Xinzhu Ma

Zengyu Qiu, Xinzhu Ma, Kunlin Yang et al.

Knowledge distillation (KD) has shown very promising capabilities in transferring learning representations from large models (teachers) to small models (students). However, as the capacity gap between students and teachers becomes larger, existing KD methods fail to achieve better results. Our work shows that the `prior knowledge' is vital to KD, especially when applying large teachers. Particularly, we propose the dynamic prior knowledge (DPK), which integrates part of teacher's features as the prior knowledge before the feature distillation. This means that our method also takes the teacher's feature as `input', not just `target'. Besides, we dynamically adjust the ratio of the prior knowledge during the training phase according to the feature gap, thus guiding the student in an appropriate difficulty. To evaluate the proposed method, we conduct extensive experiments on two image classification benchmarks (i.e. CIFAR100 and ImageNet) and an object detection benchmark (i.e. MS COCO. The results demonstrate the superiority of our method in performance under varying settings. Besides, our DPK makes the performance of the student model positively correlated with that of the teacher model, which means that we can further boost the accuracy of students by applying larger teachers. More importantly, DPK provides a fast solution in teacher model selection for any given model.

Xinzhu Ma, Yongtao Wang, Yinmin Zhang et al.

In this work, we build a modular-designed codebase, formulate strong training recipes, design an error diagnosis toolbox, and discuss current methods for image-based 3D object detection. In particular, different from other highly mature tasks, e.g., 2D object detection, the community of image-based 3D object detection is still evolving, where methods often adopt different training recipes and tricks resulting in unfair evaluations and comparisons. What is worse, these tricks may overwhelm their proposed designs in performance, even leading to wrong conclusions. To address this issue, we build a module-designed codebase and formulate unified training standards for the community. Furthermore, we also design an error diagnosis toolbox to measure the detailed characterization of detection models. Using these tools, we analyze current methods in-depth under varying settings and provide discussions for some open questions, e.g., discrepancies in conclusions on KITTI-3D and nuScenes datasets, which have led to different dominant methods for these datasets. We hope that this work will facilitate future research in image-based 3D object detection. Our codes will be released at \url{https://github.com/OpenGVLab/3dodi}

Xinzhu Ma, Yuan Meng, Yinmin Zhang et al.

Image-based 3D detection is an indispensable component of the perception system for autonomous driving. However, it still suffers from the unsatisfying performance, one of the main reasons for which is the limited training data. Unfortunately, annotating the objects in the 3D space is extremely time/resource-consuming, which makes it hard to extend the training set arbitrarily. In this work, we focus on the semi-supervised manner and explore the feasibility of a cheaper alternative, i.e. pseudo-labeling, to leverage the unlabeled data. For this purpose, we conduct extensive experiments to investigate whether the pseudo-labels can provide effective supervision for the baseline models under varying settings. The experimental results not only demonstrate the effectiveness of the pseudo-labeling mechanism for image-based 3D detection (e.g. under monocular setting, we achieve 20.23 AP for moderate level on the KITTI-3D testing set without bells and whistles, improving the baseline model by 6.03 AP), but also show several interesting and noteworthy findings (e.g. the models trained with pseudo-labels perform better than that trained with ground-truth annotations based on the same training data). We hope this work can provide insights for the image-based 3D detection community under a semi-supervised setting. The codes, pseudo-labels, and pre-trained models will be publicly available.

Ye Li, Chen Tang, Yuan Meng et al.

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}.

Yan Lu, Xinzhu Ma, Lei Yang et al.

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.

Chaoqi Liang, Lifeng Qiao, Peng Ye et al.

With the success of large-scale pre-training in language tasks, there is an increasing trend of applying it to the domain of life sciences. In particular, pre-training methods based on DNA sequences have received increasing attention because of their potential to capture general information about genes. However, existing pre-training methods for DNA sequences largely rely on direct adoptions of BERT pre-training from NLP, lacking a comprehensive understanding and a specifically tailored approach. To address this research gap, we provide the first empirical study with three insightful observations. Based on the empirical study, we notice that overlapping tokenizer can benefit the fine-tuning of downstream tasks but leads to inadequate pre-training with fast convergence. To unleash the pre-training potential, we introduce a novel approach called RandomMask, which gradually increases the task difficulty of BERT-like pre-training by continuously expanding its mask boundary, forcing the model to learn more knowledge. RandomMask is simple but effective, achieving state-of-the-art performance across 6 downstream tasks. RandomMask achieves a staggering 68.16\% in Matthew's correlation coefficient for Epigenetic Mark Prediction, a groundbreaking increase of 19.85\% over the baseline and a remarkable 3.69\% improvement over the previous state-of-the-art result.

