The increasing use of 360 images across various domains has emphasized the need for robust depth estimation techniques tailored for omnidirectional images. However, obtaining large-scale labeled datasets for 360 depth estimation remains a significant challenge. In this paper, we propose RPG360, a training-free robust 360 monocular depth estimation method that leverages perspective foundation models and graph optimization. Our approach converts 360 images into sixface cubemap representations, where a perspective foundation model is employed to estimate depth and surface normals. To address depth scale inconsistencies across different faces of the cubemap, we introduce a novel depth scale alignment technique using graph-based optimization, which parameterizes the predicted depth and normal maps while incorporating an additional per-face scale parameter. This optimization ensures depth scale consistency across the six-face cubemap while preserving 3D structural integrity. Furthermore, as foundation models exhibit inherent robustness in zero-shot settings, our method achieves superior performance across diverse datasets, including Matterport3D, Stanford2D3D, and 360Loc. We also demonstrate the versatility of our depth estimation approach by validating its benefits in downstream tasks such as feature matching 3.2 5.4% and Structure from Motion 0.2 9.7% in AUC@5 .

Scaling laws motivate the development of Time Series Foundation Models (TSFMs) that pre-train vast parameters and achieve remarkable zero-shot forecasting performance. Surprisingly, even after fine-tuning, TSFMs cannot consistently outperform smaller, specialized models trained on full-shot downstream data. A key question is how to realize effective adaptation of TSFMs for a target forecasting task. Through empirical studies on various TSFMs, the pre-trained models often exhibit inherent sparsity and redundancy in computation, suggesting that TSFMs have learned to activate task-relevant network substructures to accommodate diverse forecasting tasks. To preserve this valuable prior knowledge, we propose a structured pruning method to regularize the subsequent fine-tuning process by focusing it on a more relevant and compact parameter space. Extensive experiments on seven TSFMs and six benchmarks demonstrate that fine-tuning a smaller, pruned TSFM significantly improves forecasting performance compared to fine-tuning original models. This "prune-then-finetune" paradigm often enables TSFMs to achieve state-of-the-art performance and surpass strong specialized baselines.

Randomized experiments are the preferred approach for evaluating the effects of interventions, but they are costly and often yield estimates with substantial uncertainty. On the other hand, in silico experiments leveraging foundation models offer a cost-effective alternative that can potentially attain higher statistical precision. However, the benefits of in silico experiments come with a significant risk: statistical inferences are not valid if the models fail to accurately predict experimental responses to interventions. In this paper, we propose a novel approach that integrates the predictions from multiple foundation models with experimental data while preserving valid statistical inference. Our estimator is consistent and asymptotically normal, with asymptotic variance no larger than the standard estimator based on experimental data alone. Importantly, these statistical properties hold even when model predictions are arbitrarily biased. Empirical results across several randomized experiments show that our estimator offers substantial precision gains, equivalent to a reduction of up to 20% in the sample size needed to match the same precision as the standard estimator based on experimental data alone.

Electroencephalography (EEG) has wide-ranging applications, from clinical diagnosis to brain-computer interfaces (BCIs). With the increasing volume and variety of EEG data, there has been growing interest in establishing foundation models (FMs) to scale up and generalize neural decoding. Despite showing early potential, applying FMs to EEG remains challenging due to substantial inter-subject, intertask, and inter-condition variability, as well as diverse electrode configurations across recording setups. To tackle these open challenges, we propose NEURIPT, a foundation model developed for diverse EEG-based Neural Interfaces with a Pre-trained Transformer by capturing both homogeneous and heterogeneous spatio-temporal characteristics inherent in EEG signals. Temporally, we introduce Amplitude-Aware Masked Pretraining (AAMP), masking based on signal amplitude rather than random intervals, to learn robust representations across varying signal intensities beyond local interpolation. Moreover, this temporal representation is enhanced by a Progressive Mixture-of-Experts (PMoE) architecture, where specialized expert subnetworks are progressively introduced at deeper layers, adapting effectively to the diverse temporal characteristics of EEG signals.

