Positive-unlabeled (PU) learning addresses binary classification when only a set of labeled positives is available alongside a pool of unlabeled samples drawn from a mixture of positives and negatives. Existing PU methods typically require dataset-specific training or iterative optimization, which limits their applicability when many tasks must be solved quickly or with little tuning. We introduce PUICL, a pretrained transformer that solves PU classification entirely through in-context learning. PUICL is pretrained on synthetic PU datasets generated from randomly instantiated structural causal models, exposing it to a wide range of feature-label relationships and class-prior configurations. At inference time, PUICL receives the labeled positives and the unlabeled samples as a single input and returns class probabilities for the unlabeled rows in one forward pass, with no gradient updates or per-task fitting. On 20 semi-synthetic PU benchmarks derived from the UCI Machine Learning Repository, OpenML, and scikit-learn, PUICL outperforms four standard PU learning baselines in average AUC and accuracy, and is competitive on F1-score. These results show that the in-context learning paradigm extends naturally beyond fully supervised tabular prediction to the semi-supervised PU setting.

The standard constraint-based paradigm for causal discovery with incomplete data -- impute first, test second -- is frequently miscalibrated: any consistent conditional independence (CI) test rejects a true null with probability approaching 1 when imputation error induces spurious conditional dependence. We introduce PAIR-CI, a nonparametric CI test that restores calibration by integrating multiple imputation directly into the inferential procedure via a paired permutation design. PAIR-CI compares cross-validated models that include and exclude the candidate variable while receiving the same imputed conditioning set, forcing imputation error to cancel in their loss difference rather than contaminate the test statistic. A provably consistent variance estimator jointly accounts for uncertainty arising from cross-validation and multiple imputation -- to our knowledge, the first formal unification of these two inferential frameworks. In simulations, existing imputation-based CI tests exhibit false positive rates of 28--45% when data are missing not at random (MNAR), whereas PAIR-CI averages below the nominal 5% level across data-generating processes and missingness mechanisms. These gains are largest in nonlinear settings and grow with causal graph size: when integrated into the PC algorithm, PAIR-CI reduces structural Hamming distance by 8% on 10-variable nonlinear graphs, 15% on 30-variable equivalents, and up to 44% on the 56-variable HAILFINDER network, with stable performance in all settings.

Despite theoretical advantages, causal methods for Gene Regulatory Network (GRN) inference from single-cell RNA-seq data consistently fail to match or outperform correlation-based baselines in many realistic benchmarks, a persistent puzzle which casts doubt on the value of causality for this task. We argue that existing benchmarks are insufficiently controlled to answer this question because they evaluate on real or semi-real data where multiple pathologies co-occur, confounding failure modes, and obscuring the specific conditions under which different inference methods excel or fail. To address this gap, we introduce a controlled diagnostic framework that isolates seven biologically motivated pathologies (dropout, latent confounders, cell-type mixing, feedback loops, network density, sample size, and pseudotime drift) and measure how six representative methods spanning three inference paradigms degrade as each pathology intensifies. Across 6,120 controlled experiments, we find that causal methods genuinely dominate in clean and structurally favorable regimes, but specific pathologies (notably dropout and latent confounders) selectively neutralize their advantages. We further introduce an errortype decomposition that reveals methods with similar aggregate accuracy commit qualitatively different errors. To probe whether single-pathology effects persist when multiple stressors co-occur, we perform an interaction sweep over the three most impactful pathologies and find that their joint effects are sub-additive, while also exposing density-conditional cross-overs invisible to single-dial analysis. Our findings offer a nuanced understanding of when and why different methods succeed or fail for GRN inference, providing actionable insights for method development and practical guidance for practitioners.3

We develop graph-based methods for semi-supervised learning based on label propagation on a data similarity graph. When data is abundant or arrive in a stream, the problems of computation and data storage arise for any graph-based method. We propose a fast approximate online algorithm that solves for the harmonic solution on an approximate graph. We show, both empirically and theoretically, that good behavior can be achieved by collapsing nearby points into a set of local representative points that minimize distortion. Moreover, we regularize the harmonic solution to achieve better stability properties. We also present graph-based methods for detecting conditional anomalies and apply them to the identification of unusual clinical actions in hospitals. Our hypothesis is that patient-management actions that are unusual with respect to the past patients may be due to errors and that it is worthwhile to raise an alert if such a condition is encountered. Conditional anomaly detection extends standard unconditional anomaly framework but also faces new problems known as fringe and isolated points. We devise novel nonparametric graph-based methods to tackle these problems. Our methods rely on graph connectivity analysis and soft harmonic solution. Finally, we conduct an extensive human evaluation study of our conditional anomaly methods by 15 experts in critical care.

The Brier score conflates two distinct properties of probabilistic predictions: reliability (calibration error) and resolution (discriminatory power). We introduce the Manokhin Probability Matrix, a BCG-style two-dimensional diagnostic framework that separates them. Classifiers are placed on a 2x2 grid by Spiegelhalter Z-statistic and AUC-ROC expected rank, then assigned to one of four archetypes: Eagle (good on both axes), Bull (strong discrimination, poor calibration), Sloth (well-calibrated, weak discriminator), and Mole (poor on both). Each archetype carries a distinct prescription. We populate the matrix from a large-scale empirical study spanning 21 classifiers, 5 post-hoc calibrators, and 30 real-world binary classification tasks from the TabArena-v0.1 suite. The assignment is unambiguous. CatBoost, TabICL, EBM, TabPFN, GBC, and Random Forest are Eagles. XGBoost, LightGBM, and HGB are Bulls; Venn-Abers calibration cuts log-loss by 6.5 to 12.6% on Bulls but degrades Eagles by 2.1%. SVM, LR, LDA, and the empirical base-rate predictor are Sloths. MLP, KNN, Naive Bayes, and ExtraTrees are Moles. A theoretical asymmetry follows: no order-preserving post-hoc calibrator can add discriminatory power (Proposition 1), so calibration is the fixable part and discrimination is the hard part. The practical rule is direct: do not optimise aggregate Brier score without first decomposing it; optimise discrimination first, then fix calibration post-hoc. Code and raw experimental data are available at https://github.com/valeman/classifier_calibration.

Neural Information Processing Systems http://nips.cc/

Labeling articulated objects in unconstrained settings has a wide variety of applications including entertainment, neuroscience, psychology, ethology, and many fields of medicine. Large offline labeled datasets do not exist for all but the most common articulated object categories (e.g., humans). Hand labeling these landmarks within a video sequence is a laborious task. Learned landmark detectors can help, but can be error-prone when trained from only a few examples. Multi-camera systems that train fine-grained detectors have shown significant promise in detecting such errors, allowing for self-supervised solutions that only need a small percentage of the video sequence to be hand-labeled.