Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5.

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise–the disagreement between model and metric defined candidate rankings–minimized.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

Transformer architecture achieves great success in abundant natural language processing tasks. The over-parameterization of the Transformer model has motivated plenty of works to alleviate its overfitting for superior performances. With some explorations, we find simple techniques such as dropout, can greatly boost model performance with a careful design. Therefore, in this paper, we integrate different dropout techniques into the training of Transformer models. Specifically, we propose an approach named UniDrop to unites three different dropout techniques from fine-grain to coarse-grain, i.e., feature dropout, structure dropout, and data dropout. Theoretically, we demonstrate that these three dropouts play different roles from regularization perspectives. Empirically, we conduct experiments on both neural machine translation and text classification benchmark datasets. Extensive results indicate that Transformer with UniDrop can achieve around 1.5 BLEU improvement on IWSLT14 translation tasks, and better accuracy for the classification even using strong pre-trained RoBERTa as backbone.

Data augmentation, which refers to manipulating the inputs (e.g., adding random noise,masking specific parts) to enlarge the dataset,has been widely adopted in machine learning. Most data augmentation techniques operate on a single input, which limits the diversity of the training corpus. In this paper, we propose a simple yet effective data augmentation technique for neural machine translation, mixSeq, which operates on multiple inputs and their corresponding targets. Specifically, we randomly select two input sequences,concatenate them together as a longer input aswell as their corresponding target sequencesas an enlarged target, and train models on theaugmented dataset. Experiments on nine machine translation tasks demonstrate that such asimple method boosts the baselines by a non-trivial margin. Our method can be further combined with single input based data augmentation methods to obtain further improvements.

We Microsoft Research Asia made submissions to 11 language directions in the WMT19 news translation tasks. We won the first place for 8 of the 11 directions and the second place for the other three. Our basic systems are built on Transformer, back translation and knowledge distillation. We integrate several of our rececent techniques to enhance the baseline systems: multi-agent dual learning (MADL), masked sequence-to-sequence pre-training (MASS), neural architecture optimization (NAO), and soft contextual data augmentation (SCA).

Multilingual neural machine translation (NMT), which translates multiple languages using a single model, is of great practical importance due to its advantages in simplifying the training process, reducing online maintenance costs, and enhancing low-resource and zero-shot translation. Given there are thousands of languages in the world and some of them are very different, it is extremely burdensome to handle them all in a single model or use a separate model for each language pair. Therefore, given a fixed resource budget, e.g., the number of models, how to determine which languages should be supported by one model is critical to multilingual NMT, which, unfortunately, has been ignored by previous work. In this work, we develop a framework that clusters languages into different groups and trains one multilingual model for each cluster. We study two methods for language clustering: (1) using prior knowledge, where we cluster languages according to language family, and (2) using language embedding, in which we represent each language by an embedding vector and cluster them in the embedding space. In particular, we obtain the embedding vectors of all the languages by training a universal neural machine translation model. Our experiments on 23 languages show that the first clustering method is simple and easy to understand but leading to suboptimal translation accuracy, while the second method sufficiently captures the relationship among languages well and improves the translation accuracy for almost all the languages over baseline methods.

While target-side monolingual data has been proven to be very useful to improve neural machine translation (briefly, NMT) through back translation, source-side monolingual data is not well investigated. In this work, we study how to use both the source-side and target-side monolingual data for NMT, and propose an effective strategy leveraging both of them. First, we generate synthetic bitext by translating monolingual data from the two domains into the other domain using the models pretrained on genuine bitext. Next, a model is trained on a noised version of the concatenated synthetic bitext where each source sequence is randomly corrupted. Finally, the model is fine-tuned on the genuine bitext and a clean version of a subset of the synthetic bitext without adding any noise. Our approach achieves state-of-the-art results on WMT16, WMT17, WMT18 English↔German translations and WMT19 German→French translations, which demonstrate the effectiveness of our method. We also conduct a comprehensive study on how each part in the pipeline works.

While data augmentation is an important trick to boost the accuracy of deep learning methods in computer vision tasks, its study in natural language tasks is still very limited. In this paper, we present a novel data augmentation method for neural machine translation. Different from previous augmentation methods that randomly drop, swap or replace words with other words in a sentence, we softly augment a randomly chosen word in a sentence by its contextual mixture of multiple related words. More accurately, we replace the one-hot representation of a word by a distribution (provided by a language model) over the vocabulary, i.e., replacing the embedding of this word by a weighted combination of multiple semantically similar words. Since the weights of those words depend on the contextual information of the word to be replaced,the newly generated sentences capture much richer information than previous augmentation methods. Experimental results on both small scale and large scale machine translation data sets demonstrate the superiority of our method over strong baselines.

While very deep neural networks have shown effectiveness for computer vision and text classification applications, how to increase the network depth of the neural machine translation (NMT) models for better translation quality remains a challenging problem. Directly stacking more blocks to the NMT model results in no improvement and even drop in performance. In this work, we propose an effective two-stage approach with three specially designed components to construct deeper NMT models, which result in significant improvements over the strong Transformer baselines on WMT14 English→German and English→French translation tasks.