Yixuan Wang

Tao Shen, Zhihang Hu, Siqi Sun et al.

Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to scarcity of experimentally determined data, complicates computational prediction efforts. Here, we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences. By integrating an RNA language model pre-trained on ~23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end pipeline for RNA 3D structure prediction. Retrospective evaluations on RNA-Puzzles and CASP15 natural RNA targets demonstrate RhoFold+'s superiority over existing methods, including human expert groups. Its efficacy and generalizability are further validated through cross-family and cross-type assessments, as well as time-censored benchmarks. Additionally, RhoFold+ predicts RNA secondary structures and inter-helical angles, providing empirically verifiable features that broaden its applicability to RNA structure and function studies.

Bo Ai, Stephen Tian, Haochen Shi et al.

Tactile feedback is critical for understanding the dynamics of both rigid and deformable objects in many manipulation tasks, such as non-prehensile manipulation and dense packing. We introduce an approach that combines visual and tactile sensing for robotic manipulation by learning a neural, tactile-informed dynamics model. Our proposed framework, RoboPack, employs a recurrent graph neural network to estimate object states, including particles and object-level latent physics information, from historical visuo-tactile observations and to perform future state predictions. Our tactile-informed dynamics model, learned from real-world data, can solve downstream robotics tasks with model-predictive control. We demonstrate our approach on a real robot equipped with a compliant Soft-Bubble tactile sensor on non-prehensile manipulation and dense packing tasks, where the robot must infer the physics properties of objects from direct and indirect interactions. Trained on only an average of 30 minutes of real-world interaction data per task, our model can perform online adaptation and make touch-informed predictions. Through extensive evaluations in both long-horizon dynamics prediction and real-world manipulation, our method demonstrates superior effectiveness compared to previous learning-based and physics-based simulation systems.

Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang et al.

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic binning, clustering the assembled contigs into draft genomes. Despite the existing computational tools, most of them neglect one important property of the metagenomic data, that is, the noise. To further improve the metagenomic binning step and reconstruct better metagenomes, we propose a deep Contrastive Learning framework for Metagenome Binning (CLMB), which can efficiently eliminate the disturbance of noise and produce more stable and robust results. Essentially, instead of denoising the data explicitly, we add simulated noise to the training data and force the deep learning model to produce similar and stable representations for both the noise-free data and the distorted data. Consequently, the trained model will be robust to noise and handle it implicitly during usage. CLMB outperforms the previous state-of-the-art binning methods significantly, recovering the most near-complete genomes on almost all the benchmarking datasets (up to 17\% more reconstructed genomes compared to the second-best method). It also improves the performance of bin refinement, reconstructing 8-22 more high-quality genomes and 15-32 more middle-quality genomes than the second-best result. Impressively, in addition to being compatible with the binning refiner, single CLMB even recovers on average 15 more HQ genomes than the refiner of VAMB and Maxbin on the benchmarking datasets. CLMB is open-source and available at https://github.com/zpf0117b/CLMB/.

Yixuan Wang, Guang Yin, Binghao Huang et al.

Diffusion-based policies have shown remarkable capability in executing complex robotic manipulation tasks but lack explicit characterization of geometry and semantics, which often limits their ability to generalize to unseen objects and layouts. To enhance the generalization capabilities of Diffusion Policy, we introduce a novel framework that incorporates explicit spatial and semantic information via 3D semantic fields. We generate 3D descriptor fields from multi-view RGBD observations with large foundational vision models, then compare these descriptor fields against reference descriptors to obtain semantic fields. The proposed method explicitly considers geometry and semantics, enabling strong generalization capabilities in tasks requiring category-level generalization, resolving geometric ambiguities, and attention to subtle geometric details. We evaluate our method across eight tasks involving articulated objects and instances with varying shapes and textures from multiple object categories. Our method demonstrates its effectiveness by increasing Diffusion Policy's average success rate on unseen instances from 20% to 93%. Additionally, we provide a detailed analysis and visualization to interpret the sources of performance gain and explain how our method can generalize to novel instances.

