Revisiting Language Encoding in Learning Multilingual Representations

Transformer has demonstrated its great power to learn contextual word representations for multiple languages in a single model. To process multilingual sentences in the model, a learnable vector is usually assigned to each language, which is called "language embedding". The language embedding can be either added to the word embedding or attached at the beginning of the sentence. It serves as a language-specific signal for the Transformer to capture contextual representations across languages. In this paper, we revisit the use of language embedding and identify several problems in the existing formulations. By investigating the interaction between language embedding and word embedding in the self-attention module, we find that the current methods cannot reflect the language-specific word correlation well. Given these findings, we propose a new approach called Cross-lingual Language Projection (XLP) to replace language embedding. For a sentence, XLP projects the word embeddings into language-specific semantic space, and then the projected embeddings will be fed into the Transformer model to process with their language-specific meanings. In such a way, XLP achieves the purpose of appropriately encoding "language" in a multilingual Transformer model. Experimental results show that XLP can freely and significantly boost the model performance on extensive multilingual benchmark datasets. Codes and models will be released at https://github.com/lsj2408/XLP.

Towards Certifying $\ell_\infty$ Robustness using Neural Networks with $\ell_\infty$-dist Neurons

It is well-known that standard neural networks, even with a high classification accuracy, are vulnerable to small $\ell_\infty$-norm bounded adversarial perturbations. Although many attempts have been made, most previous works either can only provide empirical verification of the defense to a particular attack method, or can only develop a certified guarantee of the model robustness in limited scenarios. In this paper, we seek for a new approach to develop a theoretically principled neural network that inherently resists $\ell_\infty$ perturbations. In particular, we design a novel neuron that uses $\ell_\infty$-distance as its basic operation (which we call $\ell_\infty$-dist neuron), and show that any neural network constructed with $\ell_\infty$-dist neurons (called $\ell_{\infty}$-dist net) is naturally a 1-Lipschitz function with respect to $\ell_\infty$-norm. This directly provides a rigorous guarantee of the certified robustness based on the margin of prediction outputs. We also prove that such networks have enough expressive power to approximate any 1-Lipschitz function with robust generalization guarantee. Our experimental results show that the proposed network is promising. Using $\ell_{\infty}$-dist nets as the basic building blocks, we consistently achieve state-of-the-art performance on commonly used datasets: 93.09% certified accuracy on MNIST ($\epsilon=0.3$), 79.23% on Fashion MNIST ($\epsilon=0.1$) and 35.10% on CIFAR-10 ($\epsilon=8/255$).

CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics

Accurate and robust prediction of patient's response to drug treatments is critical for developing precision medicine. However, it is often difficult to obtain a sufficient amount of coherent drug response data from patients directly for training a generalized machine learning model. Although the utilization of rich cell line data provides an alternative solution, it is challenging to transfer the knowledge obtained from cell lines to patients due to various confounding factors. Few existing transfer learning methods can reliably disentangle common intrinsic biological signals from confounding factors in the cell line and patient data. In this paper, we develop a Coherent Deconfounding Autoencoder (CODE-AE) that can extract both common biological signals shared by incoherent samples and private representations unique to each data set, transfer knowledge learned from cell line data to tissue data, and separate confounding factors from them. Extensive studies on multiple data sets demonstrate that CODE-AE significantly improves the accuracy and robustness over state-of-the-art methods in both predicting patient drug response and de-confounding biological signals. Thus, CODE-AE provides a useful framework to take advantage of in vitro omics data for developing generalized patient predictive models. The source code is available at https://github.com/XieResearchGroup/CODE-AE.

A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine

An unsolved fundamental problem in biology and ecology is to predict observable traits (phenotypes) from a new genetic constitution (genotype) of an organism under environmental perturbations (e.g., drug treatment). The emergence of multiple omics data provides new opportunities but imposes great challenges in the predictive modeling of genotype-phenotype associations. Firstly, the high-dimensionality of genomics data and the lack of labeled data often make the existing supervised learning techniques less successful. Secondly, it is a challenging task to integrate heterogeneous omics data from different resources. Finally, the information transmission from DNA to phenotype involves multiple intermediate levels of RNA, protein, metabolite, etc. The higher-level features (e.g., gene expression) usually have stronger discriminative power than the lower level features (e.g., somatic mutation). To address above issues, we proposed a novel Cross-LEvel Information Transmission network (CLEIT) framework. CLEIT aims to explicitly model the asymmetrical multi-level organization of the biological system. Inspired by domain adaptation, CLEIT first learns the latent representation of high-level domain then uses it as ground-truth embedding to improve the representation learning of the low-level domain in the form of contrastive loss. In addition, we adopt a pre-training-fine-tuning approach to leveraging the unlabeled heterogeneous omics data to improve the generalizability of CLEIT. We demonstrate the effectiveness and performance boost of CLEIT in predicting anti-cancer drug sensitivity from somatic mutations via the assistance of gene expressions when compared with state-of-the-art methods.

GraphNorm: A Principled Approach to Accelerating Graph Neural Network Training

Normalization plays an important role in the optimization of deep neural networks. While there are standard normalization methods in computer vision and natural language processing, there is limited understanding of how to effectively normalize neural networks for graph representation learning. In this paper, we propose a principled normalization method, Graph Normalization (GraphNorm), where the key idea is to normalize the feature values across all nodes for each individual graph with a learnable shift. Theoretically, we show that GraphNorm serves as a preconditioner that smooths the distribution of the graph aggregation's spectrum, leading to faster optimization. Such an improvement cannot be well obtained if we use currently popular normalization methods, such as BatchNorm, which normalizes the nodes in a batch rather than in individual graphs, due to heavy batch noises. Moreover, we show that for some highly regular graphs, the mean of the feature values contains graph structural information, and directly subtracting the mean may lead to an expressiveness degradation. The learnable shift in GraphNorm enables the model to learn to avoid such degradation for those cases. Empirically, Graph neural networks (GNNs) with GraphNorm converge much faster compared to GNNs with other normalization methods, e.g., BatchNorm. GraphNorm also improves generalization of GNNs, achieving better performance on graph classification benchmarks.

