arXiv subjects

Yang Song

Publications and source records attributed to Yang Song.

At least 271 records · Page 15Linked to original sources

arXiv2021

3D Medical Point Transformer: Introducing Convolution to Attention Networks for Medical Point Cloud Analysis

General point clouds have been increasingly investigated for different tasks, and recently Transformer-based networks are proposed for point cloud analysis. However, there are barely related works for medical point clouds, which are important for disease detection and treatment. In this work, we propose an attention-based model specifically for medical point clouds, namely 3D medical point Transformer (3DMedPT), to examine the complex biological structures. By augmenting contextual information and summarizing local responses at query, our attention module can capture both local context and global content feature interactions. However, the insufficient training samples of medical data may lead to poor feature learning, so we apply position embeddings to learn accurate local geometry and Multi-Graph Reasoning (MGR) to examine global knowledge propagation over channel graphs to enrich feature representations. Experiments conducted on IntrA dataset proves the superiority of 3DMedPT, where we achieve the best classification and segmentation results. Furthermore, the promising generalization ability of our method is validated on general 3D point cloud benchmarks: ModelNet40 and ShapeNetPart. Code is released.

eess.IV↗

arXiv2021

Score-Based Generative Classifiers

The tremendous success of generative models in recent years raises the question whether they can also be used to perform classification. Generative models have been used as adversarially robust classifiers on simple datasets such as MNIST, but this robustness has not been observed on more complex datasets like CIFAR-10. Additionally, on natural image datasets, previous results have suggested a trade-off between the likelihood of the data and classification accuracy. In this work, we investigate score-based generative models as classifiers for natural images. We show that these models not only obtain competitive likelihood values but simultaneously achieve state-of-the-art classification accuracy for generative classifiers on CIFAR-10. Nevertheless, we find that these models are only slightly, if at all, more robust than discriminative baseline models on out-of-distribution tasks based on common image corruptions. Similarly and contrary to prior results, we find that score-based are prone to worst-case distribution shifts in the form of adversarial perturbations. Our work highlights that score-based generative models are closing the gap in classification accuracy compared to standard discriminative models. While they do not yet deliver on the promise of adversarial and out-of-domain robustness, they provide a different approach to classification that warrants further research.

stat.ML↗

arXiv2021

Estimating High Order Gradients of the Data Distribution by Denoising

The first order derivative of a data density can be estimated efficiently by denoising score matching, and has become an important component in many applications, such as image generation and audio synthesis. Higher order derivatives provide additional local information about the data distribution and enable new applications. Although they can be estimated via automatic differentiation of a learned density model, this can amplify estimation errors and is expensive in high dimensional settings. To overcome these limitations, we propose a method to directly estimate high order derivatives (scores) of a data density from samples. We first show that denoising score matching can be interpreted as a particular case of Tweedie's formula. By leveraging Tweedie's formula on higher order moments, we generalize denoising score matching to estimate higher order derivatives. We demonstrate empirically that models trained with the proposed method can approximate second order derivatives more efficiently and accurately than via automatic differentiation. We show that our models can be used to quantify uncertainty in denoising and to improve the mixing speed of Langevin dynamics via Ozaki discretization for sampling synthetic data and natural images.

cs.LG↗

arXiv2021

Pseudo-Spherical Contrastive Divergence

Energy-based models (EBMs) offer flexible distribution parametrization. However, due to the intractable partition function, they are typically trained via contrastive divergence for maximum likelihood estimation. In this paper, we propose pseudo-spherical contrastive divergence (PS-CD) to generalize maximum likelihood learning of EBMs. PS-CD is derived from the maximization of a family of strictly proper homogeneous scoring rules, which avoids the computation of the intractable partition function and provides a generalized family of learning objectives that include contrastive divergence as a special case. Moreover, PS-CD allows us to flexibly choose various learning objectives to train EBMs without additional computational cost or variational minimax optimization. Theoretical analysis on the proposed method and extensive experiments on both synthetic data and commonly used image datasets demonstrate the effectiveness and modeling flexibility of PS-CD, as well as its robustness to data contamination, thus showing its superiority over maximum likelihood and $f$-EBMs.