Yuzhuang Xu, Xu Han, Yuanchi Zhang et al. · tsinghua

Large Language Models (LLMs) with Mixture-of-Experts (MoE) architectures are distinguished by their strong performance scaling with increasing parameters across a wide range of tasks, yet they also suffer from substantial computational and storage overheads. Notably, the performance gains of MoE models do not scale proportionally with the growth in expert parameters. While prior works attempt to reduce parameters via expert-level pruning, merging, or decomposition, they still suffer from challenges in both performance and computational efficiency. In this paper, we address these challenges by introducing micro-expert as a finer-grained compression unit that spans across matrices. We first establish a more fundamental perspective, viewing MoE layers as mixtures of micro-experts, and present CAMERA, a lightweight and training-free framework for identifying micro-expert redundancy. Our analysis uncovers significant variance in micro-expert contributions during decoding. Based on this insight, we further propose CAMERA-P, a structured micro-expert pruning framework, and CAMERA-Q, a mixed-precision quantization idea designed for micro-experts. Extensive experiments on nine downstream tasks show that CAMERA-P consistently outperforms strong baselines under pruning ratios ranging from 20% to 60%. Furthermore, CAMERA-Q achieves superior results under aggressive 2-bit quantization, surpassing existing matrix- and channel-level ideas. Notably, our method enables complete micro-expert analysis of Qwen2-57B-A14B in less than 5 minutes on a single NVIDIA A100-40GB GPU.

Zhiming Zhang, Qingfu Zhu, Xianzhen Luo et al.

Code translation aims to translate the code from its source language to the target language and is used in various software development scenarios. Recent developments in Large Language Models (LLMs) have showcased their capabilities in code translation, and parallel corpora play a crucial role in training models for code translation. Parallel corpora can be categorized into program-alignment (PA) and snippet-alignment (SA) data. Although PA data has complete context and is suitable for semantic alignment learning, it may not provide adequate fine-grained training signals due to its extended length, while the brevity of SA data enables more fine-grained alignment learning. Due to limited parallel corpora, researchers explore several augmentation methods for code translation. Previous studies mainly focus on augmenting PA data. In this paper, we propose a data augmentation method that leverages LLMs to generate SA data automatically. To fully leverage both PA data and SA data, we explore a simple yet effective two-stage training strategy, which consistently enhances model performance compared to fine-tuning solely on PA data. Experiments on TransCoder-test demonstrate that our augmented SA data combined with the two-stage training approach yields consistent improvements over the baseline, achieving a maximum gain of 3.78% on pass@k.

Baoxin Wang, Yumeng Luo, Yixuan Wang et al.

The primary objective of Chinese grammatical error correction (CGEC) is to detect and correct errors in Chinese sentences. Recent research shows that large language models (LLMs) have been applied to CGEC with significant results. For LLMs, selecting appropriate reference examples can help improve their performance. However, existing methods predominantly rely on text similarity for example retrieval, a strategy that frequently mismatches actual error patterns and retrieves lexically similar yet grammatically irrelevant sentences. To address this problem, we propose a method named RE$^2$, which retrieves appropriate examples with explanations of grammatical errors. Instead of using text similarity of the input sentence, we use explanations of grammatical errors to select reference examples, which are used by LLMs to improve the performance of CGEC. We conduct experiments on two CGEC datasets and create a high-quality grammatical error explanation (GEE) dataset, which is not only used in our research but also serves as a valuable resource for future studies in both CGEC and GEE. The experimental results on the two datasets indicate that our proposed method effectively improves the performance of CGEC.

Xianzhen Luo, Qingfu Zhu, Zhiming Zhang et al.

Code Sensitivity refers to the ability of Code LLMs to recognize and respond to details changes in problem descriptions. While current code benchmarks and instruction data focus on difficulty and diversity, sensitivity is overlooked. We first introduce the CTF-Code benchmark, constructed using counterfactual perturbations, minimizing input changes while maximizing output changes. The evaluation shows that many LLMs have a more than 10\% performance drop compared to the original problems. To fully utilize sensitivity, CTF-Instruct, an incremental instruction fine-tuning framework, extends on existing data and uses a selection mechanism to meet the three dimensions of difficulty, diversity, and sensitivity. Experiments show that LLMs fine-tuned with CTF-Instruct data achieve over a 2\% improvement on CTF-Code, and more than a 10\% performance boost on LiveCodeBench, validating the feasibility of enhancing LLMs' sensitivity to improve performance.

Haoyan Yang, Yixuan Wang, Keyue Tong et al.

This paper proposes a detailed prompting flow, termed Table-Logic, to investigate the performance contrasts between bigger and smaller language models (LMs) utilizing step-by-step reasoning methods in the TableQA task. The method processes tasks by sequentially identifying critical columns and rows given question and table with its structure, determining necessary aggregations, calculations, or comparisons, and finally inferring the results to generate a precise prediction. By deploying this method, we observe a 7.8% accuracy improvement in bigger LMs like Llama-3-70B compared to the vanilla on HybridQA, while smaller LMs like Llama-2-7B shows an 11% performance decline. We empirically investigate the potential causes of performance contrasts by exploring the capabilities of bigger and smaller LMs from various dimensions in TableQA task. Our findings highlight the limitations of the step-by-step reasoning method in small models and provide potential insights for making improvements.