Multimodal Large Language Models (MLLMs) exhibit impressive capabilities across a variety of tasks, especially when equipped with carefully designed visual prompts. However, existing studies primarily focus on logical reasoning and visual understanding, while the capability of MLLMs to operate effectively in 3D vision remains an ongoing area of exploration. In this paper, we introduce a novel visual prompting method, called 3DAxisPrompt, to elicit the 3D understanding capabilities of MLLMs in real-world scenes. More specifically, our method leverages the 3D coordinate axis and masks generated from the Segment Anything Model (SAM) to provide explicit geometric priors to MLLMs and then extend their impressive 2D grounding and reasoning ability to real-world 3D scenarios. Besides, we first provide a thorough investigation of the potential visual prompting formats and conclude our findings to reveal the potential and limits of 3D understanding capabilities in GPT-4o, as a representative of MLLMs. Finally, we build evaluation environments with four datasets, i.e., ScanRefer, ScanNet, FMB, and nuScene datasets, covering various 3D tasks. Based on this, we conduct extensive quantitative and qualitative experiments, which demonstrate the effectiveness of the proposed method. Overall, our study reveals that MLLMs, with the help of 3DAxisPrompt, can effectively perceive an object's 3D position in real-world scenarios. Nevertheless, a single prompt engineering approach does not consistently achieve the best outcomes for all 3D tasks. This study highlights the feasibility of leveraging MLLMs for 3D vision grounding/reasoning with prompt engineering techniques.

In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there is a lack of comparison between these recent approaches and the classical architecture convolutional networks (CNNs) on foundation model benchmarks. This raises the question: are CNNs truly being surpassed by these recent approaches based on transformer and SSM architectures? In this paper, we develop a simple but well-designed CNN-based method termed ConvNova. ConvNova identifies and proposes three effective designs: 1) dilated convolutions, 2) gated convolutions, and 3) a dual-branch framework for gating mechanisms. Through extensive empirical experiments, we demonstrate that ConvNova significantly outperforms recent methods on more than half of the tasks across several foundation model benchmarks. For example, in histone-related tasks, ConvNova exceeds the second-best method by an average of 5.8%, while generally utilizing fewer parameters and enabling faster computation. In addition, the experiments observed findings that may be related to biological characteristics. This indicates that CNNs are still a strong competitor compared to Transformers and SSMs. We anticipate that this work will spark renewed interest in CNN-based methods for DNA foundation models.

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights.

As key elements within the central dogma, DNA, RNA, and proteins play crucial roles in maintaining life by guaranteeing accurate genetic expression and implementation. Although research on these molecules has profoundly impacted fields like medicine, agriculture, and industry, the diversity of machine learning approaches-from traditional statistical methods to deep learning models and large language models-poses challenges for researchers in choosing the most suitable models for specific tasks, especially for cross-omics and multi-omics tasks due to the lack of comprehensive benchmarks. To address this, we introduce the first comprehensive multi-omics benchmark COMET (Benchmark for Biological COmprehensive Multi-omics Evaluation Tasks and Language Models), designed to evaluate models across single-omics, cross-omics, and multi-omics tasks. First, we curate and develop a diverse collection of downstream tasks and datasets covering key structural and functional aspects in DNA, RNA, and proteins, including tasks that span multiple omics levels. Then, we evaluate existing foundational language models for DNA, RNA, and proteins, as well as the newly proposed multi-omics method, offering valuable insights into their performance in integrating and analyzing data from different biological modalities. This benchmark aims to define critical issues in multi-omics research and guide future directions, ultimately promoting advancements in understanding biological processes through integrated and different omics data analysis.