Chen Tang, Yuan Meng, Jiacheng Jiang et al.

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. 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 behavior of the bad-performing bit-widths to the well-performing ones. In the second stage, an inference-only greedy search scheme is devised to evaluate the goodness of configurations without introducing any additional training costs. Extensive experiments on three representative models and three datasets demonstrate the effectiveness of the proposed method. Code can be available on \href{https://www.github.com/1hunters/retraining-free-quantization}{https://github.com/1hunters/retraining-free-quantization}.

Baoli Sun, Yihan Wang, Xinzhu Ma et al.

Fine-grained action recognition (FGAR) aims to identify subtle and distinctive differences among fine-grained action categories. However, current recognition methods often capture coarse-grained motion patterns but struggle to identify subtle details in local regions evolving over time. In this work, we introduce the Action-Region Tracking (ART) framework, a novel solution leveraging a query-response mechanism to discover and track the dynamics of distinctive local details, enabling effective distinction of similar actions. Specifically, we propose a region-specific semantic activation module that employs discriminative and text-constrained semantics as queries to capture the most action-related region responses in each video frame, facilitating interaction among spatial and temporal dimensions with corresponding video features. The captured region responses are organized into action tracklets, which characterize region-based action dynamics by linking related responses across video frames in a coherent sequence. The text-constrained queries encode nuanced semantic representations derived from textual descriptions of action labels extracted by language branches within Visual Language Models (VLMs). To optimize the action tracklets, we design a multi-level tracklet contrastive constraint among region responses at spatial and temporal levels, enabling effective discrimination within each frame and correlation between adjacent frames. Additionally, a task-specific fine-tuning mechanism refines textual semantics such that semantic representations encoded by VLMs are preserved while optimized for task preferences. Comprehensive experiments on widely used action recognition benchmarks demonstrate the superiority to previous state-of-the-art baselines.

Baoli Sun, Xinzhu Ma, Ning Wang et al.

Referring video object segmentation (RVOS) is an emerging cross-modality task that aims to generate pixel-level maps of the target objects referred by given textual expressions. The main concept involves learning an accurate alignment of visual elements and language expressions within a semantic space. Recent approaches address cross-modality alignment through conditional queries, tracking the target object using a query-response based mechanism built upon transformer structure. However, they exhibit two limitations: (1) these conditional queries lack inter-frame dependency and variation modeling, making accurate target tracking challenging amid significant frame-to-frame variations; and (2) they integrate textual constraints belatedly, which may cause the video features potentially focus on the non-referred objects. Therefore, we propose a novel RVOS architecture called ProxyFormer, which introduces a set of proxy queries to integrate visual and text semantics and facilitate the flow of semantics between them. By progressively updating and propagating proxy queries across multiple stages of video feature encoder, ProxyFormer ensures that the video features are focused on the object of interest. This dynamic evolution also enables the establishment of inter-frame dependencies, enhancing the accuracy and coherence of object tracking. To mitigate high computational costs, we decouple cross-modality interactions into temporal and spatial dimensions. Additionally, we design a Joint Semantic Consistency (JSC) training strategy to align semantic consensus between the proxy queries and the combined video-text pairs. Comprehensive experiments on four widely used RVOS benchmarks demonstrate the superiority of our ProxyFormer to the state-of-the-art methods.

Han Deng, Yuan Meng, Shixiang Tang et al.

