Taifeng Wang

Jing Gong, Minsheng Hao, Xingyi Cheng et al.

Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for humans with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGene$^α$ (or xTrimoGene for short), which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we scale up the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell type annotation, perturb-seq effect prediction, and drug combination prediction. xTrimoGene model is now available for use as a service via the following link: https://api.biomap.com/xTrimoGene/apply.

Zhihang Hu, Qinze Yu, Yucheng Guo et al.

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the vast combinatorial search space. Recently, computational approaches, specifically deep learning models have emerged as an efficient way to discover synergistic combinations. While previous methods reported fair performance, their models usually do not take advantage of multi-modal data and they are unable to handle new drugs or cell lines. In this study, we collected data from various datasets covering various drug-related aspects. Then, we take advantage of large-scale pre-training models to generate informative representations and features for drugs, proteins, and diseases. Based on that, a message-passing graph is built on top to propagate information together with graph structure learning flexibility. This is first introduced in the biological networks and enables us to generate pseudo-relations in the graph. Our framework achieves state-of-the-art results in comparison with other deep learning-based methods on synergistic prediction benchmark datasets. We are also capable of inferencing new drug combination data in a test on an independent set released by AstraZeneca, where 10% of improvement over previous methods is observed. In addition, we're robust against unseen drugs and surpass almost 15% AU ROC compared to the second-best model. We believe our framework contributes to both the future wet-lab discovery of novel drugs and the building of promising guidance for precise combination medicine.

Linlin Chao, Xiexiong Lin, Taifeng Wang et al.

Knowledge graph (KG) embedding methods which map entities and relations to unique embeddings in the KG have shown promising results on many reasoning tasks. However, the same embedding dimension for both dense entities and sparse entities will cause either over parameterization (sparse entities) or under fitting (dense entities). Normally, a large dimension is set to get better performance. Meanwhile, the inference time grows log-linearly with the number of entities for all entities are traversed and compared. Both the parameter and inference become challenges when working with huge amounts of entities. Thus, we propose PIE, a \textbf{p}arameter and \textbf{i}nference \textbf{e}fficient solution. Inspired from tensor decomposition methods, we find that decompose entity embedding matrix into low rank matrices can reduce more than half of the parameters while maintaining comparable performance. To accelerate model inference, we propose a self-supervised auxiliary task, which can be seen as fine-grained entity typing. By randomly masking and recovering entities' connected relations, the task learns the co-occurrence of entity and relations. Utilizing the fine grained typing, we can filter unrelated entities during inference and get targets with possibly sub-linear time requirement. Experiments on link prediction benchmarks demonstrate the proposed key capabilities. Moreover, we prove effectiveness of the proposed solution on the Open Graph Benchmark large scale challenge dataset WikiKG90Mv2 and achieve the state of the art performance.

Weidi Xu, Jingwei Wang, Lele Xie et al.

Integrating first-order logic constraints (FOLCs) with neural networks is a crucial but challenging problem since it involves modeling intricate correlations to satisfy the constraints. This paper proposes a novel neural layer, LogicMP, whose layers perform mean-field variational inference over an MLN. It can be plugged into any off-the-shelf neural network to encode FOLCs while retaining modularity and efficiency. By exploiting the structure and symmetries in MLNs, we theoretically demonstrate that our well-designed, efficient mean-field iterations effectively mitigate the difficulty of MLN inference, reducing the inference from sequential calculation to a series of parallel tensor operations. Empirical results in three kinds of tasks over graphs, images, and text show that LogicMP outperforms advanced competitors in both performance and efficiency.

Kunlong Chen, Weidi Xu, Xingyi Cheng et al.

Numerical reasoning over texts, such as addition, subtraction, sorting and counting, is a challenging machine reading comprehension task, since it requires both natural language understanding and arithmetic computation. To address this challenge, we propose a heterogeneous graph representation for the context of the passage and question needed for such reasoning, and design a question directed graph attention network to drive multi-step numerical reasoning over this context graph. The code link is at: https://github.com/emnlp2020qdgat/QDGAT

Xingyi Cheng, Weidi Xu, Kunlong Chen et al.

Chinese Spelling Check (CSC) is a task to detect and correct spelling errors in Chinese natural language. Existing methods have made attempts to incorporate the similarity knowledge between Chinese characters. However, they take the similarity knowledge as either an external input resource or just heuristic rules. This paper proposes to incorporate phonological and visual similarity knowledge into language models for CSC via a specialized graph convolutional network (SpellGCN). The model builds a graph over the characters, and SpellGCN is learned to map this graph into a set of inter-dependent character classifiers. These classifiers are applied to the representations extracted by another network, such as BERT, enabling the whole network to be end-to-end trainable. Experiments (The dataset and all code for this paper are available at https://github.com/ACL2020SpellGCN/SpellGCN) are conducted on three human-annotated datasets. Our method achieves superior performance against previous models by a large margin.