As large language models (LLMs) continue to advance, the demand for higher quality and faster processing of long contexts across various applications is growing. KV cache is widely adopted as it stores previously generated key and value tokens, effectively reducing redundant computations during inference. However, as memory overhead becomes a significant concern, efficient compression of KV cache has gained increasing attention. Most existing methods perform compression from two perspectives: identifying important tokens and designing compression strategies. However, these approaches often produce biased distributions of important tokens due to the influence of accumulated attention scores or positional encoding. Furthermore, they overlook the sparsity and redundancy across different heads, which leads to difficulties in preserving the most effective information at the head level. To this end, we propose EMS to overcome these limitations, while achieving better KV cache compression under extreme compression ratios. Specifically, we introduce a Global-Local score that combines accumulated attention scores from both global and local KV tokens to better identify the token importance. Additionally, we implement the head-wise parallel compression through a zero-class mechanism to enhance efficiency. Extensive experiments demonstrate our SOTA performance even under extreme compression ratios. EMS consistently achieves the lowest perplexity, improves scores by over 1.28 points across four LLMs on LongBench under a 256 cache budget, and preserves 95% retrieval accuracy with a cache budget less than 2% of the context length in the Needle-in-a-Haystack task. With growing application demands for LLMs, the requirement to manage long sequences (Chen et al., 2024b; Jin et al., 2024; Chen et al., 2023) is also increasing.

Recent advancements in diffusion models, particularly the trend of architectural transformation from UNet-based Diffusion to Diffusion Transformer (DiT), have significantly improved the quality and scalability of image synthesis. Despite the incredible generative quality, the large computational requirements of these large-scale models significantly hinder the deployments in real-world scenarios. Post-training Quantization (PTQ) offers a promising solution by compressing model sizes and speeding up inference for the pretrained models while eliminating model retraining. However, we have observed the existing PTQ frameworks exclusively designed for both ViT and conventional Diffusion models fall into biased quantization and result in remarkable performance degradation. In this paper, we find that the DiTs typically exhibit considerable variance in terms of both weight and activation, which easily runs out of the limited numerical representations. To address this issue, we devise Q-DiT, which seamlessly integrates three techniques: fine-grained quantization to manage substantial variance across input channels of weights and activations, an automatic search strategy to optimize the quantization granularity and mitigate redundancies, and dynamic activation quantization to capture the activation changes across timesteps. Extensive experiments on the ImageNet dataset demonstrate the effectiveness of the proposed Q-DiT. Specifically, when quantizing DiT-XL/2 to W8A8 on ImageNet 256x256, Q-DiT achieves a remarkable reduction in FID by 1.26 compared to the baseline. Under a W4A8 setting, it maintains high fidelity in image generation, showcasing only a marginal increase in FID and setting a new benchmark for efficient, high-quality quantization in diffusion transformers. Code is available at \href{https://github.com/Juanerx/Q-DiT}{https://github.com/Juanerx/Q-DiT}.

Large language models (LLMs) have exhibited exciting progress in multiple scenarios, while the huge computational demands hinder their deployments in lots of real-world applications. As an effective means to reduce memory footprint and inference cost, quantization also faces challenges in performance degradation at low bit-widths. Understanding the impact of quantization on LLM capabilities, especially the generalization ability, is crucial. However, the community's main focus remains on the algorithms and models of quantization, with insufficient attention given to whether the quantized models can retain the strong generalization abilities of LLMs. In this work, we fill this gap by providing a comprehensive benchmark suite for this research topic, including an evaluation system, detailed analyses, and a general toolbox. Specifically, based on the dominant pipeline in LLM quantization, we primarily explore the impact of calibration data distribution on the generalization of quantized LLMs and conduct the benchmark using more than 40 datasets within two main scenarios. Based on this benchmark, we conduct extensive experiments with two well-known LLMs (English and Chinese) and four quantization algorithms to investigate this topic in-depth, yielding several counter-intuitive and valuable findings, e.g., models quantized using a calibration set with the same distribution as the test data are not necessarily optimal. Besides, to facilitate future research, we also release a modular-designed toolbox, which decouples the overall pipeline into several separate components, e.g., base LLM module, dataset module, quantizer module, etc. and allows subsequent researchers to easily assemble their methods through a simple configuration.

