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Yuxing Peng

Publications and source records attributed to Yuxing Peng.

At least 19 recordsLinked to original sources

Dense Weak Hiding: Closing Complexity Gaps in Nonconvex and PL Finite-Sum Optimization under Individual Smoothness

Under individual smoothness, the optimal incremental first-order oracle (IFO) complexity of nonconvex finite-sum optimization has remained open. Known algorithms use $O(n+\sqrt{n}\,\Delta L_{\max}/\varepsilon^2)$ calls, while prior lower bounds miss a factor of $\sqrt{n}$. We prove the matching lower bound for randomized IFO algorithms whose component indices and query points may depend on the complete preceding transcript and private randomness. This determines the minimax IFO complexity up to universal constants under both individual and mean-squared smoothness. Under the global Polyak-Lojasiewicz (PL) condition, the standard PAGE guarantee is not tight when $\kappa_{\mathrm{ms}}<\sqrt{n}$. Restarted PAGE attains $O(n+n\log(\Delta/\varepsilon)/(1+\log(\sqrt{n}/\kappa_{\mathrm{ms}})))$ for $1\leq\kappa_{\mathrm{ms}}\leq\sqrt{n}$, and $O(n+\kappa_{\mathrm{ms}}\sqrt{n}\log(\Delta/\varepsilon))$ for $\kappa_{\mathrm{ms}}\geq\sqrt{n}$. We prove matching lower bounds under individual smoothness for every $\kappa_{\max}\geq 3$; the same hard instances also give the mean-squared lower bounds. In the small-$\kappa_{\max}$ range, their average objective is globally strongly convex. Our lower bounds use dense weak hiding. A fixed sign table spreads each hidden direction across the components. Each queried row carries little information, while the exact row average preserves the full signal after rescaling. A bounded radial map handles arbitrary query points, and a smooth gate makes unopened links invisible to both function values and gradients. Balancing the rows needed to reveal one stage with the number of stages allowed by individual smoothness yields the missing $\sqrt{n}$ factor.

cs.DS

Fold-CP: A Context Parallelism Framework for Biomolecular Modeling

Understanding cellular machinery requires atomic-scale reconstruction of large biomolecular assemblies. However, predicting the structures of these systems has been constrained by hardware memory requirements of models like AlphaFold 3, imposing a practical ceiling of a few thousand residues that can be processed on a single GPU. Here we present NVIDIA BioNeMo Fold-CP, a context parallelism framework that overcomes this barrier by distributing the inference and training pipelines of co-folding models across multiple GPUs. We use the Boltz models as open source reference architectures and implement custom multidimensional primitives that efficiently parallelize both the dense triangular updates and the irregular, data-dependent pattern of window-batched local attention. Our approach achieves efficient memory scaling; for an N-token input distributed across P GPUs, per-device memory scales as $O(N^2/P)$, enabling the structure prediction of assemblies exceeding 30,000 residues on 64 NVIDIA B300 GPUs. We demonstrate the scientific utility of this approach through successful developer use cases: Fold-CP enabled the scoring of over 90% of Comprehensive Resource of Mammalian protein complexes (CORUM) database, as well as folding of disease-relevant PI4KA lipid kinase complex bound to an intrinsically disordered region without cropping. By providing a scalable pathway for modeling massive systems with full global context, Fold-CP represents a significant step toward the realization of a virtual cell.

q-bio.QM

Coupled Level-Set Lattice Boltzmann Method on Adaptive Cartesian Grids

A novel coupled level-set lattice Boltzmann method on adaptive Cartesian grids for simulating liquid-gas multiphase flows is presented. The approach addresses the inherent challenges of accurately modeling multiphase systems characterized by sharp interfaces and large density ratios. By employing separate solution algorithms for each fluid phase which are coupled through boundary conditions at the interface the method is more accurate and more efficient. The study highlights the advantages of using lattice Boltzmann methods together with level-set techniques to track interfaces effectively while facilitating adaptive mesh refinement. Applications to various test cases, e.g., immiscible stratified flow and rising bubbles, demonstrate the method's capability to capture complex interfacial dynamics and validate its accuracy against literature data.