Variance-reduced Language Pretraining via a Mask Proposal Network

Self-supervised learning, a.k.a., pretraining, is important in natural language processing. Most of the pretraining methods first randomly mask some positions in a sentence and then train a model to recover the tokens at the masked positions. In such a way, the model can be trained without human labeling, and the massive data can be used with billion parameters. Therefore, the optimization efficiency becomes critical. In this paper, we tackle the problem from the view of gradient variance reduction. In particular, we first propose a principled gradient variance decomposition theorem, which shows that the variance of the stochastic gradient of the language pretraining can be naturally decomposed into two terms: the variance that arises from the sample of data in a batch, and the variance that arises from the sampling of the mask. The second term is the key difference between selfsupervised learning and supervised learning, which makes the pretraining slower. In order to reduce the variance of the second part, we leverage the importance sampling strategy, which aims at sampling the masks according to a proposal distribution instead of the uniform distribution. It can be shown that if the proposal distribution is proportional to the gradient norm, the variance of the sampling is reduced. To improve efficiency, we introduced a MAsk Proposal Network (MAPNet), which approximates the optimal mask proposal distribution and is trained end-to-end along with the model. According to the experimental result, our model converges much faster and achieves higher performance than the baseline BERT model.

Taking Notes on the Fly Helps BERT Pre-training

How to make unsupervised language pre-training more efficient and less resource-intensive is an important research direction in NLP. In this paper, we focus on improving the efficiency of language pre-training methods through providing better data utilization. It is well-known that in language data corpus, words follow a heavy-tail distribution. A large proportion of words appear only very few times and the embeddings of rare words are usually poorly optimized. We argue that such embeddings carry inadequate semantic signals. They could make the data utilization inefficient and slow down the pre-training of the entire model. To solve this problem, we propose Taking Notes on the Fly (TNF). TNF takes notes for rare words on the fly during pre-training to help the model understand them when they occur next time. Specifically, TNF maintains a note dictionary and saves a rare word's context information in it as notes when the rare word occurs in a sentence. When the same rare word occurs again in training, TNF employs the note information saved beforehand to enhance the semantics of the current sentence. By doing so, TNF provides a better data utilization since cross-sentence information is employed to cover the inadequate semantics caused by rare words in the sentences. Experimental results show that TNF significantly expedite the BERT pre-training and improve the model's performance on downstream tasks. TNF's training time is $60\%$ less than BERT when reaching the same performance. When trained with same number of iterations, TNF significantly outperforms BERT on most of downstream tasks and the average GLUE score.

Transferred Discrepancy: Quantifying the Difference Between Representations

Understanding what information neural networks capture is an essential problem in deep learning, and studying whether different models capture similar features is an initial step to achieve this goal. Previous works sought to define metrics over the feature matrices to measure the difference between two models. However, different metrics sometimes lead to contradictory conclusions, and there has been no consensus on which metric is suitable to use in practice. In this work, we propose a novel metric that goes beyond previous approaches. Recall that one of the most practical scenarios of using the learned representations is to apply them to downstream tasks. We argue that we should design the metric based on a similar principle. For that, we introduce the transferred discrepancy (TD), a new metric that defines the difference between two representations based on their downstream-task performance. Through an asymptotic analysis, we show how TD correlates with downstream tasks and the necessity to define metrics in such a task-dependent fashion. In particular, we also show that under specific conditions, the TD metric is closely related to previous metrics. Our experiments show that TD can provide fine-grained information for varied downstream tasks, and for the models trained from different initializations, the learned features are not the same in terms of downstream-task predictions. We find that TD may also be used to evaluate the effectiveness of different training strategies. For example, we demonstrate that the models trained with proper data augmentations that improve the generalization capture more similar features in terms of TD, while those with data augmentations that hurt the generalization will not. This suggests a training strategy that leads to more robust representation also trains models that generalize better.

Rethinking Positional Encoding in Language Pre-training

How to explicitly encode positional information into neural networks is important in learning the representation of natural languages, such as BERT. Based on the Transformer architecture, the positional information is simply encoded as embedding vectors, which are used in the input layer, or encoded as a bias term in the self-attention module. In this work, we investigate the problems in the previous formulations and propose a new positional encoding method for BERT called Transformer with Untied Positional Encoding (TUPE). Different from all other works, TUPE only uses the word embedding as input. In the self-attention module, the word contextual correlation and positional correlation are computed separately with different parameterizations and then added together. This design removes the addition over heterogeneous embeddings in the input, which may potentially bring randomness, and gives more expressiveness to characterize the relationship between words/positions by using different projection matrices. Furthermore, TUPE unties the [CLS] symbol from other positions to provide it with a more specific role to capture the global representation of the sentence. Extensive experiments and ablation studies on GLUE benchmark demonstrate the effectiveness and efficiency of the proposed method: TUPE outperforms several baselines on almost all tasks by a large margin. In particular, it can achieve a higher score than baselines while only using 30% pre-training computational costs. We release our code at https://github.com/guolinke/TUPE.