Diffusion models have emerged as preeminent contenders in the realm of generative models. Distinguished by their distinctive sequential generative processes, characterized by hundreds or even thousands of timesteps, diffusion models progressively reconstruct images from pure Gaussian noise, with each timestep necessitating full inference of the entire model. However, the substantial computational demands inherent to these models present challenges for deployment, quantization is thus widely used to lower the bit-width for reducing the storage and computing overheads. Current quantization methodologies primarily focus on model-side optimization, disregarding the temporal dimension, such as the length of the timestep sequence, thereby allowing redundant timesteps to continue consuming computational resources, leaving substantial scope for accelerating the generative process. In this paper, we introduce TMPQ-DM, which jointly optimizes timestep reduction and quantization to achieve a superior performance-efficiency trade-off, addressing both temporal and model optimization aspects. For timestep reduction, we devise a non-uniform grouping scheme tailored to the non-uniform nature of the denoising process, thereby mitigating the explosive combinations of timesteps. In terms of quantization, we adopt a fine-grained layer-wise approach to allocate varying bit-widths to different layers based on their respective contributions to the final generative performance, thus rectifying performance degradation observed in prior studies. To expedite the evaluation of fine-grained quantization, we further devise a super-network to serve as a precision solver by leveraging shared quantization results. These two design components are seamlessly integrated within our framework, enabling rapid joint exploration of the exponentially large decision space via a gradient-free evolutionary search algorithm.

Geometry plays a significant role in monocular 3D object detection. It can be used to estimate object depth by using the perspective projection between object's physical size and 2D projection in the image plane, which can introduce mathematical priors into deep models. However, this projection process also introduces error amplification, where the error of the estimated height is amplified and reflected into the projected depth. It leads to unreliable depth inferences and also impairs training stability. To tackle this problem, we propose a novel Geometry Uncertainty Propagation Network (GUPNet++) by modeling geometry projection in a probabilistic manner. This ensures depth predictions are well-bounded and associated with a reasonable uncertainty. The significance of introducing such geometric uncertainty is two-fold: (1). It models the uncertainty propagation relationship of the geometry projection during training, improving the stability and efficiency of the end-to-end model learning. (2). It can be derived to a highly reliable confidence to indicate the quality of the 3D detection result, enabling more reliable detection inference. Experiments show that the proposed approach not only obtains (state-of-the-art) SOTA performance in image-based monocular 3D detection but also demonstrates superiority in efficacy with a simplified framework.

With the success of large-scale pretraining in NLP, there is an increasing trend of applying it to the domain of life sciences. In particular, pretraining methods based on DNA sequences have garnered growing attention due to their potential to capture generic information about genes. However, existing pretraining methods for DNA sequences largely rely on direct adoptions of BERT pretraining from NLP, lacking a comprehensive understanding and a specifically tailored approach. To address this research gap, we first conducted a series of exploratory experiments and gained several insightful observations: 1) In the fine-tuning phase of downstream tasks, when using K-mer overlapping tokenization instead of K-mer non-overlapping tokenization, both overlapping and non-overlapping pretraining weights show consistent performance improvement.2) During the pre-training process, using K-mer overlapping tokenization quickly produces clear K-mer embeddings and reduces the loss to a very low level, while using K-mer non-overlapping tokenization results in less distinct embeddings and continuously decreases the loss. 3) Using overlapping tokenization causes the self-attention in the intermediate layers of pre-trained models to tend to overly focus on certain tokens, reflecting that these layers are not adequately optimized. In summary, overlapping tokenization can benefit the fine-tuning of downstream tasks but leads to inadequate pretraining with fast convergence. To unleash the pretraining potential, we introduce a novel approach called RandomMask, which gradually increases the task difficulty of BERT-like pretraining by continuously expanding its mask boundary, forcing the model to learn more knowledge. RandomMask is simple but effective, achieving top-tier performance across 26 datasets of 28 datasets spanning 7 downstream tasks.