Competitive programming benchmarks are widely used in scenarios such as programming contests and large language model assessments. However, the growing presence of duplicate or highly similar problems raises concerns not only about competition fairness, but also about the validity of competitive programming as a benchmark for model evaluation. In this paper, we propose a new problem, similar question retrieval, to tackle this issue. Due to the lack of both data and models, solving this problem is challenging. To this end, we introduce CPRet, a retrieval-oriented benchmark suite for competitive programming, covering four retrieval tasks: two code-centric (i.e., Text-to-Code, Code-to-Code) and two newly proposed problem-centric tasks (i.e., Problem-to-Duplicate, Simplified-to-Full) built from a combination of automatically crawled problem-solution data and manually curated annotations. Our contribution includes both high-quality training data and temporally separated test sets for reliable evaluation. Besides, we further develop two task-specialized retrievers based on this dataset: CPRetriever-Code, trained with a novel Group-InfoNCE loss for problem-code alignment, and CPRetriever-Prob, fine-tuned for identifying problem-level similarity. Both models achieve strong results and are open-sourced for local use. Finally, we analyze LiveCodeBench and find that high-similarity problems inflate model pass rates and reduce differentiation, underscoring the need for similarity-aware evaluation in future benchmarks. Github: https://github.com/coldchair/CPRet Online Demo: https://www.cpret.online/

Lei Chen, Yuan Meng, Chen Tang et al.

Recent advancements in diffusion models, particularly the architectural transformation from UNet-based models to Diffusion Transformers (DiTs), significantly improve the quality and scalability of image and video generation. However, despite their impressive capabilities, the substantial computational costs of these large-scale models pose significant challenges for real-world deployment. Post-Training Quantization (PTQ) emerges as a promising solution, enabling model compression and accelerated inference for pretrained models, without the costly retraining. However, research on DiT quantization remains sparse, and existing PTQ frameworks, primarily designed for traditional diffusion models, tend to suffer from biased quantization, leading to notable performance degradation. In this work, we identify that DiTs typically exhibit significant spatial variance in both weights and activations, along with temporal variance in activations. To address these issues, we propose Q-DiT, a novel approach that seamlessly integrates two key techniques: automatic quantization granularity allocation to handle the significant variance of weights and activations across input channels, and sample-wise dynamic activation quantization to adaptively capture activation changes across both timesteps and samples. Extensive experiments conducted on ImageNet and VBench demonstrate the effectiveness of the proposed Q-DiT. Specifically, when quantizing DiT-XL/2 to W6A8 on ImageNet ($256 \times 256$), Q-DiT achieves a remarkable reduction in FID by 1.09 compared to the baseline. Under the more challenging W4A8 setting, it maintains high fidelity in image and video generation, establishing a new benchmark for efficient, high-quality quantization in DiTs. Code is available at \href{https://github.com/Juanerx/Q-DiT}{https://github.com/Juanerx/Q-DiT}.

Yijun Liu, Yuan Meng, Fang Wu et al.

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. Our benchmark suite is publicly available at https://github.com/TsingmaoAI/MI-optimize

Yuchen Ren, Zhiyuan Chen, Lifeng Qiao et al.

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.

Chen Tang, Xinzhu Ma, Encheng Su et al.

Traditional spatiotemporal models generally rely on task-specific architectures, which limit their generalizability and scalability across diverse tasks due to domain-specific design requirements. In this paper, we introduce \textbf{UniSTD}, a unified Transformer-based framework for spatiotemporal modeling, which is inspired by advances in recent foundation models with the two-stage pretraining-then-adaption paradigm. Specifically, our work demonstrates that task-agnostic pretraining on 2D vision and vision-text datasets can build a generalizable model foundation for spatiotemporal learning, followed by specialized joint training on spatiotemporal datasets to enhance task-specific adaptability. To improve the learning capabilities across domains, our framework employs a rank-adaptive mixture-of-expert adaptation by using fractional interpolation to relax the discrete variables so that can be optimized in the continuous space. Additionally, we introduce a temporal module to incorporate temporal dynamics explicitly. We evaluate our approach on a large-scale dataset covering 10 tasks across 4 disciplines, demonstrating that a unified spatiotemporal model can achieve scalable, cross-task learning and support up to 10 tasks simultaneously within one model while reducing training costs in multi-domain applications. Code will be available at https://github.com/1hunters/UniSTD.

Zhiyu Chong, Xinzhu Ma, Hong Zhang et al.

