Neural processes amortize Gaussian process inference, replacing the exact $O(n^3)$ posterior with a learned $O(n)$ map from context sets to predictive distributions. For a class of latent neural processes, we bound the Kullback--Leibler (KL) divergence between the GP and LNP predictives, decomposing it into three interpretable sources, namely label contamination as the neural process uses label values to estimate a quantity that is label-independent in the exact GP, an information bottleneck because the finite-dimensional representation cannot resolve the full context geometry, and amortization error from a single encoder network shared across all contexts. The bottleneck truncation term decays in the representation dimension $d$ as $O(e^{-cd^{2/d_x}})$ for squared-exponential kernels on $\mathbb{R}^{d_x}$ where $c > 0$ is a kernel-dependent constant and as $O(d^{-2ν/d_x})$ for Matérn-$ν$ kernels, directly linking architecture sizing to kernel smoothness and input dimension. The label contamination term is $O(1)$ in general, with only the observation-noise component decaying as $O(1/n)$, identifying a persistent cost of routing uncertainty estimation through a label-dependent representation. These results characterize the costs of amortization within the analyzed class and yield architectural recommendations to predict variance from context locations alone in the GP-amortization regime, and replace mean aggregation with second-order pooling to close the dominant amortization gap.

Heavy-tailed distributions are prevalent in performance evaluation, network traffic, and risk modeling. This behavior poses a fundamental challenge for modern deep generative models. Standard Variational Autoencoders (VAEs) employ Gaussian decoder likelihoods and Lipschitz-constrained neural networks, a combination that is structurally incapable of producing heavy-tailed outputs: the Gaussian tail decays exponentially, and Lipschitz continuity prevents the decoder from amplifying rare events from the latent space input to sufficiently overcome this decay. We provide both a theoretical characterization of this limitation and a controlled empirical demonstration using synthetic Pareto data across a grid of tail indices $α$ $\in$ {2, 3, 5, 30} and dimensions d $\in$ {1, 5, 10}. As a solution, we replace the Gaussian decoder with a Phase-Type (PH) distribution based on Markov chains, while keeping the encoder, latent space, and training procedure identical. PH distributions allow for arbitrarily precise approximations of any positive-valued distributions, including heavy-tailed families. Experiments showed that the PH-based model reduces tail Kolmogorov-Smirnov distance by up to x6 and extreme quantile error by up to x10 compared to the Gaussian baseline for heavy-tailed data. These results demonstrate that integrating Markov chain-based distributions into the decoder of a generative model institutes a principled and practically effective solution to the heavy-tail generation problem.

While deep learning has revolutionised inverse problems, its safe deployment is hindered by three primary reliability concerns: hallucinations, instabilities, and performance volatility [48]. Hallucinations manifest as high-fidelity features that are factually false; instabilities reflect heightened sensitivity to measurement noise; and performance volatility refers to significant fluctuations in reconstruction quality across the data, yielding high-fidelity results for some samples while failing on seemingly similar images. In many applications, the risk of generating realistic but unfaithful content can impede the safe deployment of AI methods for inverse problems. The choice of "hallucinate" as the Cambridge Dictionary's word of the year in 2023 illustrates this open problem [53]. The problem of AI hallucinations persists, as the Financial Times [44] highlighted that, "AI hallucinations haunt users more than job losses." A first step toward training AI methods that do not suffer from hallucinations is the assessment and identification of hallucinated outputs. Consider the inverse problem of recovering xfrom noisy measurements y " Fpx,eq, x PM1 ĂX, e PEĂY, (1.1)

Link prediction (inferring missing or future connections between nodes in a graph) is a fundamental problem in network science with widespread applications in, e.g., biological systems, recommender systems, finance and cybersecurity. The ability to accurately predict links has significant real-world applications, such as detecting fraudulent financial transactions or identifying drug-target interactions in biomedicine. Despite a rich literature, link prediction is still challenging, especially for graphs enriched with information on edges (direction) and nodes (attributes). In fact, research on link prediction, especially the one based on Graph Deep Learning (GDL), has mostly focused on undirected graphs, without fully leveraging node attributes. Here, we fill this gap by proposing Gravity-GraphSAGE (GG-SAGE), a modified version of GraphSAGE, a GDL model for node embeddings, composed of a gravity-inspired decoder. This implementation is the first example in the literature of a GraphSAGE backbone adopted for directed link prediction. Using the benchmark datasets Cora, Citeseer, PubMed and 16 real-world graphs from the online Netzschleuder repository, we show that our proposed model outperforms state-of-the-art GDL link prediction techniques. Using further experimental evidence, we relate the quality of the output of our model with various characteristics of the graph, suggesting that our framework scales well when applied to data of increasing complexity.