This work presents a systematic investigation into the latent knowledge encoded within Network Foundation Models (NFMs). Different from existing efforts, we focus on hidden representations analysis rather than pure downstream task performance and analyze NFMs through a three-part evaluation: Embedding Geometry Analysis to assess representation space utilization, Metric Alignment Assessment to measure correspondence with domain-expert features, and Causal Sensitivity Testing to evaluate robustness to protocol perturbations. Using five diverse network datasets spanning controlled and real-world environments, we evaluate four stateof-the-art NFMs, revealing that they all exhibit significant anisotropy, inconsistent feature sensitivity patterns, an inability to separate the high-level context, payload dependency, and other properties. Our work identifies numerous limitations across all models and demonstrates that addressing them can significantly improve model performance (up to 0.35 increase in F1 scores without architectural changes).

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single-cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling.

The proposed research on pre-training temporal graph neural networks across multiple networks has the potential to advance the field of machine learning and its applications significantly. By introducing methodologies to enhance the scalability and transferability of TGNNs, this work could revolutionize areas like network security, financial fraud detection, and real-time social network analysis, where dynamic and adaptive models are essential. The publicly available dataset of 84 Ethereum-based temporal networks will serve as a valuable resource for the research community, fostering innovation and collaboration. Furthermore, the principles of multi-network pre-training introduced here can inspire analogous advances in other temporal data domains, such as healthcare, transportation, and climate science. This research opens up a new direction in training generalizable temporal graph models that, for the first time, can be trained on distinct temporal networks, paving the way for Temporal Graph Foundation Models. This work also introduces a set of Ethereum transaction token networks, which are publicly available to users who have the necessary resources, such as fast SSDs, large RAM, and ample disk space, to synchronize Ethereum clients and manually extract blocks. Additionally, all Ethereum data is accessible on numerous Ethereum explorer sites such as etherscan.io. An Ethereum user's privacy depends on whether personally identifiable information (PII) is associated with any of their blockchain address, which serves as account handles and are considered pseudonymous. If such PII were obtained from other sources, our datasets could potentially be used to link Ethereum addresses. However, real-life identities can only be discovered using IP tracking information, which we neither have nor share. Our data does not contain any PII. Furthermore, we have developed a request to exclude an address from the dataset. Benchmark datasets have become fundamental for advancing graph machine learning, providing a common ground to evaluate models and facilitate the development of graph foundation models. Early graph ML studies often relied on a handful of small, static benchmark graphs (e.g., citation networks like Cora/Citeseer and molecular graphs from the TU collection [37]).

Temporal Graph Learning (TGL) aims to discover patterns in evolving networks or temporal graphs and leverage these patterns to predict future interactions. However, most existing research focuses on learning from a single network in isolation, leaving the challenges of within-domain and cross-domain generalization largely unaddressed. In this study, we introduce a new benchmark of 84 real-world temporal transaction networks and propose Temporal Multi-network Transfer (MiNT), a pre-training framework designed to capture transferable temporal dynamics across diverse networks. We train MiNT models on up to 64 transaction networks and evaluate their generalization ability on 20 held-out, unseen networks. Our results show that MiNT consistently outperforms individually trained models, revealing a strong relation between the number of pre-training networks and transfer performance. These findings highlight scaling trends in temporal graph learning and underscore the importance of network diversity in improving generalization. This work establishes the first large-scale benchmark for studying transferability in TGL and lays the groundwork for developing Temporal Graph Foundation Models.

Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both Hi-C contact maps and epigenomic tracks, which obtains unified and comprehensive semantics.

Discovering novel molecules requires accurate out-of-distribution (OOD) predictions, but ML models struggle to generalize OOD. Currently, no systematic benchmarks exist for molecular OOD prediction tasks.