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.

Contrastive learning--a modern approach to extract useful representations from unlabeled data by training models to distinguish similar samples from dissimilar ones--has driven significant progress in foundation models. In this work, we develop a new theoretical framework for analyzing data augmentation-based contrastive learning, with a focus on SimCLR as a representative example. Our approach is based on the concept of approximate sufficient statistics, which we extend beyond its original definition in Oko et al. [28] for contrastive languageimage pretraining (CLIP) using KL-divergence. We generalize it to equivalent forms and general f-divergences, and show that minimizing SimCLR and other contrastive losses yields encoders that are approximately sufficient. Furthermore, we demonstrate that these near-sufficient encoders can be effectively adapted to downstream regression and classification tasks, with performance depending on their sufficiency and the error induced by data augmentation in contrastive learning. Concrete examples in linear regression and topic classification are provided to illustrate the broad applicability of our results.

Multimodal learning plays a pivotal role in advancing artificial intelligence systems by incorporating information from multiple modalities to build a more comprehensive representation. Despite its importance, current state-of-the-art models still suffer from severe limitations that prevent the successful development of a fully multimodal model. Such methods may not provide indicators that all the involved modalities are effectively aligned. As a result, some modalities may not be aligned, undermining the effectiveness of the model in downstream tasks where multiple modalities should provide additional information that the model fails to exploit. In this paper, we present TRIANGLE: TRI-modAl Neural Geometric LEarning, the novel proposed similarity measure that is directly computed in the higher-dimensional space spanned by the modality embeddings. TRIANGLE improves the joint alignment of three modalities via a triangle-area similarity, avoiding additional fusion layers or pairwise similarities. When incorporated in contrastive losses replacing cosine similarity, TRIANGLE significantly boosts the performance of multimodal modeling, while yielding interpretable alignment rationales. Extensive evaluation in three-modal tasks such as video-text and audio-text retrieval or audio-video classification, demonstrates that TRIANGLE achieves state-of-the-art results across different datasets improving the performance of cosine-based methods up to 9 points of Recall@1.

Neural networks generally prefer simple and easy-to-learn features. When these features are spuriously correlated with the labels, the network's performance can suffer, particularly for underrepresented classes or concepts. Self-supervised representation learning methods, such as contrastive learning, are especially prone to this issue, often resulting in worse performance on downstream tasks. We identify a key spectral signature of this failure: early reliance on dominant singular modes of the learned feature matrix. To mitigate this, we propose a novel framework that promotes a uniform eigenspectrum of the feature covariance matrix, encouraging diverse and semantically rich representations. Our method operates in a fully self-supervised setting, without relying on ground-truth labels or any additional information. Empirical results on SimCLR and SimSiam demonstrate consistent gains in robustness and transfer performance, suggesting broad applicability across self-supervised learning paradigms.

Foundation Vision Encoders have become essential for a wide range of dense vision tasks. However, their low-resolution spatial feature outputs necessitate feature upsampling to produce the high-resolution modalities required for downstream tasks. In this work, we introduce JAFAR, a lightweight and flexible feature upsampler that enhances the spatial resolution of visual features from any Foundation Vision Encoder to an arbitrary target resolution. JAFAR employs an attention-based module designed to promote semantic alignment between high-resolution queries, derived from low-level image features, and semantically enriched low-resolution keys, using Spatial Feature Transform (SFT) modulation. Notably, despite the absence of high-resolution supervision, we demonstrate that learning at low upsampling ratios and resolutions generalizes remarkably well to significantly higher output scales. Extensive experiments show that JAFAR effectively recovers fine-grained spatial details and consistently outperforms existing feature upsampling methods across a diverse set of downstream tasks.

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.1

Mixture-of-Experts (MoE) models enable efficient scaling of large language models (LLMs) by activating only a subset of experts per input. However, we observe that the commonly used auxiliary load balancing loss often leads to expert overlap and overly uniform routing, which hinders expert specialization and degrades overall performance during post-training. To address this, we propose a simple yet effective solution that introduces two complementary objectives: (1) an orthogonality loss to encourage experts to process distinct types of tokens, and (2) a variance loss to encourage more discriminative routing decisions. Gradient-level analysis demonstrates that these objectives are compatible with the existing auxiliary loss and contribute to optimizing the training process. Experimental results over various model architectures and across multiple benchmarks show that our method significantly enhances expert specialization. Notably, our method improves classic MoE baselines with auxiliary loss by up to 23.79%, while also maintaining load balancing in downstream tasks, without any architectural modifications or additional components. Our code is available at this link.

Contrastive Language-Image Pretraining (CLIP) has demonstrated strong zero-shot performance across diverse downstream text-image tasks. Existing CLIP methods typically optimize a contrastive objective using negative samples drawn from each minibatch. To achieve robust representation learning, these methods require extremely large batch sizes and escalate computational demands to hundreds or even thousands of GPUs. Prior approaches to mitigate this issue often compromise downstream performance, prolong training duration, or face scalability challenges with very large datasets. To overcome these limitations, we propose AMORLIP, an efficient CLIP pretraining framework that amortizes expensive computations involved in contrastive learning through lightweight neural networks, which substantially improves training efficiency and performance. Leveraging insights from a spectral factorization of energy-based models, we introduce novel amortization objectives along with practical techniques to improve training stability. Extensive experiments across 38 downstream tasks demonstrate the superior zero-shot classification and retrieval capabilities of AMORLIP, consistently outperforming standard CLIP baselines with substantial relative improvements of up to 12.24%.

Length generalization--the ability to solve problems longer than those seen during training--remains a critical challenge for large language models (LLMs). Previous work modifies positional encodings (PEs) and data formats to improve length generalization on specific symbolic tasks such as addition and sorting. However, these approaches are fundamentally limited to special tasks, often degrading general language performance. Furthermore, they are typically evaluated on small transformers trained from scratch on single tasks and can cause performance drop when applied during post-training stage of practical LLMs with general capabilities. Hu et al. [19] proposed Rule-Following Fine-Tuning (RFFT) to improve length generalization in the post-training stage of LLMs.

With the increasing number of time series pre-trained models, designing transferability evaluation metrics for time series has become an urgent problem to address. While transferability evaluation has been extensively studied in computer vision, we aim to address a critical gap by developing tailored metrics for time series analysis. In this paper, we introduce TEMPLATE, a transferability estimation framework specifically tailored for versatile time series analysis, comprising three complementary metrics: (1) Dependency Learning Score quantifies a model's capacity to capture temporal dependencies.