Yuxing Peng

Zheng Qin, Hao Yu, Changjian Wang et al.

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}.

Zheng Qin, Hao Yu, Changjian Wang et al.

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.

Dejun Lin, Simon Chu, Vishanth Iyer et al.

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.

Boqing Zhu, Kele Xu, Changjian Wang et al.

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.

Honghui Liu, Changjian Wang, Kele Xu et al.

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.

Seul Lee, Karsten Kreis, Srimukh Prasad Veccham et al.

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.

Peter St. John, Dejun Lin, Polina Binder et al.

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.

Zheng Qin, Hao Yu, Changjian Wang et al.

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.

Minghao Hu, Yuxing Peng, Zhen Huang et al.

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.

Zheng Qin, Zeming Li, Zhaoning Zhang et al.

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}.

Boqing Zhu, Kele Xu, Qiuqiang Kong et al.

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.

Liang Gao, Kele Xu, Huaimin Wang et al.

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.

Minghao Hu, Yuxing Peng, Zhen Huang et al.

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.

Minghao Hu, Yuxing Peng, Zhen Huang et al.

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.

Minghao Hu, Yuxing Peng, Furu Wei et al.

Despite that current reading comprehension systems have achieved significant advancements, their promising performances are often obtained at the cost of making an ensemble of numerous models. Besides, existing approaches are also vulnerable to adversarial attacks. This paper tackles these problems by leveraging knowledge distillation, which aims to transfer knowledge from an ensemble model to a single model. We first demonstrate that vanilla knowledge distillation applied to answer span prediction is effective for reading comprehension systems. We then propose two novel approaches that not only penalize the prediction on confusing answers but also guide the training with alignment information distilled from the ensemble. Experiments show that our best student model has only a slight drop of 0.4% F1 on the SQuAD test set compared to the ensemble teacher, while running 12x faster during inference. It even outperforms the teacher on adversarial SQuAD datasets and NarrativeQA benchmark.

Minghao Hu, Furu Wei, Yuxing Peng et al.

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).

Boqing Zhu, Kele Xu, Dezhi Wang et al.

Motivated by the fact that characteristics of different sound classes are highly diverse in different temporal scales and hierarchical levels, a novel deep convolutional neural network (CNN) architecture is proposed for the environmental sound classification task. This network architecture takes raw waveforms as input, and a set of separated parallel CNNs are utilized with different convolutional filter sizes and strides, in order to learn feature representations with multi-temporal resolutions. On the other hand, the proposed architecture also aggregates hierarchical features from multi-level CNN layers for classification using direct connections between convolutional layers, which is beyond the typical single-level CNN features employed by the majority of previous studies. This network architecture also improves the flow of information and avoids vanishing gradient problem. The combination of multi-level features boosts the classification performance significantly. Comparative experiments are conducted on two datasets: the environmental sound classification dataset (ESC-50), and DCASE 2017 audio scene classification dataset. Results demonstrate that the proposed method is highly effective in the classification tasks by employing multi-temporal resolution and multi-level features, and it outperforms the previous methods which only account for single-level features.

Zheng Qin, Zhaoning Zhang, Dongsheng Li et al.

Depthwise convolutions provide significant performance benefits owing to the reduction in both parameters and mult-adds. However, training depthwise convolution layers with GPUs is slow in current deep learning frameworks because their implementations cannot fully utilize the GPU capacity. To address this problem, in this paper we present an efficient method (called diagonalwise refactorization) for accelerating the training of depthwise convolution layers. Our key idea is to rearrange the weight vectors of a depthwise convolution into a large diagonal weight matrix so as to convert the depthwise convolution into one single standard convolution, which is well supported by the cuDNN library that is highly-optimized for GPU computations. We have implemented our training method in five popular deep learning frameworks. Evaluation results show that our proposed method gains $15.4\times$ training speedup on Darknet, $8.4\times$ on Caffe, $5.4\times$ on PyTorch, $3.5\times$ on MXNet, and $1.4\times$ on TensorFlow, compared to their original implementations of depthwise convolutions.

Boqing Zhu, Changjian Wang, Feng Liu et al.

Deep learning has dramatically improved the performance of sounds recognition. However, learning acoustic models directly from the raw waveform is still challenging. Current waveform-based models generally use time-domain convolutional layers to extract features. The features extracted by single size filters are insufficient for building discriminative representation of audios. In this paper, we propose multi-scale convolution operation, which can get better audio representation by improving the frequency resolution and learning filters cross all frequency area. For leveraging the waveform-based features and spectrogram-based features in a single model, we introduce two-phase method to fuse the different features. Finally, we propose a novel end-to-end network called WaveMsNet based on the multi-scale convolution operation and two-phase method. On the environmental sounds classification datasets ESC-10 and ESC-50, the classification accuracies of our WaveMsNet achieve 93.75% and 79.10% respectively, which improve significantly from the previous methods.