3D object detection is a fundamental and challenging task for 3D scene understanding, and the monocular-based methods can serve as an economical alternative to the stereo-based or LiDAR-based methods. However, accurately detecting objects in the 3D space from a single image is extremely difficult due to the lack of spatial cues. To mitigate this issue, we propose a simple and effective scheme to introduce the spatial information from LiDAR signals to the monocular 3D detectors, without introducing any extra cost in the inference phase. In particular, we first project the LiDAR signals into the image plane and align them with the RGB images. After that, we use the resulting data to train a 3D detector (LiDAR Net) with the same architecture as the baseline model. Finally, this LiDAR Net can serve as the teacher to transfer the learned knowledge to the baseline model. Experimental results show that the proposed method can significantly boost the performance of the baseline model and ranks the $1^{st}$ place among all monocular-based methods on the KITTI benchmark. Besides, extensive ablation studies are conducted, which further prove the effectiveness of each part of our designs and illustrate what the baseline model has learned from the LiDAR Net. Our code will be released at \url{https://github.com/monster-ghost/MonoDistill}.

Yinmin Zhang, Xinzhu Ma, Shuai Yi et al.

As a crucial task of autonomous driving, 3D object detection has made great progress in recent years. However, monocular 3D object detection remains a challenging problem due to the unsatisfactory performance in depth estimation. Most existing monocular methods typically directly regress the scene depth while ignoring important relationships between the depth and various geometric elements (e.g. bounding box sizes, 3D object dimensions, and object poses). In this paper, we propose to learn geometry-guided depth estimation with projective modeling to advance monocular 3D object detection. Specifically, a principled geometry formula with projective modeling of 2D and 3D depth predictions in the monocular 3D object detection network is devised. We further implement and embed the proposed formula to enable geometry-aware deep representation learning, allowing effective 2D and 3D interactions for boosting the depth estimation. Moreover, we provide a strong baseline through addressing substantial misalignment between 2D annotation and projected boxes to ensure robust learning with the proposed geometric formula. Experiments on the KITTI dataset show that our method remarkably improves the detection performance of the state-of-the-art monocular-based method without extra data by 2.80% on the moderate test setting. The model and code will be released at https://github.com/YinminZhang/MonoGeo.

Xinzhu Ma, Yinmin Zhang, Dan Xu et al.

Estimating 3D bounding boxes from monocular images is an essential component in autonomous driving, while accurate 3D object detection from this kind of data is very challenging. In this work, by intensive diagnosis experiments, we quantify the impact introduced by each sub-task and found the `localization error' is the vital factor in restricting monocular 3D detection. Besides, we also investigate the underlying reasons behind localization errors, analyze the issues they might bring, and propose three strategies. First, we revisit the misalignment between the center of the 2D bounding box and the projected center of the 3D object, which is a vital factor leading to low localization accuracy. Second, we observe that accurately localizing distant objects with existing technologies is almost impossible, while those samples will mislead the learned network. To this end, we propose to remove such samples from the training set for improving the overall performance of the detector. Lastly, we also propose a novel 3D IoU oriented loss for the size estimation of the object, which is not affected by `localization error'. We conduct extensive experiments on the KITTI dataset, where the proposed method achieves real-time detection and outperforms previous methods by a large margin. The code will be made available at: https://github.com/xinzhuma/monodle.

Xinzhu Ma, Shinan Liu, Zhiyi Xia et al.

The recently proposed pseudo-LiDAR based 3D detectors greatly improve the benchmark of monocular/stereo 3D detection task. However, the underlying mechanism remains obscure to the research community. In this paper, we perform an in-depth investigation and observe that the efficacy of pseudo-LiDAR representation comes from the coordinate transformation, instead of data representation itself. Based on this observation, we design an image based CNN detector named Patch-Net, which is more generalized and can be instantiated as pseudo-LiDAR based 3D detectors. Moreover, the pseudo-LiDAR data in our PatchNet is organized as the image representation, which means existing 2D CNN designs can be easily utilized for extracting deep features from input data and boosting 3D detection performance. We conduct extensive experiments on the challenging KITTI dataset, where the proposed PatchNet outperforms all existing pseudo-LiDAR based counterparts. Code has been made available at: https://github.com/xinzhuma/patchnet.

Haojun Sun, Chen Tang, Zhi Wang et al.

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.

Lintao Wang, Encheng Su, Jiaqi Liu et al.