Linlin Chao, Jianshan He, Taifeng Wang et al.

Distance based knowledge graph embedding methods show promising results on link prediction task, on which two topics have been widely studied: one is the ability to handle complex relations, such as N-to-1, 1-to-N and N-to-N, the other is to encode various relation patterns, such as symmetry/antisymmetry. However, the existing methods fail to solve these two problems at the same time, which leads to unsatisfactory results. To mitigate this problem, we propose PairRE, a model with paired vectors for each relation representation. The paired vectors enable an adaptive adjustment of the margin in loss function to fit for complex relations. Besides, PairRE is capable of encoding three important relation patterns, symmetry/antisymmetry, inverse and composition. Given simple constraints on relation representations, PairRE can encode subrelation further. Experiments on link prediction benchmarks demonstrate the proposed key capabilities of PairRE. Moreover, We set a new state-of-the-art on two knowledge graph datasets of the challenging Open Graph Benchmark.

Xianpei Han, Zhichun Wang, Jiangtao Zhang et al.

Knowledge graph models world knowledge as concepts, entities, and the relationships between them, which has been widely used in many real-world tasks. CCKS 2019 held an evaluation track with 6 tasks and attracted more than 1,600 teams. In this paper, we give an overview of the knowledge graph evaluation tract at CCKS 2019. By reviewing the task definition, successful methods, useful resources, good strategies and research challenges associated with each task in CCKS 2019, this paper can provide a helpful reference for developing knowledge graph applications and conducting future knowledge graph researches.

Weidi Xu, Xingyi Cheng, Kunlong Chen et al.

The ability of semantic reasoning over the sentence pair is essential for many natural language understanding tasks, e.g., natural language inference and machine reading comprehension. A recent significant improvement in these tasks comes from BERT. As reported, the next sentence prediction (NSP) in BERT, which learns the contextual relationship between two sentences, is of great significance for downstream problems with sentence-pair input. Despite the effectiveness of NSP, we suggest that NSP still lacks the essential signal to distinguish between entailment and shallow correlation. To remedy this, we propose to augment the NSP task to a 3-class categorization task, which includes a category for previous sentence prediction (PSP). The involvement of PSP encourages the model to focus on the informative semantics to determine the sentence order, thereby improves the ability of semantic understanding. This simple modification yields remarkable improvement against vanilla BERT. To further incorporate the document-level information, the scope of NSP and PSP is expanded into a broader range, i.e., NSP and PSP also include close but nonsuccessive sentences, the noise of which is mitigated by the label-smoothing technique. Both qualitative and quantitative experimental results demonstrate the effectiveness of the proposed method. Our method consistently improves the performance on the NLI and MRC benchmarks, including the challenging HANS dataset \cite{hans}, suggesting that the document-level task is still promising for the pre-training.

Weipeng Huang, Xingyi Cheng, Taifeng Wang et al.

In this paper, we report our method for the Information Extraction task in 2019 Language and Intelligence Challenge. We incorporate BERT into the multi-head selection framework for joint entity-relation extraction. This model extends existing approaches from three perspectives. First, BERT is adopted as a feature extraction layer at the bottom of the multi-head selection framework. We further optimize BERT by introducing a semantic-enhanced task during BERT pre-training. Second, we introduce a large-scale Baidu Baike corpus for entity recognition pre-training, which is of weekly supervised learning since there is no actual named entity label. Third, soft label embedding is proposed to effectively transmit information between entity recognition and relation extraction. Combining these three contributions, we enhance the information extracting ability of the multi-head selection model and achieve F1-score 0.876 on testset-1 with a single model. By ensembling four variants of our model, we finally achieve F1 score 0.892 (1st place) on testset-1 and F1 score 0.8924 (2nd place) on testset-2.

Weipeng Huang, Xingyi Cheng, Kunlong Chen et al.

The ambiguous annotation criteria lead to divergence of Chinese Word Segmentation (CWS) datasets in various granularities. Multi-criteria Chinese word segmentation aims to capture various annotation criteria among datasets and leverage their common underlying knowledge. In this paper, we propose a domain adaptive segmenter to exploit diverse criteria of various datasets. Our model is based on Bidirectional Encoder Representations from Transformers (BERT), which is responsible for introducing open-domain knowledge. Private and shared projection layers are proposed to capture domain-specific knowledge and common knowledge, respectively. We also optimize computational efficiency via distillation, quantization, and compiler optimization. Experiments show that our segmenter outperforms the previous state of the art (SOTA) models on 10 CWS datasets with superior efficiency.

Xingyi Cheng, Weidi Xu, Taifeng Wang et al.

