The Silent Failures in Agentic Data Science

Xue Li, Hongqian Xia, Daniel Gomm, Aécio Santos, Cornelius Wolff, Madelon Hulsebos
Centrum Wiskunde & Informatica (CWI)
Bar chart: share of pipelines with at least one failure mode, per agent and model. Between 95% and 100% for all configurations except MLEvolve with Gemini-3.7 at 68%.
Almost every agentic DS pipeline contains at least one failure mode, regardless of the agent scaffold or the underlying model.

Abstract

Large language models have significantly lowered the barrier to writing code. Naturally, this has also led to the development of data science agents that promise automating the design and execution of data science from task formulation to model development. Existing evaluations of agentic data science (agentic DS) assess downstream predictive performance and code correctness, providing preliminary insight in agentic DS capabilities. We argue that these evaluations overlook the fundamental principles of data science: methodological data science- and domain knowledge. As such, only assessing downstream performance masks methodological failures such as data leakage and inappropriate validation, limiting the development of robust agentic DS systems. In this paper, we evaluate agentic DS beyond accuracy from three different angles: 1) a large-scale analysis of failure modes in common agentic DS frameworks and models across 220 data science tasks, 2) a reusable and extensible test suite with curated data science tasks that test for six specific failures in a controlled manner, and 3) a qualitative assessment of agentic DS pipelines against expert solutions on Kaggle competitions.

We find that the majority of agentic solutions contain at least one failure mode despite the complexity of agentic harness or model capacity. Moreover, we identify a positive correlation between the occurrence of data leakage failures and predictive performance, confirming the necessity to evaluate agents beyond accuracy. Our qualitative analysis shows that DS agents generally lack problem solving creativity and domain knowledge, compared to competition-winning data scientists. We believe that principled failure mode analysis, as presented here, should be integral part of agentic DS evaluations, and that the insights we surface will be key in developing trustworthy agentic DS pipelines.

Key findings

Which failure modes are most common?

Breaking failures down by mode shows which mistakes each agent and model makes most often.

Failure modeReActAIDEMLEvolve
Qwen-4BQwen-27BGemini-3.7Qwen-4BQwen-27BGemini-3.7Qwen-4BQwen-27BGemini-3.7
FM01Wrong task formulation0.020.010.020.010.030.010.020.010.00
FM02Peeking at test data during EDAleak0.010.120.070.020.080.150.020.080.10
FM03Not cleaning data0.280.040.300.720.210.450.860.170.10
FM04Imputation before splittingleak0.000.130.060.080.030.130.090.030.10
FM05Ignoring temporal orderleak0.000.360.480.130.150.470.020.170.36
FM06No train/val split1.000.050.400.070.010.000.690.010.00
FM07No feature engineering0.980.500.380.930.710.120.940.160.00
FM08Scaling before splittingleak0.000.000.000.020.000.030.020.000.01
FM09Feature selection before splittingleak0.000.030.080.000.020.140.000.010.06
FM10Wrong model type for task0.010.000.000.030.000.000.000.000.00
FM11No regularisation in DL–––––––0.000.00
FM12Naive ensembling–0.490.90–0.810.46–0.510.04
FM13Reusing test set across variantsleak–0.00–––0.00–0.060.01
FM14Single eval of stochastic model0.480.950.040.190.080.031.000.760.13
FM15Using only one eval metric0.150.890.140.870.850.880.340.870.43
Occurrence rate per failure modes (FM) by agent and model over the pipelines for which the FM is applicable. N/A indicates that the number of applicable pipelines for a given FM is less than 20. Red indicates leakage modes and blue indicates non-leakage modes.
Horizontal bar chart of the share of all 4,549 detected failure instances by failure mode. Most frequent: FM15 using only one eval metric (23.8%), FM07 no feature engineering (18.9%), FM14 single eval of stochastic model (12.8%), FM03 not cleaning data (11.8%). FM11 no regularisation in DL is 0%.
Failure-mode distribution. All detected failure instances (n=4,549) by failure mode over 1,761 pipelines, averaging 2.58 failures per pipeline. Red: leakage modes; blue: other modes.
Do failures inflate scores?

Leakage failure modes are associated with better predictive performance, while non-leakage failures go with worse performance. Predictive performance alone masks the silent failures.

Slopegraph of rank residual when each failure mode is absent versus present. Leakage modes (red) slope downward toward better performance; non-leakage modes such as FM06 and FM12 slope upward toward worse performance.
Adjusted effect of FMs on residual rank in the test set that is accessible to the agent. A high rank indicates worse performance, while a low rank indicates better performance (* indicates significance).
Controlled test suite

Six curated tasks each probe one specific failure. More explicit hints lower fail rates for ReAct and AIDE, but not consistently for MLEvolve.

Bar charts of fail rate per agent for six test-suite failures (TF01 to TF06) without hints, for gemini-3.7-flash and gpt-5.6-sol. Line charts of fail rate by hint level 1 to 4 for ReAct, AIDE and MLEvolve, for gemini-3.7-flash and gpt-5.6-sol.
Left: Results for the curated test suite of failure modes. Failure rate represents failure occurrences per failure mode, averaged over n = 5 runs. A failure rate of 1.0 means it occurs in every run. Right: Average FMs per hint level. Hint level 1 is no hint; higher is more explicit.
Agents vs. expert solutions

On five Kaggle challenges, no agent beats the 1st-place human solution on either the private or the public leaderboard.

Data science agentsAutoMLBaseline
ChallengeMetricReActAIDEMLEvolveAutoGluon1st place (human)
Single-Cell PerturbationsMRRMSE ↓1.1020 / 0.76900.8970 / 0.66000.8310 / 0.6170– / –0.7290 / 0.5230
Heart Disease PredictionAUC-ROC ↑0.9547 / 0.95310.9549 / 0.95330.9546 / 0.95310.9551 / 0.95360.9554 / 0.9542
Obesity RiskAccuracy ↑0.9065 / 0.90900.9059 / 0.90250.9071 / 0.90350.9074 / 0.90750.9116 / 0.9234
Problematic Internet UseQWK ↑0.4440 / 0.46800.4280 / 0.46400.4170 / 0.4480– / –0.4820 / 0.5010
Survival PredictionsC-index ↑0.6502 / 0.64650.6536 / 0.64880.3155 / 0.3233– / –0.7013 / 0.6981
Leaderboard performance across Kaggle challenges. Scores are private / public. Best overall score in bold, second-best underlined. AutoGluon applies only to challenges with CSV uploads (Heart Disease Prediction and Obesity Risk), which are simpler playground tasks.
ReAct pipeline diagram, annotated with failure modes FM02, FM03, FM07 and FM12.
AIDE pipeline diagram.
MLEvolve pipeline diagram.
1st-place Kaggle solution pipeline diagram.
Pipeline comparison. ReAct, AIDE and MLEvolve pipelines vs. the competition-winning solution.

Contact

We welcome questions and suggestions. Reach out to effy.li@cwi.nl. (Links for paper and code are coming soon).