cs.LG↗

arXiv2021

CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation

The imputation of missing values in time series has many applications in healthcare and finance. While autoregressive models are natural candidates for time series imputation, score-based diffusion models have recently outperformed existing counterparts including autoregressive models in many tasks such as image generation and audio synthesis, and would be promising for time series imputation. In this paper, we propose Conditional Score-based Diffusion models for Imputation (CSDI), a novel time series imputation method that utilizes score-based diffusion models conditioned on observed data. Unlike existing score-based approaches, the conditional diffusion model is explicitly trained for imputation and can exploit correlations between observed values. On healthcare and environmental data, CSDI improves by 40-65% over existing probabilistic imputation methods on popular performance metrics. In addition, deterministic imputation by CSDI reduces the error by 5-20% compared to the state-of-the-art deterministic imputation methods. Furthermore, CSDI can also be applied to time series interpolation and probabilistic forecasting, and is competitive with existing baselines. The code is available at https://github.com/ermongroup/CSDI.

cs.LG↗

arXiv2021

Stable Neural ODE with Lyapunov-Stable Equilibrium Points for Defending Against Adversarial Attacks

Deep neural networks (DNNs) are well-known to be vulnerable to adversarial attacks, where malicious human-imperceptible perturbations are included in the input to the deep network to fool it into making a wrong classification. Recent studies have demonstrated that neural Ordinary Differential Equations (ODEs) are intrinsically more robust against adversarial attacks compared to vanilla DNNs. In this work, we propose a stable neural ODE with Lyapunov-stable equilibrium points for defending against adversarial attacks (SODEF). By ensuring that the equilibrium points of the ODE solution used as part of SODEF is Lyapunov-stable, the ODE solution for an input with a small perturbation converges to the same solution as the unperturbed input. We provide theoretical results that give insights into the stability of SODEF as well as the choice of regularizers to ensure its stability. Our analysis suggests that our proposed regularizers force the extracted feature points to be within a neighborhood of the Lyapunov-stable equilibrium points of the ODE. SODEF is compatible with many defense methods and can be applied to any neural network's final regressor layer to enhance its stability against adversarial attacks.

cs.LG↗

arXiv2021

Maximum Likelihood Training of Score-Based Diffusion Models

Score-based diffusion models synthesize samples by reversing a stochastic process that diffuses data to noise, and are trained by minimizing a weighted combination of score matching losses. The log-likelihood of score-based diffusion models can be tractably computed through a connection to continuous normalizing flows, but log-likelihood is not directly optimized by the weighted combination of score matching losses. We show that for a specific weighting scheme, the objective upper bounds the negative log-likelihood, thus enabling approximate maximum likelihood training of score-based diffusion models. We empirically observe that maximum likelihood training consistently improves the likelihood of score-based diffusion models across multiple datasets, stochastic processes, and model architectures. Our best models achieve negative log-likelihoods of 2.83 and 3.76 bits/dim on CIFAR-10 and ImageNet 32x32 without any data augmentation, on a par with state-of-the-art autoregressive models on these tasks.

stat.ML↗

arXiv2021

Fast WordPiece Tokenization

Tokenization is a fundamental preprocessing step for almost all NLP tasks. In this paper, we propose efficient algorithms for the WordPiece tokenization used in BERT, from single-word tokenization to general text (e.g., sentence) tokenization. When tokenizing a single word, WordPiece uses a longest-match-first strategy, known as maximum matching. The best known algorithms so far are O(n^2) (where n is the input length) or O(nm) (where m is the maximum vocabulary token length). We propose a novel algorithm whose tokenization complexity is strictly O(n). Our method is inspired by the Aho-Corasick algorithm. We introduce additional linkages on top of the trie built from the vocabulary, allowing smart transitions when the trie matching cannot continue. For general text, we further propose an algorithm that combines pre-tokenization (splitting the text into words) and our linear-time WordPiece method into a single pass. Experimental results show that our method is 8.2x faster than HuggingFace Tokenizers and 5.1x faster than TensorFlow Text on average for general text tokenization.

cs.CL↗

arXiv2021

Concept-Aware Denoising Graph Neural Network for Micro-Video Recommendation

Recently, micro-video sharing platforms such as Kuaishou and Tiktok have become a major source of information for people's lives. Thanks to the large traffic volume, short video lifespan and streaming fashion of these services, it has become more and more pressing to improve the existing recommender systems to accommodate these challenges in a cost-effective way. In this paper, we propose a novel concept-aware denoising graph neural network (named CONDE) for micro-video recommendation. CONDE consists of a three-phase graph convolution process to derive user and micro-video representations: warm-up propagation, graph denoising and preference refinement. A heterogeneous tripartite graph is constructed by connecting user nodes with video nodes, and video nodes with associated concept nodes, extracted from captions and comments of the videos. To address the noisy information in the graph, we introduce a user-oriented graph denoising phase to extract a subgraph which can better reflect the user's preference. Despite the main focus of micro-video recommendation in this paper, we also show that our method can be generalized to other types of tasks. Therefore, we also conduct empirical studies on a well-known public E-commerce dataset. The experimental results suggest that the proposed CONDE achieves significantly better recommendation performance than the existing state-of-the-art solutions.

