Invariant Point Attention (IPA) is a key algorithm for geometry-aware modeling in structural biology, central to many protein and RNA models. However, its quadratic complexity limits the input sequence length. We introduce FlashIPA, a factorized reformulation of IPA that leverages hardware-efficient FlashAttention to achieve linear scaling in GPU memory and wall-clock time with sequence length. FlashIPA matches or exceeds standard IPA performance while substantially reducing computational costs. FlashIPA extends training to previously unattainable lengths, and we demonstrate this by re-training generative models without length restrictions and generating structures of thousands of residues.

We present a universal theoretical framework for understanding long-context language modeling based on a bipartite mutual information scaling law that we rigorously verify in natural language. We demonstrate that bipartite mutual information captures multi-token interactions distinct from and scaling independently of conventional two-point mutual information, and show that this provides a more complete characterization of the dependencies needed for accurately modeling long sequences. Leveraging this scaling law, we formulate the Long-context Language Modeling (L2M) condition, which lower bounds the necessary scaling of a model's history state--the latent variables responsible for storing past information--for effective long-context modeling.

State-space models (SSMs) have recently emerged as a compelling alternative to Transformers for sequence modeling tasks. This paper presents a theoretical generalization analysis of selective SSMs, the core architectural component behind the Mamba model. We derive a novel covering number-based generalization bound for selective SSMs, building upon recent theoretical advances in the analysis of Transformer models. Using this result, we analyze how the spectral abscissa of the continuous-time state matrix influences the model's stability during training and its ability to generalize across sequence lengths. We empirically validate our findings on a synthetic majority task, the IMDb sentiment classification benchmark, and the ListOps task, demonstrating how our theoretical insights translate into practical model behavior.

Marked temporal point processes (MTPPs) model sequences of events occurring at irregular time intervals, with wide-ranging applications in fields such as healthcare, finance and social networks. We propose the state-space point process (S2P2) model, a novel and performant model that leverages techniques derived for modern deep state-space models (SSMs) to overcome limitations of existing MTPP models, while simultaneously imbuing strong inductive biases for continuous-time event sequences that other discrete sequence models (i.e., RNNs, transformers) do not capture. Inspired by the classical linear Hawkes processes, we propose an architecture that interleaves stochastic jump differential equations with nonlinearities to create a highly expressive intensity-based MTPP model, without the need for restrictive parametric assumptions for the intensity. Our approach enables efficient training and inference with a parallel scan, bringing linear complexity and sublinear scaling while retaining expressivity to MTPPs. Empirically, S2P2 achieves state-of-the-art predictive likelihoods across eight real-world datasets, delivering an average improvement of 33% over the best existing approaches.

Scaling video diffusion transformers (DiTs) is limited by their quadratic 3D attention, even though most of the attention mass concentrates on a small subset of positions. We turn this observation into VSA, a trainable, hardware-efficient sparse attention that replaces full attention at both training and inference. In VSA, a lightweight coarse stage pools tokens into tiles and identifies high-weight critical tokens; a fine stage computes token-level attention only inside those tiles subjecting to block computing layout to ensure hard efficiency. This leads to a single differentiable kernel that trains end-to-end, requires no post-hoc profiling, and sustains 85% of FlashAttention3 MFU. We perform a large sweep of ablation studies and scaling-law experiments by pretraining DiTs from 60M to 1.4B parameters. VSA reaches a Pareto point that cuts training FLOPS by 2.53 with no drop in diffusion loss.

This paper presents a novel approach to addressing the long-sequence problem in high-resolution medical images for Vision Transformers (ViTs). Using smaller patches as tokens can enhance ViT performance, but quadratically increases computation and memory requirements. Therefore, the common practice for applying ViTs to high-resolution images is either to: (a) employ complex sub-quadratic attention schemes or (b) use large to medium-sized patches and rely on additional mechanisms within the model to capture the spatial hierarchy of details. We propose Symmetrical Hierarchical Forest (SHF), a lightweight approach that adaptively patches the input image to increase token information density and encode hierarchical spatial structures into the input embedding. We then apply a reverse depatching scheme to the output embeddings of the transformer encoder, eliminating the need for convolution-based decoders. Unlike previous methods that modify attention mechanisms or use a complex hierarchy of interacting models, SHFcan be retrofitted to any ViT model to allow it to learn the hierarchical structure of details in high-resolution images without requiring architectural changes. Experimental results demonstrate significant gains in computational efficiency and performance: on the PAIPWSI dataset, we achieved a 3 32 speedup or a 2.95% 7.03% increase in accuracy (measured by Dice score) at a 64K2 resolution with the same computational budget, compared to state-of-the-art production models. On the 3D medical datasets BTCV and KiTS, training was 6 faster, with accuracy gains of 6.93% and 5.9%, respectively, compared to models without SHF.