physics.flu-dyn

Investigation of Air Fluidization during Intruder Penetration in Sand

Self-burrowing robots navigating through granular media benefit from airflow-assisted burrowing, which reduces penetration resistance. However, the mechanisms underlying airflow-granular interactions remain poorly understood. To address this knowledge gap, we employ a coupled computational fluid dynamics and discrete element method (CFD-DEM) approach, supplemented by experimental cone penetration tests (CPT) under varying airflow conditions, to investigate the effects of aeration on penetration resistance. Experimental results reveal a nonlinear relationship between penetration resistance reduction and depth, wherein resistance approaches near-zero values up to a critical depth, beyond which the effectiveness of fluidization diminishes. Simulations demonstrate that higher airflow rates enhance the mobilization of overlying grains, increasing the critical depth. A detailed meso- and micro-scale analysis of particle motion, contact forces, and fluid pressure fields reveals four distinct penetration stages: particle ejection and channel formation, channel sealing, channel refill, and final compaction. These findings contribute to a deeper understanding of granular aeration mechanisms and their implications for geotechnical engineering, excavation technologies, and the development of self-burrowing robotic systems.

cond-mat.soft

GenMol: A Drug Discovery Generalist with Discrete Diffusion

Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present Generalist Molecular generative model (GenMol), a versatile framework that uses only a single discrete diffusion model to handle diverse drug discovery scenarios. GenMol generates Sequential Attachment-based Fragment Embedding (SAFE) sequences through non-autoregressive bidirectional parallel decoding, thereby allowing the utilization of a molecular context that does not rely on the specific token ordering while having better sampling efficiency. GenMol uses fragments as basic building blocks for molecules and introduces fragment remasking, a strategy that optimizes molecules by regenerating masked fragments, enabling effective exploration of chemical space. We further propose molecular context guidance (MCG), a guidance method tailored for masked discrete diffusion of GenMol. GenMol significantly outperforms the previous GPT-based model in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design. Our code is available at https://github.com/NVIDIA-Digital-Bio/genmol.

cs.LG

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

cs.LG

GeoTransformer: Fast and Robust Point Cloud Registration with Geometric Transformer

We study the problem of extracting accurate correspondences for point cloud registration. Recent keypoint-free methods have shown great potential through bypassing the detection of repeatable keypoints which is difficult to do especially in low-overlap scenarios. They seek correspondences over downsampled superpoints, which are then propagated to dense points. Superpoints are matched based on whether their neighboring patches overlap. Such sparse and loose matching requires contextual features capturing the geometric structure of the point clouds. We propose Geometric Transformer, or GeoTransformer for short, to learn geometric feature for robust superpoint matching. It encodes pair-wise distances and triplet-wise angles, making it invariant to rigid transformation and robust in low-overlap cases. The simplistic design attains surprisingly high matching accuracy such that no RANSAC is required in the estimation of alignment transformation, leading to $100$ times acceleration. Extensive experiments on rich benchmarks encompassing indoor, outdoor, synthetic, multiway and non-rigid demonstrate the efficacy of GeoTransformer. Notably, our method improves the inlier ratio by $18{\sim}31$ percentage points and the registration recall by over $7$ points on the challenging 3DLoMatch benchmark. Our code and models are available at \url{https://github.com/qinzheng93/GeoTransformer}.

cs.CV

Deep Graph-based Spatial Consistency for Robust Non-rigid Point Cloud Registration

We study the problem of outlier correspondence pruning for non-rigid point cloud registration. In rigid registration, spatial consistency has been a commonly used criterion to discriminate outliers from inliers. It measures the compatibility of two correspondences by the discrepancy between the respective distances in two point clouds. However, spatial consistency no longer holds in non-rigid cases and outlier rejection for non-rigid registration has not been well studied. In this work, we propose Graph-based Spatial Consistency Network (GraphSCNet) to filter outliers for non-rigid registration. Our method is based on the fact that non-rigid deformations are usually locally rigid, or local shape preserving. We first design a local spatial consistency measure over the deformation graph of the point cloud, which evaluates the spatial compatibility only between the correspondences in the vicinity of a graph node. An attention-based non-rigid correspondence embedding module is then devised to learn a robust representation of non-rigid correspondences from local spatial consistency. Despite its simplicity, GraphSCNet effectively improves the quality of the putative correspondences and attains state-of-the-art performance on three challenging benchmarks. Our code and models are available at https://github.com/qinzheng93/GraphSCNet.

cs.CV

Wound Segmentation with Dynamic Illumination Correction and Dual-view Semantic Fusion

Wound image segmentation is a critical component for the clinical diagnosis and in-time treatment of wounds. Recently, deep learning has become the mainstream methodology for wound image segmentation. However, the pre-processing of the wound image, such as the illumination correction, is required before the training phase as the performance can be greatly improved. The correction procedure and the training of deep models are independent of each other, which leads to sub-optimal segmentation performance as the fixed illumination correction may not be suitable for all images. To address aforementioned issues, an end-to-end dual-view segmentation approach was proposed in this paper, by incorporating a learn-able illumination correction module into the deep segmentation models. The parameters of the module can be learned and updated during the training stage automatically, while the dual-view fusion can fully employ the features from both the raw images and the enhanced ones. To demonstrate the effectiveness and robustness of the proposed framework, the extensive experiments are conducted on the benchmark datasets. The encouraging results suggest that our framework can significantly improve the segmentation performance, compared to the state-of-the-art methods.

