Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA

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.

COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models

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.

EMS: Adaptive Evict-then-Merge Strategy for Head-wise KV Cache Compression Based on Global-Local Importance

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. For the compression strategy, we design an adaptive and unified Evict-then-Merge framework that accounts for the sparsity and redundancy of KV tokens across different heads. 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.

PRANCE: Joint Token-Optimization and Structural Channel-Pruning for Adaptive ViT Inference

We introduce PRANCE, a Vision Transformer compression framework that jointly optimizes the activated channels and reduces tokens, based on the characteristics of inputs. Specifically, PRANCE~ leverages adaptive token optimization strategies for a certain computational budget, aiming to accelerate ViTs' inference from a unified data and architectural perspective. However, the joint framework poses challenges to both architectural and decision-making aspects. Firstly, while ViTs inherently support variable-token inference, they do not facilitate dynamic computations for variable channels. To overcome this limitation, we propose a meta-network using weight-sharing techniques to support arbitrary channels of the Multi-head Self-Attention and Multi-layer Perceptron layers, serving as a foundational model for architectural decision-making. Second, simultaneously optimizing the structure of the meta-network and input data constitutes a combinatorial optimization problem with an extremely large decision space, reaching up to around $10^{14}$, making supervised learning infeasible. To this end, we design a lightweight selector employing Proximal Policy Optimization for efficient decision-making. Furthermore, we introduce a novel "Result-to-Go" training mechanism that models ViTs' inference process as a Markov decision process, significantly reducing action space and mitigating delayed-reward issues during training. Extensive experiments demonstrate the effectiveness of PRANCE~ in reducing FLOPs by approximately 50\%, retaining only about 10\% of tokens while achieving lossless Top-1 accuracy. Additionally, our framework is shown to be compatible with various token optimization techniques such as pruning, merging, and sequential pruning-merging strategies. The code is available at \href{https://github.com/ChildTang/PRANCE}{https://github.com/ChildTang/PRANCE}.

Q-DiT: Accurate Post-Training Quantization for Diffusion Transformers

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}.

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (\textbf{BE}nchm\textbf{A}rk for \textbf{CO}mprehensive R\textbf{N}A Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

TMPQ-DM: Joint Timestep Reduction and Quantization Precision Selection for Efficient Diffusion Models

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.

Retraining-free Model Quantization via One-Shot Weight-Coupling Learning

Quantization is of significance for compressing the over-parameterized deep neural models and deploying them on resource-limited devices. Fixed-precision quantization suffers from performance drop due to the limited numerical representation ability. Conversely, mixed-precision quantization (MPQ) is advocated to compress the model effectively by allocating heterogeneous bit-width for layers. MPQ is typically organized into a searching-retraining two-stage process. Previous works only focus on determining the optimal bit-width configuration in the first stage efficiently, while ignoring the considerable time costs in the second stage. However, retraining always consumes hundreds of GPU-hours on the cutting-edge GPUs, thus hindering deployment efficiency significantly. In this paper, we devise a one-shot training-searching paradigm for mixed-precision model compression. Specifically, in the first stage, all potential bit-width configurations are coupled and thus optimized simultaneously within a set of shared weights. However, our observations reveal a previously unseen and severe bit-width interference phenomenon among highly coupled weights during optimization, leading to considerable performance degradation under a high compression ratio. To tackle this problem, we first design a bit-width scheduler to dynamically freeze the most turbulent bit-width of layers during training, to ensure the rest bit-widths converged properly. Then, taking inspiration from information theory, we present an information distortion mitigation technique to align the behaviour of the bad-performing bit-widths to the well-performing ones.

GUPNet++: Geometry Uncertainty Propagation Network for Monocular 3D Object Detection

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.

Rethinking the BERT-like Pretraining for DNA Sequences

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.