Dynamic graph modeling aims to uncover evolutionary patterns in real-world systems, enabling accurate social recommendation and early detection of cancer cells. Inspired by the success of recent state space models in efficiently capturing long-term dependencies, we propose DyG-Mamba by translating dynamic graph modeling into a long-term sequence modeling problem. Specifically, inspired by Ebbinghaus' forgetting curve, we treat the irregular timespans between events as control signals, allowing DyG-Mamba to dynamically adjust the forgetting of historical information. This mechanism ensures effective usage of irregular timespans, thereby improving both model effectiveness and inductive capability. In addition, inspired by Ebbinghaus' review cycle, we redefine core parameters to ensure that DyG-Mamba selectively reviews historical information and filters out noisy inputs, further enhancing the model's robustness. Through exhaustive experiments on 12 datasets covering dynamic link prediction and node classification tasks, we show that DyG-Mamba achieves state-of-the-art performance on most datasets, while demonstrating significantly improved computational and memory efficiency.

Long-context supervised fine-tuning (Long-SFT) plays a vital role in enhancing the performance of large language models (LLMs) on long-context tasks. To smoothly adapt LLMs to long-context scenarios, this process typically entails training on mixed datasets containing both long and short sequences. However, this heterogeneous sequence length distribution poses significant challenges for existing training systems, as they fail to simultaneously achieve high training efficiency for both long and short sequences, resulting in sub-optimal end-to-end system performance in Long-SFT. In this paper, we present a novel perspective on data scheduling to address the challenges posed by the heterogeneous data distributions in Long-SFT. We propose Skrull, a dynamic data scheduler specifically designed for efficient long-SFT.

Training Transformer models on long sequences in a distributed setting poses significant challenges in terms of efficiency and scalability. Current methods are either constrained by the number of attention heads or excessive communication overheads. To address this problem, we propose StarTrail, a multi-dimensional concentric distributed training system for long sequences, fostering an efficient communication paradigm and providing additional tuning flexibility for communication arrangements. Specifically, StarTrail introduces an extra parallel dimension and divides the peer-to-peer communication into sub-rings to substantially reduce communication volume and avoid bandwidth bottlenecks. Through comprehensive experiments across diverse hardware environments and on both Natural Language Processing (NLP) and Computer Vision (CV) tasks, we demonstrate that our approach significantly surpasses state-of-the-art methods that support Long sequence lengths, achieving performance improvements of up to 77.12% on GPT-style models and up to 114.33% on DiT (Diffusion Transformer) models without affecting the computation results.

We argue that diffusion models' success in modeling complex distributions is, for the most part, coming from their input conditioning. This paper investigates the representation used to condition diffusion models from the perspective that ideal representations should improve sample fidelity, be easy to generate, and be compositional to allow out-of-training samples generation. We introduce Discrete Latent Code (DLC), an image representation derived from Simplicial Embeddings trained with a self-supervised learning objective. DLCs are sequences of discrete tokens, as opposed to the standard continuous image embeddings. They are easy to generate and their compositionality enables sampling of novel images beyond the training distribution. Diffusion models trained with DLCs have improved generation fidelity, establishing a new state-of-the-art for unconditional image generation on ImageNet. Additionally, we show that composing DLCs allows the image generator to produce out-of-distribution samples that coherently combine the semantics of images in diverse ways. Finally, we showcase how DLCs can enable text-to-image generation by leveraging large-scale pretrained language models. We efficiently finetune a text diffusion language model to generate DLCs that produce novel samples outside of the image generator training distribution.