.
Figure 3: Sanity check results on BLADE datasets. (a) KDEs of the null and alternative response distributions for each dataset. (b) Each dataset’s OVL and alternative response mean, colored by category (Table 2 ). Vertical and horizontal dashed lines mark the OVL decision boundary and the scale midpoint, respectively. (c) Agreement between subsampled and full-sample classifications as a function of the number of alternative runs (Appendix A.5 ).
Figure 4: Multi-faceted analysis of agentic instability.
Appendix figures & tables15 assets
Supplementary material from the paper’s appendix.
Appendix
| Dataset | Blocked | Unblocked | |
| affairs | 0.045 | 0.040 | 0.005 |
| amtl | 0.140 | 0.122 | 0.018 |
| boxes | 0.041 | 0.038 | 0.003 |
| caschools | 0.057 | 0.050 | 0.007 |
| crofoot | 0.037 | 0.021 | 0.016 |
| hurricane | 0.040 | 0.032 | 0.008 |
Table A1: Empirical rejection rates ( ) at for the bootstrap mean test. replicates per dataset, bootstrap resamples per test. is unblocked minus blocked.
Figure A1: QQ plots comparing observed -value quantiles to theoretical quantiles for the blocked (left) and unblocked (right) bootstrap tests, pooled across all 11 datasets and replicates. The blocked test tracks the diagonal closely. The unblocked test’s curve falls slightly above the diagonal at low quantiles, reflecting its mild conservatism.
| Dataset Name | Question | Source Paper(s) |
| affairs | Does having children decrease (if at all) the engagement in extramarital affairs? | Fair (1978) ; Long and Freese (2006) ; Kleiber and Zeileis (2008) |
| amtl | Do modern humans ( Homo sapiens ) have higher frequencies of antemortem tooth loss (AMTL) compared to non-human primate genera ( Pan, Pongo, Papio ), after accounting for the effects of age, sex, and tooth class? | Gilmore (2013) ; Konigsberg and Frankenberg (2013) ; McElreath (2018) |
| boxes | Do children’s reliance on social information and preference for majority cues vary across cultures and developmental stages? | Van Leeuwen et al. (2018) ; McElreath (2018) |
| caschools | Is a lower student-teacher ratio associated with higher academic performance? | Kleiber and Zeileis (2008) ; Stock and Watson (2020) |
| crofoot | Do relative group size and contest location influence the probability of a capuchin monkey group winning an intergroup contest? | Crofoot et al. (2008) ; McElreath (2018) |
| fish | How many fish on average do visitors takes per hour, when fishing? | McElreath (2018) |
Table A2: Summary of BLADE datasets and their corresponding questions.
Figure A2: We observe that datasets tend to move out of the “Failed both checks” quadrant as PVE increases, demonstrating that the two agentic stability checks corroborate the signal present in the data.
Figure A3: Empirical null and alternative distributions, with the alternative distribution being produced on a PVE-controlled dataset. Note the rightward shift of the alternative distribution as PVE increases.
| Dataset | Null Mean (SD) | Alt Mean (SD) | -Value | OVL | Checks Passed |
| teachingratings | 7.18 (5.72) | 69.94 (3.54) | 0.0001 | 0.000 | Both |
| amtl | 26.50 (16.51) | 93.85 (6.56) | 0.0001 | 0.019 | Both |
| panda_nuts | 30.38 (10.92) | 70.04 (6.70) | 0.0001 | 0.069 | Both |
| soccer | 23.20 (5.44) | 64.25 (9.82) | 0.0001 | 0.052 | Both |
| mortgage | 29.83 (5.78) | 53.46 (16.44) | 0.0228 | 0.102 | Both |
| caschools | 17.26 (11.14) | 55.81 (19.89) | 0.0016 | 0.280 | Yes Check |
Table A3: Results of the sanity check on eleven BLADE datasets.
Figure A4: Classification agreement vs. sample size under random subsampling (both distributions reduced). Most datasets stabilize within 5–10 runs. caschools and mortgage require substantially more.
Figure A5: Classification agreement vs. alternative sample size (full null retained). The pattern is similar to Fig. A4 , confirming that the alternative distribution is the primary driver of instability at small sample sizes.
Figure A6: Component-level agreement under random subsampling. Left: Bootstrap test (significant or not). Right: Overlap coefficient (low or high).
Figure A7: Component-level agreement under alt-only subsampling. The decomposition mirrors Fig. A6 , with the same bottleneck checks driving instability for the borderline datasets.
Figure A8: Empirical null and alternative distributions, with the “null” distribution being produced on datasets with a very small signal-to-noise ratio.
Figure A9: Within-perturbation volatility. Each cell shows the mean across all within-perturbation run pairs for a given perturbation and pipeline step, averaged over ten datasets. High values indicate that the perturbation makes the pipeline’s output unpredictable relative to the unperturbed reference.
Figure A10: Baseline-vs-perturbation divergence. Each cell shows the mean for comparisons between an unperturbed run and a perturbed run. High values indicate that perturbed outputs differ from unperturbed outputs by more than unperturbed outputs differ from each other.
Figure A11: The three independent raters tend to agree on the scores for each human-performed data analysis. The raters were asked to put the conclusion of each team’s analysis on the same Likert scale that the agent was prompted with.
Figure A12: Comparison of individual rater values shows general agreement.