Physics problem-solving is a challenging domain for large AI models, requiring integration of conceptual understanding, mathematical reasoning, and interpretation of physical diagrams. Current evaluation methodologies show notable limitations in capturing the breadth and complexity of undergraduate-level physics, underscoring the need for more rigorous assessments. To this end, we present PhysUniBench, a large-scale multimodal benchmark designed to evaluate and improve the reasoning capabilities of multimodal large language models (MLLMs) specifically on undergraduate-level physics problems. PhysUniBench consists of 3,304 physics questions spanning 8 major sub-disciplines of physics, each accompanied by one visual diagrams. The benchmark includes both open-ended and multiple-choice questions, systematically curated and difficulty-rated through an iterative model-in-the-loop process. The benchmark's construction involved a rigorous multi-stage process, including multiple roll-outs, expert-level evaluation, automated filtering of easily solved problems, and a nuanced difficulty grading system with five levels. Through extensive experiments, we observe that current state-of-the-art models encounter substantial challenges in physics reasoning. For example, GPT-4o mini achieves only about 34.2% accuracy in the proposed PhysUniBench. These results highlight that current MLLMs struggle with advanced physics reasoning, especially on multi-step problems and those requiring precise diagram interpretation. By providing a broad and rigorous assessment tool, PhysUniBench aims to drive progress in AI for Science, encouraging the development of models with stronger physical reasoning, problem-solving skills, and multimodal understanding. The benchmark and evaluation scripts are available at https://prismax-team.github.io/PhysUniBenchmark/.

Lifeng Qiao, Peng Ye, Yuchen Ren et al.

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.

Yu Bo, Weian Mao, Yanjun Shao et al.

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.

Yingxin Li, Ye Li, Yuan Meng et al.

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.

Xinzhu Ma, Cheng Wang, Chen Tang et al.

Recovering CAD models from point clouds requires reconstructing their topology and sketch-based extrusion primitives. A dominant paradigm for representing sketches involves implicit neural representations such as Signed Distance Fields (SDFs). However, this indirect approach inherently struggles with precision, leading to unintended curved edges and models that are difficult to edit. In this paper, we propose Point2Primitive, a framework that learns to directly predict the explicit, parametric primitives of CAD models. Our method treats sketch reconstruction as a set prediction problem, employing a improved transformer-based decoder with explicit position queries to directly detect and predict the fundamental sketch curves (i.e., type and parameter) from the point cloud. Instead of approximating a continuous field, we formulate curve parameters as explicit position queries, which are optimized autoregressively to achieve high accuracy. The overall topology is rebuilt via extrusion segmentation. Extensive experiments demonstrate that this direct prediction paradigm significantly outperforms implicit methods in both primitive accuracy and overall geometric fidelity.

Jianyu Wu, Yizhou Wang, Xiangyu Yue et al.

While accurate and user-friendly Computer-Aided Design (CAD) is crucial for industrial design and manufacturing, existing methods still struggle to achieve this due to their over-simplified representations or architectures incapable of supporting multimodal design requirements. In this paper, we attempt to tackle this problem from both methods and datasets aspects. First, we propose a cascade MAR with topology predictor (CMT), the first multimodal framework for CAD generation based on Boundary Representation (B-Rep). Specifically, the cascade MAR can effectively capture the ``edge-counters-surface'' priors that are essential in B-Reps, while the topology predictor directly estimates topology in B-Reps from the compact tokens in MAR. Second, to facilitate large-scale training, we develop a large-scale multimodal CAD dataset, mmABC, which includes over 1.3 million B-Rep models with multimodal annotations, including point clouds, text descriptions, and multi-view images. Extensive experiments show the superior of CMT in both conditional and unconditional CAD generation tasks. For example, we improve Coverage and Valid ratio by +10.68% and +10.3%, respectively, compared to state-of-the-art methods on ABC in unconditional generation. CMT also improves +4.01 Chamfer on image conditioned CAD generation on mmABC.

Yuchen Ren, Wenwei Han, Qianyuan Zhang et al.

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.

Zixuan Hu, Dongxiao Li, Xinzhu Ma et al.

