Compositional training has been the de-facto paradigm in existing Multimodal Large Language Models (MLLMs), where pre-trained visual encoders are connected with pre-trained LLMs through continuous multimodal pre-training. However, the multimodal scaling property of this paradigm remains difficult to explore due to the separated training. In this paper, we focus on the native training of MLLMs in an end-to-end manner and systematically study its design space and scaling property under a practical setting, i.e., data constraint. Through careful study of various choices in MLLM, we obtain the optimal meta-architecture that best balances performance and training cost. After that, we further explore the scaling properties of the native MLLM and indicate the positively correlated scaling relationship between visual encoders and LLMs. Based on these findings, we propose a native MLLM called NaViL, combined with a simple and cost-effective recipe. Experimental results on 14 multimodal benchmarks confirm the competitive performance of NaViL against existing MLLMs. Besides that, our findings and results provide in-depth insights for the future study of native MLLMs.

We study the problem of entropy calibration, which asks whether a language model's entropy over generations matches its log loss on human text. Past work found that models are miscalibrated, with entropy per step increasing as generations grow longer, due to error accumulation. To calibrate the model and improve text quality, it has become standard practice to truncate the distribution, but this approach reduces output diversity, which we would like to avoid. Therefore, in this paper, we ask: does miscalibration improve automatically with scale, and if not, is it theoretically possible to calibrate without tradeoffs? To build intuition, we first study a simplified theoretical setting to characterize the scaling behavior of miscalibration with respect to dataset size. We find that the rate of scaling depends on the power law exponent of the data distribution -- in particular, for a power law exponent close to 1, the scaling exponent is close to 0, meaning that miscalibration improves very slowly with scale.

Multimodal Large Language Models (MLLMs) have achieved considerable accuracy in Optical Character Recognition (OCR) from static images. However, their efficacy in video OCR is significantly diminished due to factors such as motion blur, temporal variations, and visual effects inherent in video content. To provide clearer guidance for training practical MLLMs, we introduce MMEVideoOCR benchmark, which encompasses a comprehensive range of video OCR application scenarios.

Discrete Flow-based Models (DFMs) are powerful generative models for highquality discrete data but typically suffer from slow sampling speeds due to their reliance on iterative decoding processes. This reliance on a multi-step process originates from the factorization approximation of DFMs, which is necessary for handling high-dimensional data. In this paper, we analyze the factorization approximation error using Conditional Total Correlation (TC), and reveal its dependence on the coupling. To address the challenge of efficient few-step generation, we propose Rectified Discrete Flow (ReDi), a novel iterative method that reduces the underlying factorization error (measured as Conditional TC) by rectifying the coupling between source and target distributions. We theoretically prove that each ReDi step guarantees a monotonic decreasing Conditional TC, ensuring its convergence. Empirically, ReDi significantly reduces Conditional TC and enables few-step generation. Moreover, we demonstrate that the rectified couplings are well-suited for training efficient one-step models on image generation. ReDi offers a simple and theoretically grounded approach for tackling the few-step challenge, providing a new perspective on efficient discrete data synthesis.

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Occlusion is one of the fundamental challenges in crowd counting. In the community, various data-driven approaches have been developed to address this issue, yet their effectiveness is limited. This is mainly because most existing crowd counting datasets on which the methods are trained are based on passive cameras, restricting their ability to fully sense the environment. Recently, embodied navigation methods have shown significant potential in precise object detection in interactive scenes. These methods incorporate active camera settings, holding promise in addressing the fundamental issues in crowd counting.

Realignment becomes necessary when a language model (LM) fails to meet expected performance. We propose a flexible realignment framework that supports quantitative control of alignment degree during training and inference. This framework incorporates Training-time Realignment (TrRa), which efficiently realigns the reference model by leveraging the controllable fusion of logits from both the reference and already aligned models. For example, TrRa reduces token usage by 54.63% on DeepSeek-R1-Distill-Qwen-1.5B without any performance degradation, outperforming DeepScaleR-1.5B's

Despite the remarkable successes of general-purpose neural networks, such as MLPs and Transformers, we find that they exhibit notable shortcomings in modeling and reasoning about periodic phenomena, achieving only marginal performance within the training domain and failing to generalize effectively to out-of-domain (OOD) scenarios. Periodicity is ubiquitous throughout nature and science. Therefore, neural networks should be equipped with the essential ability to model and handle periodicity. In this work, we propose FAN, a novel neural network that effectively addresses periodicity modeling challenges while offering broad applicability similar to MLP with fewer parameters and FLOPs. Periodicity is naturally integrated into FAN's structure and computational processes by introducing the Fourier Principle. Unlike existing Fourier-based networks, which possess particular periodicity modeling abilities but face challenges in scaling to deeper networks and are typically designed for specific tasks, our approach overcomes this challenge to enable scaling to large-scale models and maintains the capability to be applied to more types of tasks. Through extensive experiments, we demonstrate the superiority of FAN in periodicity modeling tasks and the effectiveness and generalizability of FAN across a range of real-world tasks. Moreover, we reveal that compared to existing Fourier-based networks, FAN accommodates both periodicity modeling and general-purpose modeling well.

Recent advances in graph machine learning have shifted to data-centric paradigms, driven by two emerging research fields: (1) Federated graph learning (FGL) facilitates multi-client collaboration but struggles with data and task heterogeneity, resulting in limited practicality; (2) Graph foundation model (GFM) enables desirable domain generalization but is typically confined to single-machine training, neglecting the potential of cross-silo data and computational resources. It is evident that these two paradigms are complementary, and their integration offers substantial advantages. Motivated by this, we present a pioneering study about the federated graph foundation model (FedGFM), a novel decentralized GFM training paradigm. Despite the promising vision of FedGFM, knowledge entanglement has emerged as a critical challenge, where multi-domain knowledge is encoded into indistinguishable representations, thereby limiting downstream adaptation. To this end, we propose FedGFM+, an effective FedGFM framework with two key modules to mitigate knowledge entanglement in a dual-pronged manner.

While large language models (LLMs) demonstrate impressive capabilities across numerous applications, their robustness remains a critical concern. This paper is motivated by a specific vulnerability: the order sensitivity of LLMs. This vulnerability manifests itself as the order bias observed when LLMs decide between possible options (for example, a preference for the first option) and the tendency of LLMs to provide different answers when options are reordered. The use cases for this scenario extend beyond the classical case of multiple-choice question answering to the use of LLMs for multidocument tasks and as automated evaluators in AI pipelines. We introduce Set-LLM, a novel architectural adaptation for pretrained LLMs that enables the processing of mixed set-text inputs with permutation invariance guarantees. The adaptations involve a new attention mask and new positional encodings specifically designed for sets. We provide a theoretical proof of invariance and demonstrate through experiments that Set-LLM can be trained effectively, achieving comparable or improved performance and maintaining the runtime of the original model, while altogether eliminating order sensitivity.