Chuan Cao

Yanbo Wang, Wentao Zhao, Chuan Cao et al.

Although LiDAR semantic segmentation advances rapidly, state-of-the-art methods often incorporate specifically designed inductive bias derived from benchmarks originating from mechanical spinning LiDAR. This can limit model generalizability to other kinds of LiDAR technologies and make hyperparameter tuning more complex. To tackle these issues, we propose a generalized framework to accommodate various types of LiDAR prevalent in the market by replacing window-attention with our sparse focal point modulation. Our SFPNet is capable of extracting multi-level contexts and dynamically aggregating them using a gate mechanism. By implementing a channel-wise information query, features that incorporate both local and global contexts are encoded. We also introduce a novel large-scale hybrid-solid LiDAR semantic segmentation dataset for robotic applications. SFPNet demonstrates competitive performance on conventional benchmarks derived from mechanical spinning LiDAR, while achieving state-of-the-art results on benchmark derived from solid-state LiDAR. Additionally, it outperforms existing methods on our novel dataset sourced from hybrid-solid LiDAR. Code and dataset are available at https://github.com/Cavendish518/SFPNet and https://www.semanticindustry.top.

Zhao Yang, Hengchang Liu, Chuan Cao et al.

Early DNA foundation models adopted BERT-style training, achieving good performance on DNA understanding tasks but lacking generative capabilities. Recent autoregressive models enable DNA generation, but employ left-to-right causal modeling that is suboptimal for DNA where regulatory relationships are inherently bidirectional. We present D3LM (\textbf{D}iscrete \textbf{D}NA \textbf{D}iffusion \textbf{L}anguage \textbf{M}odel), which unifies bidirectional representation learning and DNA generation through masked diffusion. D3LM directly adopts the Nucleotide Transformer (NT) v2 architecture but reformulates the training objective as masked diffusion in discrete DNA space, enabling both bidirectional understanding and generation capabilities within a single model. Compared to NT v2 of the same size, D3LM achieves improved performance on understanding tasks. Notably, on regulatory element generation, D3LM achieves an SFID of 10.92, closely approaching real DNA sequences (7.85) and substantially outperforming the previous best result of 29.16 from autoregressive models. Our work suggests diffusion language models as a promising paradigm for unified DNA foundation models. We further present the first systematic study of masked diffusion models in the DNA domain, investigating practical design choices such as tokenization schemes and sampling strategies, thereby providing empirical insights and a solid foundation for future research. D3LM has been released at https://huggingface.co/collections/Hengchang-Liu/d3lm.

Lei Zhao, Xingyi Li, Tianchen Deng et al.

Maintaining stable and accurate localization during fast motion or on rough terrain remains highly challenging for mobile robots with onboard resources. Currently, multi-sensor fusion methods based on continuous-time representation offer a potential and effective solution to this challenge. Among these, spline-based methods provide an efficient and intuitive approach for continuous-time representation. Previous continuous-time odometry works based on B-splines either treat control points as variables to be estimated or perform estimation in quaternion space, which introduces complexity in deriving analytical Jacobians and often overlooks the fitting error between the spline and the true trajectory over time. To address these issues, we first propose representing the increments of control points on matrix Lie groups as variables to be estimated. Leveraging the feature of the cumulative form of B-splines, we derive a more compact formulation that yields simpler analytical Jacobians without requiring additional boundary condition considerations. Second, we utilize forward propagation information from IMU measurements to estimate fitting errors online and further introduce a hybrid feature-based voxel map management strategy, enhancing system accuracy and robustness. Finally, we propose a re-estimation policy that significantly improves system computational efficiency and robustness. The proposed method is evaluated on multiple challenging public datasets, demonstrating superior performance on most sequences. Detailed ablation studies are conducted to analyze the impact of each module on the overall pose estimation system.

Zhao Yang, Yi Duan, Jiwei Zhu et al.

Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target genes from hundreds of kilobases away. Our work first reveals that for current models, long sequence modeling can decrease performance. Even carefully designed algorithms only mitigate the performance degradation caused by long sequences. Instead, we find that proximal multimodal epigenomic signals near target genes prove more essential. Hence we focus on how to better integrate these signals, which has been overlooked. We find that different signal types serve distinct biological roles, with some directly marking active regulatory elements while others reflect background chromatin patterns that may introduce confounding effects. Simple concatenation may lead models to develop spurious associations with these background patterns. To address this challenge, we propose Prism, a framework that learns multiple combinations of high-dimensional epigenomic features to represent distinct background chromatin states and uses backdoor adjustment to mitigate confounding effects. Our experimental results demonstrate that proper modeling of multimodal epigenomic signals achieves state-of-the-art performance using only short sequences for gene expression prediction.

Yanbo Wang, Yongtao Chen, Chuan Cao et al.

We propose a flexible Semi-Automatic Labeling Tool (SALT) for general LiDAR point clouds with cross-scene adaptability and 4D consistency. Unlike recent approaches that rely on camera distillation, SALT operates directly on raw LiDAR data, automatically generating pre-segmentation results. To achieve this, we propose a novel zero-shot learning paradigm, termed data alignment, which transforms LiDAR data into pseudo-images by aligning with the training distribution of vision foundation models. Additionally, we design a 4D-consistent prompting strategy and 4D non-maximum suppression module to enhance SAM2, ensuring high-quality, temporally consistent presegmentation. SALT surpasses the latest zero-shot methods by 18.4% PQ on SemanticKITTI and achieves nearly 40-50% of human annotator performance on our newly collected low-resolution LiDAR data and on combined data from three LiDAR types, significantly boosting annotation efficiency. We anticipate that SALT's open-sourcing will catalyze substantial expansion of current LiDAR datasets and lay the groundwork for the future development of LiDAR foundation models. Code is available at https://github.com/Cavendish518/SALT.

Zhao Yang, Bing Su, Chuan Cao et al.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Xingrui Qin, Wentao Zhao, Chuan Cao et al.

Dense depth estimation using millimeter-wave radar typically requires dense LiDAR supervision, generated via multi-frame projection and interpolation, for guiding the learning of accurate depth from sparse radar measurements and RGB images. However, this paradigm is both costly and data-intensive. To address this, we propose RaCalNet, a novel framework that eliminates the need for dense supervision by using sparse LiDAR to supervise the learning of refined radar measurements, resulting in a supervision density of merely around 1\% compared to dense-supervised methods. RaCalNet is composed of two key modules. The Radar Recalibration module performs radar point screening and pixel-wise displacement refinement, producing accurate and reliable depth priors from sparse radar inputs. These priors are then used by the Metric Depth Optimization module, which learns to infer scene-level scale priors and fuses them with monocular depth predictions to achieve metrically accurate outputs. This modular design enhances structural consistency and preserves fine-grained geometric details. Despite relying solely on sparse supervision, RaCalNet produces depth maps with clear object contours and fine-grained textures, demonstrating superior visual quality compared to state-of-the-art dense-supervised methods. Quantitatively, it achieves performance comparable to existing methods on the ZJU-4DRadarCam dataset and yields a 34.89\% RMSE reduction in real-world deployment scenarios. We plan to gradually release the code and models in the future at https://github.com/818slam/RaCalNet.git.

Yingce Xia, Peiran Jin, Shufang Xie et al. · microsoft-research

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, RNA and even cells. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) top performance across different domains, matching or surpassing state-of-the-art specialist models. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Mingqian Ma, Guoqing Liu, Chuan Cao et al. · microsoft-research

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".