Data leakage remains a recurrent source of optimistic bias in biomedical machine learning studies. Standard row-wise cross-validation and globally estimated preprocessing steps are often inappropriate for data with repeated measurements, study-level heterogeneity, batch effects, or temporal dependencies. This paper describes bioLeak, an R package for constructing leakage-aware resampling workflows and for auditing fitted models for common leakage mechanisms. The package provides leakage-aware split construction, train-fold-only preprocessing, cross-validated model fitting, nested hyperparameter tuning, post hoc leakage audits, and HTML reporting. The implementation supports binary classification, multiclass classification, regression, and survival analysis, with task-specific metrics and S4 containers for splits, fits, audits, and inflation summaries. The simulation artifacts show how apparent performance changes under controlled leakage mechanisms, and the case study illustrates how guarded and leaky pipelines can yield materially different conclusions on multi-study transcriptomic data. The emphasis throughout is on software design, reproducible workflows, and interpretation of diagnostic output.

Preprocessing leakage arises when scaling, imputation, or other data-dependent transformations are estimated before resampling, inflating apparent performance while remaining hard to detect. We present fastml, an R package that provides a single-call interface for leakage-aware machine learning through guarded resampling, where preprocessing is re-estimated inside each resample and applied to the corresponding assessment data. The package supports grouped and time-ordered resampling, blocks high-risk configurations, audits recipes for external dependencies, and includes sandboxed execution and integrated model explanation. We evaluate fastml with a Monte Carlo simulation contrasting global and fold-local normalization, a usability comparison with tidymodels under matched specifications, and survival benchmarks across datasets of different sizes. The simulation demonstrates that global preprocessing substantially inflates apparent performance relative to guarded resampling. fastml matched held-out performance obtained with tidymodels while reducing workflow orchestration, and it supported consistent benchmarking of multiple survival model classes through a unified interface.

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However, a gradient is often insufficient to reconstruct the user data without any prior knowledge. By exploiting a generative model pretrained on the data distribution, we demonstrate that data privacy can be easily breached.

According to our experimental findings, inaccurate cross-attention maps are at the root of this problem.

When learning from sensitive data, care must be taken to ensure that training algorithms address privacy concerns. The canonical Private Aggregation of Teacher Ensembles, or P A TE, computes output labels by aggregating the predictions of a (possibly distributed) collection of teacher models via a voting mechanism. The mechanism adds noise to attain a differential privacy guarantee with respect to the teachers' training data. In this work, we observe that this use of noise, which makes P A TE predictions stochastic, enables new forms of leakage of sensitive information. For a given input, our adversary exploits this stochasticity to extract high-fidelity histograms of the votes submitted by the underlying teachers. From these histograms, the adversary can learn sensitive attributes of the input such as race, gender, or age. Although this attack does not directly violate the differential privacy guarantee, it clearly violates privacy norms and expectations, and would not be possible at all without the noise inserted to obtain differential privacy. In fact, counter-intuitively, the attack becomes easier as we add more noise to provide stronger differential privacy. We hope this encourages future work to consider privacy holistically rather than treat differential privacy as a panacea.

The rapid advancement and widespread use of large language models (LLMs) have raised significant concerns regarding the potential leakage of personally identifiable information (PII). These models are often trained on vast quantities of web-collected data, which may inadvertently include sensitive personal data.

Ahumansupervisorcaninterpret and understand the label predictions by inspecting the concept predictions.