Aspect-term sentiment analysis (ATSA) is a longstanding challenge in natural language understanding. It requires fine-grained semantical reasoning about a target entity appeared in the text. As manual annotation over the aspects is laborious and time-consuming, the amount of labeled data is limited for supervised learning. This paper proposes a semi-supervised method for the ATSA problem by using the Variational Autoencoder based on Transformer (VAET), which models the latent distribution via variational inference. By disentangling the latent representation into the aspect-specific sentiment and the lexical context, our method induces the underlying sentiment prediction for the unlabeled data, which then benefits the ATSA classifier. Our method is classifier agnostic, i.e., the classifier is an independent module and various advanced supervised models can be integrated. Experimental results are obtained on the SemEval 2014 task 4 and show that our method is effective with four classical classifiers. The proposed method outperforms two general semisupervised methods and achieves state-of-the-art performance.

Quanming Yao, James T. Kwok, Taifeng Wang et al.

Low-rank modeling has many important applications in computer vision and machine learning. While the matrix rank is often approximated by the convex nuclear norm, the use of nonconvex low-rank regularizers has demonstrated better empirical performance. However, the resulting optimization problem is much more challenging. Recent state-of-the-art requires an expensive full SVD in each iteration. In this paper, we show that for many commonly-used nonconvex low-rank regularizers, a cutoff can be derived to automatically threshold the singular values obtained from the proximal operator. This allows such operator being efficiently approximated by power method. Based on it, we develop a proximal gradient algorithm (and its accelerated variant) with inexact proximal splitting and prove that a convergence rate of O(1/T) where T is the number of iterations is guaranteed. Furthermore, we show the proposed algorithm can be well parallelized, which achieves nearly linear speedup w.r.t the number of threads. Extensive experiments are performed on matrix completion and robust principal component analysis, which shows a significant speedup over the state-of-the-art. Moreover, the matrix solution obtained is more accurate and has a lower rank than that of the nuclear norm regularizer.

Qi Meng, Wei Chen, Jingcheng Yu et al.

Regularized empirical risk minimization (R-ERM) is an important branch of machine learning, since it constrains the capacity of the hypothesis space and guarantees the generalization ability of the learning algorithm. Two classic proximal optimization algorithms, i.e., proximal stochastic gradient descent (ProxSGD) and proximal stochastic coordinate descent (ProxSCD) have been widely used to solve the R-ERM problem. Recently, variance reduction technique was proposed to improve ProxSGD and ProxSCD, and the corresponding ProxSVRG and ProxSVRCD have better convergence rate. These proximal algorithms with variance reduction technique have also achieved great success in applications at small and moderate scales. However, in order to solve large-scale R-ERM problems and make more practical impacts, the parallel version of these algorithms are sorely needed. In this paper, we propose asynchronous ProxSVRG (Async-ProxSVRG) and asynchronous ProxSVRCD (Async-ProxSVRCD) algorithms, and prove that Async-ProxSVRG can achieve near linear speedup when the training data is sparse, while Async-ProxSVRCD can achieve near linear speedup regardless of the sparse condition, as long as the number of block partitions are appropriately set. We have conducted experiments on a regularized logistic regression task. The results verified our theoretical findings and demonstrated the practical efficiency of the asynchronous stochastic proximal algorithms with variance reduction.

Shuxin Zheng, Qi Meng, Taifeng Wang et al.

With the fast development of deep learning, it has become common to learn big neural networks using massive training data. Asynchronous Stochastic Gradient Descent (ASGD) is widely adopted to fulfill this task for its efficiency, which is, however, known to suffer from the problem of delayed gradients. That is, when a local worker adds its gradient to the global model, the global model may have been updated by other workers and this gradient becomes "delayed". We propose a novel technology to compensate this delay, so as to make the optimization behavior of ASGD closer to that of sequential SGD. This is achieved by leveraging Taylor expansion of the gradient function and efficient approximation to the Hessian matrix of the loss function. We call the new algorithm Delay Compensated ASGD (DC-ASGD). We evaluated the proposed algorithm on CIFAR-10 and ImageNet datasets, and the experimental results demonstrate that DC-ASGD outperforms both synchronous SGD and asynchronous SGD, and nearly approaches the performance of sequential SGD.

Yuyu Zhang, Hanjun Dai, Chang Xu et al.

Click prediction is one of the fundamental problems in sponsored search. Most of existing studies took advantage of machine learning approaches to predict ad click for each event of ad view independently. However, as observed in the real-world sponsored search system, user's behaviors on ads yield high dependency on how the user behaved along with the past time, especially in terms of what queries she submitted, what ads she clicked or ignored, and how long she spent on the landing pages of clicked ads, etc. Inspired by these observations, we introduce a novel framework based on Recurrent Neural Networks (RNN). Compared to traditional methods, this framework directly models the dependency on user's sequential behaviors into the click prediction process through the recurrent structure in RNN. Large scale evaluations on the click-through logs from a commercial search engine demonstrate that our approach can significantly improve the click prediction accuracy, compared to sequence-independent approaches.