eess.IV

Unsupervised Voice-Face Representation Learning by Cross-Modal Prototype Contrast

We present an approach to learn voice-face representations from the talking face videos, without any identity labels. Previous works employ cross-modal instance discrimination tasks to establish the correlation of voice and face. These methods neglect the semantic content of different videos, introducing false-negative pairs as training noise. Furthermore, the positive pairs are constructed based on the natural correlation between audio clips and visual frames. However, this correlation might be weak or inaccurate in a large amount of real-world data, which leads to deviating positives into the contrastive paradigm. To address these issues, we propose the cross-modal prototype contrastive learning (CMPC), which takes advantage of contrastive methods and resists adverse effects of false negatives and deviate positives. On one hand, CMPC could learn the intra-class invariance by constructing semantic-wise positives via unsupervised clustering in different modalities. On the other hand, by comparing the similarities of cross-modal instances from that of cross-modal prototypes, we dynamically recalibrate the unlearnable instances' contribution to overall loss. Experiments show that the proposed approach outperforms state-of-the-art unsupervised methods on various voice-face association evaluation protocols. Additionally, in the low-shot supervision setting, our method also has a significant improvement compared to previous instance-wise contrastive learning.

cs.SD

ThunderNet: Towards Real-time Generic Object Detection

Real-time generic object detection on mobile platforms is a crucial but challenging computer vision task. However, previous CNN-based detectors suffer from enormous computational cost, which hinders them from real-time inference in computation-constrained scenarios. In this paper, we investigate the effectiveness of two-stage detectors in real-time generic detection and propose a lightweight two-stage detector named ThunderNet. In the backbone part, we analyze the drawbacks in previous lightweight backbones and present a lightweight backbone designed for object detection. In the detection part, we exploit an extremely efficient RPN and detection head design. To generate more discriminative feature representation, we design two efficient architecture blocks, Context Enhancement Module and Spatial Attention Module. At last, we investigate the balance between the input resolution, the backbone, and the detection head. Compared with lightweight one-stage detectors, ThunderNet achieves superior performance with only 40% of the computational cost on PASCAL VOC and COCO benchmarks. Without bells and whistles, our model runs at 24.1 fps on an ARM-based device. To the best of our knowledge, this is the first real-time detector reported on ARM platforms. Our code and models are available at \url{https://github.com/qinzheng93/ThunderNet}.

cs.CV

Geometric Transformer for Fast and Robust Point Cloud Registration

We study the problem of extracting accurate correspondences for point cloud registration. Recent keypoint-free methods bypass the detection of repeatable keypoints which is difficult in low-overlap scenarios, showing great potential in registration. They seek correspondences over downsampled superpoints, which are then propagated to dense points. Superpoints are matched based on whether their neighboring patches overlap. Such sparse and loose matching requires contextual features capturing the geometric structure of the point clouds. We propose Geometric Transformer to learn geometric feature for robust superpoint matching. It encodes pair-wise distances and triplet-wise angles, making it robust in low-overlap cases and invariant to rigid transformation. The simplistic design attains surprisingly high matching accuracy such that no RANSAC is required in the estimation of alignment transformation, leading to $100$ times acceleration. Our method improves the inlier ratio by $17{\sim}30$ percentage points and the registration recall by over $7$ points on the challenging 3DLoMatch benchmark. Our code and models are available at https://github.com/qinzheng93/GeoTransformer.

cs.CV

Audio Tagging by Cross Filtering Noisy Labels

High quality labeled datasets have allowed deep learning to achieve impressive results on many sound analysis tasks. Yet, it is labor-intensive to accurately annotate large amount of audio data, and the dataset may contain noisy labels in the practical settings. Meanwhile, the deep neural networks are susceptive to those incorrect labeled data because of their outstanding memorization ability. In this paper, we present a novel framework, named CrossFilter, to combat the noisy labels problem for audio tagging. Multiple representations (such as, Logmel and MFCC) are used as the input of our framework for providing more complementary information of the audio. Then, though the cooperation and interaction of two neural networks, we divide the dataset into curated and noisy subsets by incrementally pick out the possibly correctly labeled data from the noisy data. Moreover, our approach leverages the multi-task learning on curated and noisy subsets with different loss function to fully utilize the entire dataset. The noisy-robust loss function is employed to alleviate the adverse effects of incorrect labels. On both the audio tagging datasets FSDKaggle2018 and FSDKaggle2019, empirical results demonstrate the performance improvement compared with other competing approaches. On FSDKaggle2018 dataset, our method achieves state-of-the-art performance and even surpasses the ensemble models.