We study sparse recovery when observations come from mixed-quality sources: a small collection of high-quality measurements with small noise variance and a larger collection of lower-quality measurements with higher variance. For this heterogeneous-noise setting, we establish sample-size conditions for information-theoretic and algorithmic recovery. On the information-theoretic side, we show that it is sufficient for $(n_1, n_2)$ to satisfy a linear trade-off defining the Price of Quality: the number of low-quality samples needed to replace one high-quality sample. In the agnostic setting, where the decoder is completely agnostic to the quality of the data, it is uniformly bounded, and in particular one high-quality sample is never worth more than two low-quality samples for this sufficient condition to hold. In the informed setting, where the decoder is informed of per-sample variances, the price of quality can grow arbitrarily large. On the algorithmic side, we analyze the LASSO in the agnostic setting and show that the recovery threshold matches the homogeneous-noise case and only depends on the average noise level, revealing a striking robustness of computational recovery to data heterogeneity. Together, these results give the first conditions for sparse recovery with mixed-quality data and expose a fundamental difference between how the information-theoretic and algorithmic thresholds adapt to changes in data quality.

Evolutionary methods have long been useful for analysis and explanation in genetics, biology, ecology, and related fields. In this work, we extend these methods to neural networks, specifically large language models (LLMs), to better analyze and explain relationships among models. We show how relating weights to genotypes and output text to phenotypes can improve our understanding of model lineage, important datasets, the roles of different model layers, and visualization of model relationships. We demonstrate this in a controlled experiment, where our estimated evolutionary trees reliably recover the topology of the ground-truth training tree. We further identify the most important weight layers according to weight differences and show through phenotypic experiments that one training dataset appears to contribute more useful information than the others. Finally, we generate an unsupervised evolutionary tree of black-box foundation models. Throughout, we provide visualizations that support a clearer understanding of evolutionary relationships among LLMs.

Generative models for time-series imputation achieve strong reconstruction accuracy, yet provide no finite-sample reliability guarantees, a critical limitation in power systems where imputed values inform dispatch and planning. We introduce SPLICE (Self-supervised Predictive Latent Inpainting with Conformal Envelopes), a modular framework coupling latent generative imputation with distribution-free, online-adaptive prediction intervals. A JEPA encoder maps daily load segments into a 64-dimensional latent space; a conditional latent bridge with four sampling modes generates candidate gap trajectories; an hourly-conditioned decoder maps back to signal space; and Adaptive Conformal Inference (ACI) wraps the output with coverage-guaranteed prediction bands. The flow-matching variant achieves comparable quality to DDIM in 5--10 ODE steps (5-10x speedup). On thirteen load datasets (nine proprietary, three UCI Electricity, ETTh1), SPLICE achieves the lowest mean Load-only MSE (0.056), winning 9/12 non-degenerate datasets at 91-day gaps and 18/32 across all gap lengths vs. five established baselines, and produces the best CRPS (0.161, -18.3% vs. the strongest competitor). ACI delivers 93--95% empirical coverage, correcting under-coverage failures of up to 7.5 pp observed with static conformal prediction. A pooled JEPA encoder trained on nine feeds transfers to four unseen domains, matching or exceeding per-dataset oracles with only a quick bridge fine-tuning.

This paper reveals a characteristic of DEtection Transformer (DETR) that negatively impacts its training efficacy, i.e., the cross-attention and self-attention layers in DETR decoder have opposing impacts on the object queries (though both impacts are important). Specifically, we observe the cross-attention tends to gather multiple queries around the same object, while the self-attention disperses these queries far away. To improve the training efficacy, we propose a Divide-And-Conquer DETR (DAC-DETR) that separates out the cross-attention to avoid these competing objectives. During training, DAC-DETR employs an auxiliary decoder that focuses on learning the cross-attention layers. The auxiliary decoder, while sharing all the other parameters, has NO self-attention layers and employs one-to-many label assignment to improve the gathering effect. Experiments show that DAC-DETR brings remarkable improvement over popular DETRs. For example, under the 12 epochs training scheme on MS-COCO, DAC-DETR improves Deformable DETR (ResNet50) by +3.4AP and achieves 50.9 (ResNet-50) / 58.1 AP (Swin-Large) based on some popular methods (i.e., DINO and an IoU-related loss).

Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for humans with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGeneα (or xTrimoGene for short)4, which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we scale up the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell type annotation, perturb-seq effect prediction, and drug combination prediction.

The neural population spiking activity recorded by intracortical brain-computer interfaces (iBCIs) contain rich structure. Current models of such spiking activity are largely prepared for individual experimental contexts, restricting data volume to that collectable within a single session and limiting the effectiveness of deep neural networks (DNNs). The purported challenge in aggregating neural spiking data is the pervasiveness of context-dependent shifts in the neural data distributions. However, large scale unsupervised pretraining by nature spans heterogeneous data, and has proven to be a fundamental recipe for successful representation learning across deep learning. We thus develop Neural Data Transformer 2 (NDT2), a spatiotemporal Transformer for neural spiking activity, and demonstrate that pretraining can leverage motor BCI datasets that span sessions, subjects, and experimental tasks. NDT2 enables rapid adaptation to novel contexts in downstream decoding tasks and opens the path to deployment of pretrained DNNs for iBCI control.