Due to the difficulty in collecting all unexpected abnormal patterns, One-Class Classification (OCC) has become the most popular approach to anomaly detection (AD). Reconstruction-based AD method relies on the discrepancy between inputs and reconstructed results to identify unobserved anomalies. However, recent methods trained only on normal samples may generalize to certain abnormal inputs, leading to well-reconstructed anomalies and degraded performance. To address this, we constrain reconstructions to remain on the normal manifold using a novel AD framework based on contraction mapping. This mapping guarantees that any input converges to a fixed point through iterations of this mapping.

Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biology. In the zero-shot setting, variant impact is estimated by comparing the likelihoods of sequences, under the assumption that likelihood serves as a proxy for fitness. However, this assumption often breaks down in practice: sequence likelihood reflects not only evolutionary fitness constraints, but also phylogenetic structure and sampling biases, especially as model capacity increases. We introduce Likelihood-Fitness Bridging (LFB), a simple and general strategy that improves variant effect prediction by averaging model scores across sequences subject to similar selective pressures. Assuming an Ornstein-Uhlenbeck model of evolution, LFB can be viewed as a way to marginalize the effects of genetic drift, although its benefits appear to extend more broadly. LFB applies to existing protein and genomic language models without requiring retraining, and incurs only modest computational overhead. Evaluated on largescale deep mutational scans and clinical benchmarks, LFB consistently improves predictive performance across model families and sizes. Notably, it reverses the performance plateau observed in larger protein language models, making the largest models the most accurate when combined with LFB. These results suggest that accounting for phylogenetic and sampling biases is essential to realizing the full potential of large sequence models in variant effect prediction.

Neural processes (NPs) are a class of models that learn stochastic processes directly from data and can be used for inference, sampling and conditional sampling. We introduce a new NP model based on flow matching, a generative modeling paradigm that has demonstrated strong performance on various data modalities. Following the NP training framework, the model provides amortized predictions of conditional distributions over any arbitrary points in the data. Compared to previous NP models, our model is simple to implement and can be used to sample from conditional distributions using an ODE solver, without requiring auxiliary conditioning methods. In addition, the model provides a controllable tradeoff between accuracy and running time via the number of steps in the ODE solver. We show that our model outperforms previous state-of-the-art neural process methods on various benchmarks including synthetic 1DGaussian processes data, 2D images, and real-world weather data.

Model-based clustering integrated with variable selection is a powerful tool for uncovering latent structures within complex data. However, its effectiveness is often hindered by challenges such as identifying relevant variables that define heterogeneous subgroups and handling data that are missing not at random, a prevalent issue in fields like transcriptomics. While several notable methods have been proposed to address these problems, they typically tackle each issue in isolation, thereby limiting their flexibility and adaptability. This paper introduces a unified framework designed to address these challenges simultaneously. Our approach incorporates a data-driven penalty matrix into penalized clustering to enable more flexible variable selection, along with a mechanism that explicitly models the relationship between missingness and latent class membership. We demonstrate that, under certain regularity conditions, the proposed framework achieves both asymptotic consistency and selection consistency, even in the presence of missing data. This unified strategy significantly enhances the capability and efficiency of model-based clustering, advancing methodologies for identifying informative variables that define homogeneous subgroups in the presence of complex missing data patterns. The performance of the framework, including its computational efficiency, is evaluated through simulations and demonstrated using both synthetic and real-world transcriptomic datasets.

Inducing-point-based sparse variational Gaussian processes have become the standard workhorse for scaling up GP models. Recent advances show that these methods can be improved by introducing a diagonal scaling matrix to the conditional posterior density given the inducing points. This paper first considers an extension that employs a block-diagonal structure for the scaling matrix, provably tightening the variational lower bound. We then revisit the unifying framework of sparse GPs based on Power Expectation Propagation (PEP) and show that it can leverage and benefit from the new structured approximate posteriors. Through extensive regression experiments, we show that the proposed block-diagonal approximation consistently performs similarly to or better than existing diagonal approximations while maintaining comparable computational costs. Furthermore, the new PEP framework with structured posteriors provides competitive performance across various power hyperparameter settings, offering practitioners flexible alternatives to standard variational approaches.

