As datasets grow richer, an important challenge is to leverage the full features in the data to maximize the number of useful discoveries while controlling for false positives. We address this problem in the context of multiple hypotheses testing, where for each hypothesis, we observe a p-value along with a set of features specific to that hypothesis. For example, in genetic association studies, each hypothesis tests the correlation between a variant and the trait. We have a rich set of features for each variant (e.g. its location, conservation, epigenetics etc.) which could inform how likely the variant is to have a true association. However popular testing approaches, such as Benjamini-Hochberg's procedure (BH) and independent hypothesis weighting (IHW), either ignore these features or assume that the features are categorical. We propose a new algorithm, NeuralFDR, which automatically learns a discovery threshold as a function of all the hypothesis features. We parametrize the discovery threshold as a neural network, which enables flexible handling of multi-dimensional discrete and continuous features as well as efficient end-to-end optimization. We prove that NeuralFDR has strong false discovery rate (FDR) guarantees, and show that it makes substantially more discoveries in synthetic and real datasets. Moreover, we demonstrate that the learned discovery threshold is directly interpretable.

We consider the problem of active sequential hypothesis testing where a Bayesian decision maker must infer the true hypothesis from a set of hypotheses. The decision maker may choose for a set of actions, where the outcome of an action is corrupted by independent noise. In this paper we consider a special case where the decision maker has limited knowledge about the distribution of observations for each action, in that only a binary value is observed. Our objective is to infer the true hypothesis with low error, while minimizing the number of action sampled. Our main results include the derivation of a lower bound on sample size for our system under limited knowledge and the design of an active learning policy that matches this lower bound and outperforms similar known algorithms.

In the online multiple testing problem, p-values corresponding to different null hypotheses are presented one by one, and the decision of whether to reject a hypothesis must be made immediately, after which the next p-value is presented. Alpha-investing algorithms to control the false discovery rate were first formulated by Foster and Stine and have since been generalized and applied to various settings, varying from quality-preserving databases for science to multiple A/B tests for internet commerce. This paper improves the class of generalized alpha-investing algorithms (GAI) in four ways: (a) we show how to uniformly improve the power of the entire class of GAI procedures under independence by awarding more alpha-wealth for each rejection, giving a near win-win resolution to a dilemma raised by Javanmard and Montanari, (b) we demonstrate how to incorporate prior weights to indicate domain knowledge of which hypotheses are likely to be null or non-null, (c) we allow for differing penalties for false discoveries to indicate that some hypotheses may be more meaningful/important than others, (d) we define a new quantity called the \emph{decaying memory false discovery rate, or $\memfdr$} that may be more meaningful for applications with an explicit time component, using a discount factor to incrementally forget past decisions and alleviate some potential problems that we describe and name ``piggybacking'' and ``alpha-death''. Our GAI++ algorithms incorporate all four generalizations (a, b, c, d) simulatenously, and reduce to more powerful variants of earlier algorithms when the weights and decay are all set to unity.

This work constructs a hypothesis test for detecting whether an data-generating function $h: \real^p \rightarrow \real$ belongs to a specific reproducing kernel Hilbert space $\mathcal{H}_0$, where the structure of $\mathcal{H}_0$ is only partially known. Utilizing the theory of reproducing kernels, we reduce this hypothesis to a simple one-sided score test for a scalar parameter, develop a testing procedure that is robust against the mis-specification of kernel functions, and also propose an ensemble-based estimator for the null model to guarantee test performance in small samples. To demonstrate the utility of the proposed method, we apply our test to the problem of detecting nonlinear interaction between groups of continuous features. We evaluate the finite-sample performance of our test under different data-generating functions and estimation strategies for the null model. Our results revealed interesting connection between notions in machine learning (model underfit/overfit) and those in statistical inference (i.e. Type I error/power of hypothesis test), and also highlighted unexpected consequences of common model estimating strategies (e.g.

Bounding the generalization error of learning algorithms has a long history, which yet falls short in explaining various generalization successes including those of deep learning. Two important difficulties are (i) exploiting the dependencies between the hypotheses, (ii) exploiting the dependence between the algorithm's input and output. Progress on the first point was made with the chaining method, originating from the work of Kolmogorov, and used in the VC-dimension bound. More recently, progress on the second point was made with the mutual information method by Russo and Zou '15. Yet, these two methods are currently disjoint. In this paper, we introduce a technique to combine chaining and mutual information methods, to obtain a generalization bound that is both algorithm-dependent and that exploits the dependencies between the hypotheses. We provide an example in which our bound significantly outperforms both the chaining and the mutual information bounds. As a corollary, we tighten Dudley's inequality when the learning algorithm chooses its output from a small subset of hypotheses with high probability.

