xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data

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.

LogicMP: A Neuro-symbolic Approach for Encoding First-order Logic Constraints

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 Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning

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.

Keywords and Instances: A Hierarchical Contrastive Learning Framework Unifying Hybrid Granularities for Text Generation

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.

PIE: a Parameter and Inference Efficient Solution for Large Scale Knowledge Graph Embedding Reasoning

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.

PairRE: Knowledge Graph Embeddings via Paired Relation Vectors

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.

Question Directed Graph Attention Network for Numerical Reasoning over Text

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.

SpellGCN: Incorporating Phonological and Visual Similarities into Language Models for Chinese Spelling Check

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.