Accurate monocular 3D object detection (M3OD) is pivotal for safety-critical applications like autonomous driving, yet its reliability deteriorates significantly under real-world domain shifts caused by environmental or sensor variations. To address these shifts, Test-Time Adaptation (TTA) methods have emerged, enabling models to adapt to target distributions during inference. While prior TTA approaches recognize the positive correlation between low uncertainty and high generalization ability, they fail to address the dual uncertainty inherent to M3OD: semantic uncertainty (ambiguous class predictions) and geometric uncertainty (unstable spatial localization). To bridge this gap, we propose Dual Uncertainty Optimization (DUO), the first TTA framework designed to jointly minimize both uncertainties for robust M3OD. Through a convex optimization lens, we introduce an innovative convex structure of the focal loss and further derive a novel unsupervised version, enabling label-agnostic uncertainty weighting and balanced learning for high-uncertainty objects. In parallel, we design a semantic-aware normal field constraint that preserves geometric coherence in regions with clear semantic cues, reducing uncertainty from the unstable 3D representation. This dual-branch mechanism forms a complementary loop: enhanced spatial perception improves semantic classification, and robust semantic predictions further refine spatial understanding. Extensive experiments demonstrate the superiority of DUO over existing methods across various datasets and domain shift types.

Zhongyue Zhang, Jiahua Rao, Jie Zhong et al.

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

Xinzhu Ma, Wanli Ouyang, Andrea Simonelli et al.

3D object detection from images, one of the fundamental and challenging problems in autonomous driving, has received increasing attention from both industry and academia in recent years. Benefiting from the rapid development of deep learning technologies, image-based 3D detection has achieved remarkable progress. Particularly, more than 200 works have studied this problem from 2015 to 2021, encompassing a broad spectrum of theories, algorithms, and applications. However, to date no recent survey exists to collect and organize this knowledge. In this paper, we fill this gap in the literature and provide the first comprehensive survey of this novel and continuously growing research field, summarizing the most commonly used pipelines for image-based 3D detection and deeply analyzing each of their components. Additionally, we also propose two new taxonomies to organize the state-of-the-art methods into different categories, with the intent of providing a more systematic review of existing methods and facilitating fair comparisons with future works. In retrospect of what has been achieved so far, we also analyze the current challenges in the field and discuss future directions for image-based 3D detection research.

Yan Lu, Xinzhu Ma, Lei Yang et al.

Geometry Projection is a powerful depth estimation method in monocular 3D object detection. It estimates depth dependent on heights, which introduces mathematical priors into the deep model. But projection process also introduces the error amplification problem, in which the error of the estimated height will be amplified and reflected greatly at the output depth. This property leads to uncontrollable depth inferences and also damages the training efficiency. In this paper, we propose a Geometry Uncertainty Projection Network (GUP Net) to tackle the error amplification problem at both inference and training stages. Specifically, a GUP module is proposed to obtains the geometry-guided uncertainty of the inferred depth, which not only provides high reliable confidence for each depth but also benefits depth learning. Furthermore, at the training stage, we propose a Hierarchical Task Learning strategy to reduce the instability caused by error amplification. This learning algorithm monitors the learning situation of each task by a proposed indicator and adaptively assigns the proper loss weights for different tasks according to their pre-tasks situation. Based on that, each task starts learning only when its pre-tasks are learned well, which can significantly improve the stability and efficiency of the training process. Extensive experiments demonstrate the effectiveness of the proposed method. The overall model can infer more reliable object depth than existing methods and outperforms the state-of-the-art image-based monocular 3D detectors by 3.74% and 4.7% AP40 of the car and pedestrian categories on the KITTI benchmark.

Xinzhu Ma, Zhihui Wang, Haojie Li et al.

In this paper, we propose a monocular 3D object detection framework in the domain of autonomous driving. Unlike previous image-based methods which focus on RGB feature extracted from 2D images, our method solves this problem in the reconstructed 3D space in order to exploit 3D contexts explicitly. To this end, we first leverage a stand-alone module to transform the input data from 2D image plane to 3D point clouds space for a better input representation, then we perform the 3D detection using PointNet backbone net to obtain objects 3D locations, dimensions and orientations. To enhance the discriminative capability of point clouds, we propose a multi-modal feature fusion module to embed the complementary RGB cue into the generated point clouds representation. We argue that it is more effective to infer the 3D bounding boxes from the generated 3D scene space (i.e., X,Y, Z space) compared to the image plane (i.e., R,G,B image plane). Evaluation on the challenging KITTI dataset shows that our approach boosts the performance of state-of-the-art monocular approach by a large margin.