Many real-world vision problems suffer from inherent ambiguities. In clinical applications for example, it might not be clear from a CT scan alone which particular region is cancer tissue. Therefore a group of graders typically produces a set of diverse but plausible segmentations. We consider the task of learning a distribution over segmentations given an input. To this end we propose a generative segmentation model based on a combination of a U-Net with a conditional variational autoencoder that is capable of efficiently producing an unlimited number of plausible hypotheses. We show on a lung abnormalities segmentation task and on a Cityscapes segmentation task that our model reproduces the possible segmentation variants as well as the frequencies with which they occur, doing so significantly better than published approaches. These models could have a high impact in real-world applications, such as being used as clinical decision-making algorithms accounting for multiple plausible semantic segmentation hypotheses to provide possible diagnoses and recommend further actions to resolve the present ambiguities.

With the recent success of embeddings in natural language processing, research has been conducted into applying similar methods to code analysis. Most works attempt to process the code directly or use a syntactic tree representation, treating it like sentences written in a natural language. However, none of the existing methods are sufficient to comprehend program semantics robustly, due to structural features such as function calls, branching, and interchangeable order of statements. In this paper, we propose a novel processing technique to learn code semantics, and apply it to a variety of program analysis tasks. In particular, we stipulate that a robust distributional hypothesis of code applies to both human-and machine-generated programs. Following this hypothesis, we define an embedding space, inst2vec, based on an Intermediate Representation (IR) of the code that is independent of the source programming language. We provide a novel definition of contextual flow for this IR, leveraging both the underlying data-and control-flow of the program. We then analyze the embeddings qualitatively using analogies and clustering, and evaluate the learned representation on three different high-level tasks. We show that even without fine-tuning, a single RNN architecture and fixed inst2vec embeddings outperform specialized approaches for performance prediction (compute device mapping, optimal thread coarsening); and algorithm classification from raw code (104 classes), where we set a new state-of-the-art.

Stochastic network models play a central role across a wide range of scientific disciplines, and questions of statistical inference arise naturally in this context. In this paper we investigate goodness-of-fit and two-sample testing procedures for statistical networks based on the principle of maximum entropy (MaxEnt). Our approach formulates a constrained entropy-maximization problem on the space of networks, subject to prescribed structural constraints. The resulting test statistics are defined through the Lagrange multipliers associated with the constrained optimization problem, which, to our knowledge, is novel in the statistical networks literature. We establish consistency in the classical regime where the number of vertices is fixed. We then consider asymptotic regimes in which the graph size grows with the sample size, developing tests for both dense and sparse settings. In the dense case, we analyze exponential random graph models (ERGM) (including the Erdös-Rènyi models), while in the sparse regime our theory applies to Erd{ö}s-R{è}nyi graphs. Our analysis leverages recent advances in nonlinear large deviation theory for random graphs. We further show that the proposed Lagrange-multiplier framework connects naturally to classical score tests for constrained maximum likelihood estimation. The results provide a unified entropy-based framework for network model assessment across diverse growth regimes.

The proliferation of Large Language Models (LLMs) necessitates efficient mechanisms to distinguish machine-generated content from human text. While statistical watermarking has emerged as a promising solution, existing methods suffer from two critical limitations: the lack of a principled approach for selecting sampling distributions and the reliance on fixed-horizon hypothesis testing, which precludes valid early stopping. In this paper, we bridge this gap by developing the first e-value-based watermarking framework, Anchored E-Watermarking, that unifies optimal sampling with anytime-valid inference. Unlike traditional approaches where optional stopping invalidates Type-I error guarantees, our framework enables valid, anytime-inference by constructing a test supermartingale for the detection process. By leveraging an anchor distribution to approximate the target model, we characterize the optimal e-value with respect to the worst-case log-growth rate and derive the optimal expected stopping time. Our theoretical claims are substantiated by simulations and evaluations on established benchmarks, showing that our framework can significantly enhance sample efficiency, reducing the average token budget required for detection by 13-15% relative to state-of-the-art baselines.

We study one-sided and $α$-correct sequential hypothesis testing for data generated by an ergodic Markov chain. The null hypothesis is that the unknown transition matrix belongs to a prescribed set $P$ of stochastic matrices, and the alternative corresponds to a disjoint set $Q$. We establish a tight non-asymptotic instance-dependent lower bound on the expected stopping time of any valid sequential test under the alternative. Our novel analysis improves the existing lower bounds, which are either asymptotic or provably sub-optimal in this setting. Our lower bound incorporates both the stationary distribution and the transition structure induced by the unknown Markov chain. We further propose an optimal test whose expected stopping time matches this lower bound asymptotically as $α\to 0$. We illustrate the usefulness of our framework through applications to sequential detection of model misspecification in Markov Chain Monte Carlo and to testing structural properties, such as the linearity of transition dynamics, in Markov decision processes. Our findings yield a sharp and general characterization of optimal sequential testing procedures under Markovian dependence.