Zheng Qin, Zhaoning Zhang, Shiqing Zhang et al.

Compact neural networks are inclined to exploit "sparsely-connected" convolutions such as depthwise convolution and group convolution for employment in mobile applications. Compared with standard "fully-connected" convolutions, these convolutions are more computationally economical. However, "sparsely-connected" convolutions block the inter-group information exchange, which induces severe performance degradation. To address this issue, we present two novel operations named merging and evolution to leverage the inter-group information. Our key idea is encoding the inter-group information with a narrow feature map, then combining the generated features with the original network for better representation. Taking advantage of the proposed operations, we then introduce the Merging-and-Evolution (ME) module, an architectural unit specifically designed for compact networks. Finally, we propose a family of compact neural networks called MENet based on ME modules. Extensive experiments on ILSVRC 2012 dataset and PASCAL VOC 2007 dataset demonstrate that MENet consistently outperforms other state-of-the-art compact networks under different computational budgets. For instance, under the computational budget of 140 MFLOPs, MENet surpasses ShuffleNet by 1% and MobileNet by 1.95% on ILSVRC 2012 top-1 accuracy, while by 2.3% and 4.1% on PASCAL VOC 2007 mAP, respectively.

Zheng Qin, Zhaoning Zhang, Xiaotao Chen et al.

We present Fast-Downsampling MobileNet (FD-MobileNet), an efficient and accurate network for very limited computational budgets (e.g., 10-140 MFLOPs). Our key idea is applying an aggressive downsampling strategy to MobileNet framework. In FD-MobileNet, we perform 32$\times$ downsampling within 12 layers, only half the layers in the original MobileNet. This design brings three advantages: (i) It remarkably reduces the computational cost. (ii) It increases the information capacity and achieves significant performance improvements. (iii) It is engineering-friendly and provides fast actual inference speed. Experiments on ILSVRC 2012 and PASCAL VOC 2007 datasets demonstrate that FD-MobileNet consistently outperforms MobileNet and achieves comparable results with ShuffleNet under different computational budgets, for instance, surpassing MobileNet by 5.5% on the ILSVRC 2012 top-1 accuracy and 3.6% on the VOC 2007 mAP under a complexity of 12 MFLOPs. On an ARM-based device, FD-MobileNet achieves 1.11$\times$ inference speedup over MobileNet and 1.82$\times$ over ShuffleNet under the same complexity.

Minghao Hu, Yuxing Peng, Zhen Huang et al.

In this paper, we introduce the Reinforced Mnemonic Reader for machine reading comprehension tasks, which enhances previous attentive readers in two aspects. First, a reattention mechanism is proposed to refine current attentions by directly accessing to past attentions that are temporally memorized in a multi-round alignment architecture, so as to avoid the problems of attention redundancy and attention deficiency. Second, a new optimization approach, called dynamic-critical reinforcement learning, is introduced to extend the standard supervised method. It always encourages to predict a more acceptable answer so as to address the convergence suppression problem occurred in traditional reinforcement learning algorithms. Extensive experiments on the Stanford Question Answering Dataset (SQuAD) show that our model achieves state-of-the-art results. Meanwhile, our model outperforms previous systems by over 6% in terms of both Exact Match and F1 metrics on two adversarial SQuAD datasets.

Tingting Xie, Yuxing Peng, Changjian Wang

In recent years, dynamically growing data and incrementally growing number of classes pose new challenges to large-scale data classification research. Most traditional methods struggle to balance the precision and computational burden when data and its number of classes increased. However, some methods are with weak precision, and the others are time-consuming. In this paper, we propose an incremental learning method, namely, heterogeneous incremental Nearest Class Mean Random Forest (hi-RF), to handle this issue. It is a heterogeneous method that either replaces trees or updates trees leaves in the random forest adaptively, to reduce the computational time in comparable performance, when data of new classes arrive. Specifically, to keep the accuracy, one proportion of trees are replaced by new NCM decision trees; to reduce the computational load, the rest trees are updated their leaves probabilities only. Most of all, out-of-bag estimation and out-of-bag boosting are proposed to balance the accuracy and the computational efficiency. Fair experiments were conducted and demonstrated its comparable precision with much less computational time.