Many applications require statistically valid inference across many related "tasks", while using only a handful of high-quality labels per hypothesis. In AI evaluation, these tasks may correspond to model behaviors across prompts, subgroups, or hypotheses; in social science surveys, they may correspond to related questions, populations, or measurement conditions. Prediction-powered inference (PPI) uses abundant but inexpensive proxy measurements to improve inference from limited, "ground-truth" labels, but commonly used methods treat tasks independently and therefore fail to exploit shared structure across related tasks. This limitation is especially important in settings where only a small number of labels are available per task. To address this issue, we introduce a multi-task prediction-powered inference framework that uses labeled data from related tasks to improve power while preserving task-specific inference. Our methods exploit the shared structure in the proxy-ground-truth relationship through cross-task recalibration, while retaining within-task rectification and power tuning to construct accurate point estimates and confidence intervals. We prove that efficiency gains beyond power-tuned PPI are only possible when the proxy-ground-truth relationship contains nonlinear structure; affine cross-task recalibrations are asymptotically equivalent to using the original proxy. We complement our theoretical findings with experiments on synthetic and semi-synthetic datasets, as well as a case study auditing language models on election-related information during the 2024 U.S. presidential election. Using a large human-annotation study, we show that cross-task recalibration can substantially reduce confidence interval widths when labels are scarce.

Large language models (LLMs) are prone to hallucinations, i.e., statements unsupported by the input or training data, hindering reliable deployment. In parallel, numerous uncertainty estimation (UE) methods have been proposed to quantify model confidence and are often implicitly treated as proxies for model failure. However, the relationship between uncertainty and hallucinations remains insufficiently characterized. We present a systematic empirical study of the association between uncertainty estimators and hallucinations in LLMs. Rather than assuming this association, we evaluate directly when and to what extent it holds. We consider a diverse set of uncertainty estimators, including information-theoretic, sampling-based, and reflexive estimators, and examine their behavior across hallucination settings. Our experiments cover both intrinsic hallucinations (violations of input faithfulness) and extrinsic hallucinations (unsupported claims relative to training data), using four complementary benchmarks, including RAGTruth and HalluLens. We find that the association is highly variable and often weak, depending on the hallucination type and the LLM under evaluation. These results challenge the use of uncertainty as a direct signal of hallucination and clarify when it provides actionable information.

Ensembles of neural networks typically outperform individual networks but incur large computational costs, whereas weight aggregation produces less costly, yet also less accurate, aggregate models. We introduce partial fusion of networks, which interpolates between ensembles and weight aggregation and thus allows for a flexible tradeoff between computational cost and performance. A direct way to achieve this is to extend existing weight aggregation methods based on neuron-level similarity between different networks, where partial fusion then only aggregates weights of neurons which are most similar. We showcase one particular method to jointly identify which neurons are most similar and match them via partial optimal transport. Further, we consider the more general perspective of weight aggregation and partial fusion as generalized pruning of ensemble models, where neurons cannot just be deleted, but also linearly combined. Finally, we show that generalized pruning applied to a single network yields similar benefits as partial fusion by allowing for a tradeoff between isolating, deleting, and linearly combining neurons based on similarity. Our code is available at https://github.com/Fabian-Mor/partial_fusion_nn.

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

Training data attribution (TDA) should enable generative model interpretability and foster a variety of related downstream tasks. Nonetheless, current TDA approaches lack reliability and robustness, preventing their adoption in real-world setups. In this paper, we take a decisive step towards more reliable and robust TDA for diffusion models. We propose to perform TDA with mirrored unlearning and noise-consistent skew (MUCS). The idea is to fine-tune a second model with bounded mirrored gradient ascent, and to measure the normalized skew of this model with respect to the original one using consistent noise samples. We show that, while being conceptually simple and generic, MUCS systematically outperforms existing methods on three different datasets by a large margin. We additionally study the effect that core design choices have on final performance, and analyze novel aspects regarding the overlap of influential instances across generated items and the potential of ensembling TDA approaches. We believe that our findings may have broader implications for more general unlearning setups, as well as for tasks requiring the comparison of diffusion losses.

This paper studies the role of sinks and diagonal patterns as attention switch and anti-oversmoothing mechanisms. We analyze geometric conditions under which sinks can be represented, showing a necessary alignment between the embedding of the sink and all other embeddings. Next, we refine the current understanding of the role of sinks in oversmoothing prevention: we specify the conditions under which dense attention provably smooths more than sparse attention, and empirically verify that such conditions are often satisfied in practice. We further prove an equivalence between sinks and hard attention switch, in which the output of the attention is identically 0. Finally, we relax the hard attention switch by allowing token self-communication: we provide a quantitative comparison of the costs of representing sinks vs.\ diagonal patterns, showing why sinks are favored in pretrained transformers. The introduction and analysis of diagonal patterns and the generalization of the attention switch close the gap between what oversmoothing prevention requires and what sinks provide, while also establishing when and why attention layers act like MLPs if token communication is not necessary.

Activation-alignment measures such as Representational Similarity Analysis (RSA), Canonical Correlation Analysis (CCA), and Centered Kernel Alignment (CKA) are widely used to compare biological and artificial neural representations. Recent theoretical work interprets many of these methods as assessing agreement between optimal linear readouts over broad families of global tasks. However, agreement at the level of global readouts does not determine how a system uses local stimulus evidence. Specifically, representations may align in activation space yet differ in their sensitivity to small perturbations. To address this challenge, we introduce a complementary framework based on local decodable information, which focuses on a representation's ability, under noise, to discriminate small perturbations within a specified stimulus-coordinate subspace. Building on Fisher information and local representation geometry, we summarize each representation using the expected projected pullback/Fisher metric over that subspace. This formulation induces a second-moment family of local discrimination tasks, for which the resulting operator provides a minimal, complete dataset-level summary of expected discriminability. We compare these regularized signatures using a log-spectral distance on the manifold of symmetric positive definite (SPD) matrices, yielding the Spectral Riemannian Alignment Score (S-RAS) and a uniform multiplicative certificate over the corresponding family of lifted task values. Empirically, this framework enables the recovery of corresponding layers across independently trained artificial neural networks, supports transferable class-conditional probes, reveals controlled dissociations between standard and robust training, and uncovers stimulus-coordinate family effects across mouse visual cortex using the Allen Brain Observatory static gratings dataset.

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