cs.IR↗

arXiv2021

Voxel-wise Cross-Volume Representation Learning for 3D Neuron Reconstruction

Automatic 3D neuron reconstruction is critical for analysing the morphology and functionality of neurons in brain circuit activities. However, the performance of existing tracing algorithms is hinged by the low image quality. Recently, a series of deep learning based segmentation methods have been proposed to improve the quality of raw 3D optical image stacks by removing noises and restoring neuronal structures from low-contrast background. Due to the variety of neuron morphology and the lack of large neuron datasets, most of current neuron segmentation models rely on introducing complex and specially-designed submodules to a base architecture with the aim of encoding better feature representations. Though successful, extra burden would be put on computation during inference. Therefore, rather than modifying the base network, we shift our focus to the dataset itself. The encoder-decoder backbone used in most neuron segmentation models attends only intra-volume voxel points to learn structural features of neurons but neglect the shared intrinsic semantic features of voxels belonging to the same category among different volumes, which is also important for expressive representation learning. Hence, to better utilise the scarce dataset, we propose to explicitly exploit such intrinsic features of voxels through a novel voxel-level cross-volume representation learning paradigm on the basis of an encoder-decoder segmentation model. Our method introduces no extra cost during inference. Evaluated on 42 3D neuron images from BigNeuron project, our proposed method is demonstrated to improve the learning ability of the original segmentation model and further enhancing the reconstruction performance.

eess.IV↗

arXiv2021

A Right Invariant Extended Kalman Filter for Object based SLAM

With the recent advance of deep learning based object recognition and estimation, it is possible to consider object level SLAM where the pose of each object is estimated in the SLAM process. In this paper, based on a novel Lie group structure, a right invariant extended Kalman filter (RI-EKF) for object based SLAM is proposed. The observability analysis shows that the proposed algorithm automatically maintains the correct unobservable subspace, while standard EKF (Std-EKF) based SLAM algorithm does not. This results in a better consistency for the proposed algorithm comparing to Std-EKF. Finally, simulations and real world experiments validate not only the consistency and accuracy of the proposed algorithm, but also the practicability of the proposed RI-EKF for object based SLAM problem. The MATLAB code of the algorithm is made publicly available.

cs.RO↗

arXiv2021

Discriminative Latent Semantic Graph for Video Captioning

Video captioning aims to automatically generate natural language sentences that can describe the visual contents of a given video. Existing generative models like encoder-decoder frameworks cannot explicitly explore the object-level interactions and frame-level information from complex spatio-temporal data to generate semantic-rich captions. Our main contribution is to identify three key problems in a joint framework for future video summarization tasks. 1) Enhanced Object Proposal: we propose a novel Conditional Graph that can fuse spatio-temporal information into latent object proposal. 2) Visual Knowledge: Latent Proposal Aggregation is proposed to dynamically extract visual words with higher semantic levels. 3) Sentence Validation: A novel Discriminative Language Validator is proposed to verify generated captions so that key semantic concepts can be effectively preserved. Our experiments on two public datasets (MVSD and MSR-VTT) manifest significant improvements over state-of-the-art approaches on all metrics, especially for BLEU-4 and CIDEr. Our code is available at https://github.com/baiyang4/D-LSG-Video-Caption.

cs.CV↗

arXiv2021

Walk in the Cloud: Learning Curves for Point Clouds Shape Analysis

Discrete point cloud objects lack sufficient shape descriptors of 3D geometries. In this paper, we present a novel method for aggregating hypothetical curves in point clouds. Sequences of connected points (curves) are initially grouped by taking guided walks in the point clouds, and then subsequently aggregated back to augment their point-wise features. We provide an effective implementation of the proposed aggregation strategy including a novel curve grouping operator followed by a curve aggregation operator. Our method was benchmarked on several point cloud analysis tasks where we achieved the state-of-the-art classification accuracy of 94.2% on the ModelNet40 classification task, instance IoU of 86.8 on the ShapeNetPart segmentation task, and cosine error of 0.11 on the ModelNet40 normal estimation task.

