Contrastive learning has achieved impressive success in generation tasks to militate the "exposure bias" problem and discriminatively exploit the different quality of references. Existing works mostly focus on contrastive learning on the instance-level without discriminating the contribution of each word, while keywords are the gist of the text and dominant the constrained mapping relationships. Hence, in this work, we propose a hierarchical contrastive learning mechanism, which can unify hybrid granularities semantic meaning in the input text. Concretely, we first propose a keyword graph via contrastive correlations of positive-negative pairs to iteratively polish the keyword representations. Then, we construct intra-contrasts within instance-level and keyword-level, where we assume words are sampled nodes from a sentence distribution. Finally, to bridge the gap between independent contrast levels and tackle the common contrast vanishing problem, we propose an inter-contrast mechanism that measures the discrepancy between contrastive keyword nodes respectively to the instance distribution. Experiments demonstrate that our model outperforms competitive baselines on paraphrasing, dialogue generation, and storytelling tasks.

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$^\alpha$ (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.

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.

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.

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 improved expressiveness and low computational requirement. PairRE represents each relation with paired vectors, where these paired vectors project connected two entities to relation specific locations. Beyond its ability to solve the aforementioned two problems, PairRE is advantageous to represent subrelation as it can capture both the similarities and differences of subrelations effectively. Given simple constraints on relation representations, PairRE can be the first model that is capable of encoding symmetry/antisymmetry, inverse, composition and subrelation relations. Experiments on link prediction benchmarks show PairRE can achieve either state-of-the-art or highly competitive performances. In addition, PairRE has shown encouraging results for encoding subrelation.

Although NumNet achieves superior performance than Numerical reasoning over texts, such as addition, other numerically-aware models (Hu et al., 2019a; Andor subtraction, sorting and counting, is a et al., 2019; Geva et al., 2020; Chen et al., 2020), we challenging machine reading comprehension argue that NumNet is insufficient for sophisticated numerical task, since it requires both natural language understanding reasoning, since it lacks two critical ingredients and arithmetic computation. To for numerical reasoning: address this challenge, we propose a heterogeneous 1. Number Type and Entity Mention. The number graph representation for the context of comparison graph in NumNet is not able to identify the passage and question needed for such reasoning, different number types, and lacks the information of and design a question directed graph entities mentioned in the document that connect the attention network to drive multi-step numerical number nodes.

Gradient Boosting Decision Tree (GBDT) is a popular machine learning algorithm, and has quite a few effective implementations such as XGBoost and pGBRT. Although many engineering optimizations have been adopted in these implementations, the efficiency and scalability are still unsatisfactory when the feature dimension is high and data size is large. A major reason is that for each feature, they need to scan all the data instances to estimate the information gain of all possible split points, which is very time consuming. To tackle this problem, we propose two novel techniques: \emph{Gradient-based One-Side Sampling} (GOSS) and \emph{Exclusive Feature Bundling} (EFB). With GOSS, we exclude a significant proportion of data instances with small gradients, and only use the rest to estimate the information gain. We prove that, since the data instances with larger gradients play a more important role in the computation of information gain, GOSS can obtain quite accurate estimation of the information gain with a much smaller data size. With EFB, we bundle mutually exclusive features (i.e., they rarely take nonzero values simultaneously), to reduce the number of features. We prove that finding the optimal bundling of exclusive features is NP-hard, but a greedy algorithm can achieve quite good approximation ratio (and thus can effectively reduce the number of features without hurting the accuracy of split point determination by much). We call our new GBDT implementation with GOSS and EFB \emph{LightGBM}. Our experiments on multiple public datasets show that, LightGBM speeds up the training process of conventional GBDT by up to over 20 times while achieving almost the same accuracy.

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.

Many machine learning tasks can be formulated as Regularized Empirical Risk Minimization (R-ERM), and solved by optimization algorithms such as gradient descent (GD), stochastic gradient descent (SGD), and stochastic variance reduction (SVRG). Conventional analysis on these optimization algorithms focuses on their convergence rates during the training process, however, people in the machine learning community may care more about the generalization performance of the learned model on unseen test data. In this paper, we investigate on this issue, by using stability as a tool. In particular, we decompose the generalization error for R-ERM, and derive its upper bound for both convex and nonconvex cases. In convex cases, we prove that the generalization error can be bounded by the convergence rate of the optimization algorithm and the stability of the R-ERM process, both in expectation (in the order of 𝒪(1/ n )+ 𝔼ρ( T )), where ρ( T ) is the convergence error and T is the number of iterations) and in high probability (in the order of 𝒪(log{1/δ / √ n + ρ( T ) with probability 1 – δ). For nonconvex cases, we can also obtain a similar expected generalization error bound. Our theorems indicate that 1) along with the training process, the generalization error will decrease for all the optimization algorithms under our investigation; 2) Comparatively speaking, SVRG has better generalization ability than GD and SGD. We have conducted experiments on both convex and nonconvex problems, and the experimental results verify our theoretical findings.

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 versions 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.