Chain-of-thought (CoT) reasoning is critical for improving the interpretability and reliability of Large Vision-Language Models (LVLMs). However, existing training algorithms such as SFT, PPO, and GRPO may not generalize well across unseen reasoning tasks and heavily rely on a biased reward model. To address this challenge, we reformulate reasoning in LVLMs as posterior inference and propose a scalable training algorithm based on amortized variational inference. By leveraging diversity-seeking reinforcement learning algorithms, we introduce a novel sparse reward function for token-level learning signals that encourage diverse, high-likelihood latent CoT, overcoming deterministic sampling limitations and avoiding reward hacking. Additionally, we implement a Bayesian inference-scaling strategy that replaces costly Best-of-N and Beam Search with a marginal likelihood to efficiently rank optimal rationales and answers. We empirically demonstrate that the proposed method enhances the state-of-the-art LVLMs on seven reasoning benchmarks, in terms of effectiveness, generalization, and interpretability.

Large language model (LLM) benchmarks inform LLM use decisions (e.g., "is this LLM safe to deploy for my use case and context?"). However, benchmarks may be rendered unreliable by various failure modes that impact benchmark bias, variance, coverage, or people's capacity to understand benchmark evidence. Using the National Institute of Standards and Technology's risk management process as a foundation, this research iteratively analyzed 26 popular benchmarks, identifying 57 potential failure modes and 196 corresponding mitigation strategies. The mitigations reduce failure likelihood and/or severity, providing a frame for evaluating "benchmark risk," which is scored to provide a metaevaluation benchmark: BenchRisk. Higher scores indicate that benchmark users are less likely to reach an incorrect or unsupported conclusion about an LLM. All 26 scored benchmarks present significant risk within one or more of the five scored dimensions (comprehensiveness, intelligibility, consistency, correctness, and longevity), which points to important open research directions for the field of LLM benchmarking. The BenchRisk workflow allows for comparison between benchmarks; as an open-source tool, it also facilitates the identification and sharing of risks and their mitigations.

We study the problem of likelihood maximization when the likelihood function is intractable but model simulations are readily available. We propose a sequential, gradient-based optimization method that directly models the Fisher score based on a local score matching technique which uses simulations from a localized region around each parameter iterate. By employing a linear parameterization for the surrogate score model, our technique admits a closed-form, least-squares solution. This approach yields a fast, flexible, and efficient approximation to the Fisher score, effectively smoothing the likelihood objective and mitigating the challenges posed by complex likelihood landscapes. We provide theoretical guarantees for our score estimator, including bounds on the bias introduced by the smoothing. Empirical results on a range of synthetic and real-world problems demonstrate the superior performance of our method compared to existing benchmarks.

Human behavior is characterized by continuous learning to reduce uncertainties about the world in pursuit of goals. When trying to understand such behavior from observations, it is essential to account for this adaptive nature and reason about the uncertainties that may have led to seemingly suboptimal decisions. Nevertheless, most inverse approaches to sequential decision-making focus on inferring cost functions underlying stationary behavior or are limited to low-dimensional tasks. In this paper, we address this gap by considering the problem of inferring an agent's knowledge or awareness about the environment based on a given trajectory. We assume that the agent aims to reach a goal in an environment they only partially know, and integrates new information into their plan as they act. We propose a Bayesian approach to infer their latent knowledge state, leveraging an approximate navigation model that optimistically incorporates partial information while accounting for uncertainty. By combining sample-based Bayesian inference with dynamic graph algorithms, we achieve an efficient method for computing posterior beliefs about the agent's knowledge. Empirical validation using simulated behavioral data and human data from an online experiment demonstrates that our model effectively captures human navigation under uncertainty and reveals interpretable insights into their environmental knowledge.

The widespread use of generative models has created a feedback loop, in which each version of a model is trained on data partially produced by its predecessors. This process has raised concerns about model collapse: A critical degradation in performance caused by repeated training on synthetic data. However, different analyses in the literature have reached different conclusions as to the severity of model collapse. As such, it remains unclear how concerning this phenomenon is, and under which assumptions it can be avoided. To address this, we theoretically study model collapse for maximum likelihood estimation (MLE), in a natural setting where synthetic data is gradually added to the original data set. Under standard assumptions (similar to those long used for proving asymptotic consistency and normality of MLE), we establish non-asymptotic bounds showing that collapse can be avoided even as the fraction of real data vanishes. On the other hand, we prove that some assumptions (beyond MLE consistency) are indeed necessary: Without them, model collapse can occur arbitrarily quickly, even when the original data is still present in the training set. To the best of our knowledge, these are the first rigorous examples of iterative generative modeling with accumulating data that rapidly leads to model collapse.