cs.CV↗

arXiv2021

Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation

White matter fiber clustering (WMFC) enables parcellation of white matter tractography for applications such as disease classification and anatomical tract segmentation. However, the lack of ground truth and the ambiguity of fiber data (the points along a fiber can equivalently be represented in forward or reverse order) pose challenges to this task. We propose a novel WMFC framework based on unsupervised deep learning. We solve the unsupervised clustering problem as a self-supervised learning task. Specifically, we use a convolutional neural network to learn embeddings of input fibers, using pairwise fiber distances as pseudo annotations. This enables WMFC that is insensitive to fiber point ordering. In addition, anatomical coherence of fiber clusters is improved by incorporating brain anatomical segmentation data. The proposed framework enables outlier removal in a natural way by rejecting fibers with low cluster assignment probability. We train and evaluate our method using 200 datasets from the Human Connectome Project. Results demonstrate superior performance and efficiency of the proposed approach.

cs.CV↗

arXiv2021

PhotoChat: A Human-Human Dialogue Dataset with Photo Sharing Behavior for Joint Image-Text Modeling

We present a new human-human dialogue dataset - PhotoChat, the first dataset that casts light on the photo sharing behavior in onlin emessaging. PhotoChat contains 12k dialogues, each of which is paired with a user photo that is shared during the conversation. Based on this dataset, we propose two tasks to facilitate research on image-text modeling: a photo-sharing intent prediction task that predicts whether one intends to share a photo in the next conversation turn, and a photo retrieval task that retrieves the most relevant photo according to the dialogue context. In addition, for both tasks, we provide baseline models using the state-of-the-art models and report their benchmark performances. The best image retrieval model achieves 10.4% recall@1 (out of 1000 candidates) and the best photo intent prediction model achieves 58.1% F1 score, indicating that the dataset presents interesting yet challenging real-world problems. We are releasing PhotoChat to facilitate future research work among the community.

cs.IR↗

arXiv2021

BiX-NAS: Searching Efficient Bi-directional Architecture for Medical Image Segmentation

The recurrent mechanism has recently been introduced into U-Net in various medical image segmentation tasks. Existing studies have focused on promoting network recursion via reusing building blocks. Although network parameters could be greatly saved, computational costs still increase inevitably in accordance with the pre-set iteration time. In this work, we study a multi-scale upgrade of a bi-directional skip connected network and then automatically discover an efficient architecture by a novel two-phase Neural Architecture Search (NAS) algorithm, namely BiX-NAS. Our proposed method reduces the network computational cost by sifting out ineffective multi-scale features at different levels and iterations. We evaluate BiX-NAS on two segmentation tasks using three different medical image datasets, and the experimental results show that our BiX-NAS searched architecture achieves the state-of-the-art performance with significantly lower computational cost.

eess.IV↗

arXiv2021

Intrinsically Honeycomb-patterned Hydrogenated Graphene with Spin Polarized Edge-states

Since the advent of graphene ushered the era of two-dimensional materials, many forms of hydrogenated graphene have been reported, exhibiting diverse properties ranging from a tunable band gap to ferromagnetic ordering. Patterned hydrogenated graphene with micron-scale patterns has been fabricated by lithographic means. Here we report successful millimeter-scale synthesis of an intrinsically honeycomb patterned form of hydrogenated graphene on Ru(0001) by epitaxial growth followed by hydrogenation. Combining scanning tunneling microscopy observations with density-functional-theory (DFT) calculations, we reveal that an atomic-hydrogen layer intercalates between graphene and Ru(0001). The result is a hydrogen honeycomb structure that serves as a template for the final hydrogenation, which converts the graphene into graphane only over the template, yielding honeycomb-patterned hydrogenated graphene (HPHG). In effect, HPHG is a form of patterned graphane. DFT calculations find that the unhydrogenated graphene regions embedded in the patterned graphane exhibit spin-polarized edge states. This type of growth mechanism provides new pathways for the fabrication of intrinsically patterned graphene-based materials.

cond-mat.mtrl-sci↗

arXiv2021

Accelerating Feedforward Computation via Parallel Nonlinear Equation Solving

Feedforward computation, such as evaluating a neural network or sampling from an autoregressive model, is ubiquitous in machine learning. The sequential nature of feedforward computation, however, requires a strict order of execution and cannot be easily accelerated with parallel computing. To enable parallelization, we frame the task of feedforward computation as solving a system of nonlinear equations. We then propose to find the solution using a Jacobi or Gauss-Seidel fixed-point iteration method, as well as hybrid methods of both. Crucially, Jacobi updates operate independently on each equation and can be executed in parallel. Our method is guaranteed to give exactly the same values as the original feedforward computation with a reduced (or equal) number of parallelizable iterations, and hence reduced time given sufficient parallel computing power. Experimentally, we demonstrate the effectiveness of our approach in accelerating (i) backpropagation of RNNs, (ii) evaluation of DenseNets, and (iii) autoregressive sampling of MADE and PixelCNN++, with speedup factors between 2.1 and 26 under various settings.

cs.LG↗