eess.AS

Multi-Representation Knowledge Distillation For Audio Classification

As an important component of multimedia analysis tasks, audio classification aims to discriminate between different audio signal types and has received intensive attention due to its wide applications. Generally speaking, the raw signal can be transformed into various representations (such as Short Time Fourier Transform and Mel Frequency Cepstral Coefficients), and information implied in different representations can be complementary. Ensembling the models trained on different representations can greatly boost the classification performance, however, making inference using a large number of models is cumbersome and computationally expensive. In this paper, we propose a novel end-to-end collaborative learning framework for the audio classification task. The framework takes multiple representations as the input to train the models in parallel. The complementary information provided by different representations is shared by knowledge distillation. Consequently, the performance of each model can be significantly promoted without increasing the computational overhead in the inference stage. Extensive experimental results demonstrate that the proposed approach can improve the classification performance and achieve state-of-the-art results on both acoustic scene classification tasks and general audio tagging tasks.

cs.MM

A Multi-Type Multi-Span Network for Reading Comprehension that Requires Discrete Reasoning

Rapid progress has been made in the field of reading comprehension and question answering, where several systems have achieved human parity in some simplified settings. However, the performance of these models degrades significantly when they are applied to more realistic scenarios, such as answers involve various types, multiple text strings are correct answers, or discrete reasoning abilities are required. In this paper, we introduce the Multi-Type Multi-Span Network (MTMSN), a neural reading comprehension model that combines a multi-type answer predictor designed to support various answer types (e.g., span, count, negation, and arithmetic expression) with a multi-span extraction method for dynamically producing one or multiple text spans. In addition, an arithmetic expression reranking mechanism is proposed to rank expression candidates for further confirming the prediction. Experiments show that our model achieves 79.9 F1 on the DROP hidden test set, creating new state-of-the-art results. Source code\footnote{\url{https://github.com/huminghao16/MTMSN}} is released to facilitate future work.

cs.CL

Retrieve, Read, Rerank: Towards End-to-End Multi-Document Reading Comprehension

This paper considers the reading comprehension task in which multiple documents are given as input. Prior work has shown that a pipeline of retriever, reader, and reranker can improve the overall performance. However, the pipeline system is inefficient since the input is re-encoded within each module, and is unable to leverage upstream components to help downstream training. In this work, we present RE$^3$QA, a unified question answering model that combines context retrieving, reading comprehension, and answer reranking to predict the final answer. Unlike previous pipelined approaches, RE$^3$QA shares contextualized text representation across different components, and is carefully designed to use high-quality upstream outputs (e.g., retrieved context or candidate answers) for directly supervising downstream modules (e.g., the reader or the reranker). As a result, the whole network can be trained end-to-end to avoid the context inconsistency problem. Experiments show that our model outperforms the pipelined baseline and achieves state-of-the-art results on two versions of TriviaQA and two variants of SQuAD.

cs.CL

Open-Domain Targeted Sentiment Analysis via Span-Based Extraction and Classification

Open-domain targeted sentiment analysis aims to detect opinion targets along with their sentiment polarities from a sentence. Prior work typically formulates this task as a sequence tagging problem. However, such formulation suffers from problems such as huge search space and sentiment inconsistency. To address these problems, we propose a span-based extract-then-classify framework, where multiple opinion targets are directly extracted from the sentence under the supervision of target span boundaries, and corresponding polarities are then classified using their span representations. We further investigate three approaches under this framework, namely the pipeline, joint, and collapsed models. Experiments on three benchmark datasets show that our approach consistently outperforms the sequence tagging baseline. Moreover, we find that the pipeline model achieves the best performance compared with the other two models.

cs.CL

Read + Verify: Machine Reading Comprehension with Unanswerable Questions

Machine reading comprehension with unanswerable questions aims to abstain from answering when no answer can be inferred. In addition to extract answers, previous works usually predict an additional "no-answer" probability to detect unanswerable cases. However, they fail to validate the answerability of the question by verifying the legitimacy of the predicted answer. To address this problem, we propose a novel read-then-verify system, which not only utilizes a neural reader to extract candidate answers and produce no-answer probabilities, but also leverages an answer verifier to decide whether the predicted answer is entailed by the input snippets. Moreover, we introduce two auxiliary losses to help the reader better handle answer extraction as well as no-answer detection, and investigate three different architectures for the answer verifier. Our experiments on the SQuAD 2.0 dataset show that our system achieves a score of 74.2 F1 on the test set, achieving state-of-the-art results at the time of submission (Aug. 28th, 2018).

cs.CL