We present a machine learning framework for testing general relativity (GR) with gravitational wave signals from binary black hole mergers. Using the source parameters of 173 BBH events from the GWTC catalog as a realistic astrophysical population, we generate simulated GR waveforms and construct beyond GR (BGR) waveforms by applying controlled phase deformations. We introduce a response function formalism that provides a systematic framework for quantifying how any observable responds to modifications of GR. We train convolutional neural networks (CNNs) on two input representations: whitened waveforms and a response function type observable derived from the waveform mismatch, which isolates the effect of phase deviations from the bulk signal. Using response functions as the CNN input improves the classification sensitivity by a factor of approximately 33 compared to whitened waveforms, demonstrating that the choice of observable representation is as important as the classifier architecture. We study the fundamental limits of this classification through Bayes optimal error analysis, averaging methods that reveal coherent patterns hidden in noise, and a comparison between CNN accuracy and a single feature classifier as a proxy for human performance. At all deformation scales, the CNN outperforms the best single feature approach. We extend the framework to physically motivated theories using the parameterized post Einsteinian (ppE) formalism and apply it to massive gravity, where the classifier detects deviations for graviton masses of order $m_g \sim 10^{-23}\;\mathrm{eV}/c^2$ with aLIGO design sensitivity.

Mode separation, namely how sharply a distribution fragments into barrier-separated clusters, is a fundamental geometric property of densities, difficult to quantify in high dimensions. It is structurally distinct from dispersion, yet existing tools fall short: differential entropy rises with spread regardless of fragmentation, PCA orders directions by variance regardless of barriers, and mutual information requires a mixture decomposition one usually does not have. We measure mode separation through a single stochastic process intrinsic to the density: a unique reversible diffusion with $f$ as its stationary distribution and constant scalar diffusion coefficient. We extract two readouts from its autocovariance matrix: SSA (Sum of Squared Autocorrelations), a scalar barrier-sensitive measure; and DA (Dominant Autocorrelation directions), linear projections ordered by metastability rather than variance. Under an isotropic-Gaussian null, we derive a closed-form spectrum for the empirical autocovariance that generalizes Marchenko--Pastur, with an analytic upper edge that selects the lag at which DA is read off. Both readouts use only samples and a score function, scaling to high dimensions through pretrained score-based generative models via Tweedie's identity. We apply our framework to three settings: (i) synthetic Gaussian mixtures, where SSA tracks mutual information; (ii) SDXL text-to-image generations, where SSA and DA capture structure that entropy and PCA miss; and (iii) molecular dynamics of alanine dipeptide, where DA recovers the known slow backbone dihedrals from static samples alone.

We present a theoretically grounded Gaussian process framework that leverages neural feature maps to construct expressive kernels. We show that the learned feature map can be interpreted as an optimal low-rank approximation to a Gram matrix derived from an implied RKHS, from which we establish consistency of the GP posterior. We further analyse the spectral properties of the induced kernels and introduce product feature-map kernels to address oversmoothing. This simple yet powerful approach enables fast, scalable, and accurate exact GP inference with minimal upfront work. The flexibility of kernel design supports seamless application to both regression and classification tasks across diverse data modalities, including tabular inputs and structured domains such as images.

As datasets continue to expand in size and complexity, these models have become increasingly sophisticated, with deeper architectures and greater expressive power. Despite these advances, DNNs trained on imbalanced class distributions often exhibit a tendency to favor majority classes, leading to degraded performance on underrepresented classes [18, 39, 27, 17]. Because many real-world datasets follow long-tailed distributions in which minority classes can contain critical and informative patterns, developing methods that enable DNNs to learn effectively from imbalanced data is essential to prevent the loss of valuable information from these rare classes [26, 34, 16]. Moreover, data encountered in real-world applications are frequently multi-modal, meaning that observations originate from heterogeneous sources [6, 29, 7, 35]. To make effective use of such heterogeneous inputs, a wide range of multi-modal learning approaches have been proposed that exploit complementary information across modalities to enhance predictive performance [10, 5]. Common strategies integrate multiple modalities into a unified representation, using techniques that span from straightforward feature-level concatenation [19, 11, 12] to more sophisticated neural architectures that learn joint representations in an end-to-end manner [20, 32]. Although prior research has extensively studied class imbalance and multi-modal data separately, relatively little attentionhas beengiven to settings where bothchallenges arise si2 multaneously. Developing methods that can effectively handle long-tailed class distributions in conjunction with multi-modal inputs is therefore essential in many real-world applications. In the medical domain, for instance, datasets often contain far more samples from healthy individuals than from patients with specific conditions, while also encompassing diverse datatypes such asimagingdata(e.g., X-rays)alongsideauxiliary informationincluding demographics and clinical histories.

LLM-as-a-Judge evaluation has become a standard tool for assessing base model performance. However, characterizing performance via the naive estimator, i.e., raw judge outputs, is systematically biased. Recent work has proposed estimators to correct this bias, but their reliability depends critically on judge quality and, for model comparisons, on calibration stability. Sharing calibration across compared models is practically attractive but can introduce severe bias, including cases where the comparison estimate points in the wrong direction with high apparent confidence. We study these failure modes through analytical results, simulations over judge quality ($J$) and cross-model calibration instability ($ΔJ$), and a real-data MMLU-Pro case study with sign reversal. We propose $J$ and $ΔJ$ as diagnostics for when corrected estimates, especially shared-calibration comparisons, are likely unreliable, and provide reporting guidance for LaaJ evaluation.

Large Language Models often improve accuracy on reasoning tasks by sampling multiple Chain-of-Thought (CoT) traces and aggregating them with majority voting (MV), a test-time technique called self-consistency. When we truncate a CoT partway through and regenerate the remainder, we observe that traces with correct answers reproduce their original answer more often than traces with wrong answers. We use this difference as a reliability signal, prefix consistency, that weights each candidate answer by how often it reappears under regeneration. It requires no access to token log-probabilities or self-rating prompts. Across five reasoning models and four math and science benchmarks, prefix consistency is the best correctness predictor in most settings, and reweighting votes by it reaches Standard MV plateau accuracy at up to 21x fewer tokens (median 4.6x). Our code is available at https://github.com/naoto-iwase/prefix-consistency.

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.