Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

Dense retrieval, which aims to encode the semantic information of arbitrary text into dense vector representations or embeddings, has emerged as an effective and efficient paradigm for text retrieval, consequently becoming an essential component in various natural language processing systems. These systems typically focus on optimizing the embedding space by attending to the relevance of text pairs, while overlooking the Boolean logic inherent in language, which may not be captured by current training objectives. In this work, we first investigate whether current retrieval systems can comprehend the Boolean logic implied in language. To answer this question, we formulate the task of Boolean Dense Retrieval and collect a benchmark dataset, BoolQuestions, which covers complex queries containing basic Boolean logic and corresponding annotated passages. Through extensive experimental results on the proposed task and benchmark dataset, we draw the conclusion that current dense retrieval systems do not fully understand Boolean logic in language, and there is a long way to go to improve our dense retrieval systems. Furthermore, to promote further research on enhancing the understanding of Boolean logic for language models, we explore Boolean operation on decomposed query and propose a contrastive continual training method that serves as a strong baseline for the research community.

This paper presents our enhanced BioT5+ method for the Language + Molecules shared task at the ACL 2024 Workshop. The task involves “translating” between molecules and natural language, including molecule captioning and text-based molecule generation using the L+M-24 dataset. Our method consists of three stages. In the first stage, we distill data from various models. In the second stage, combined with extra version of the provided dataset, we train diverse models for subsequent voting ensemble.We also adopt Transductive Ensemble Learning (TEL) to enhance these base models. Lastly, all models are integrated using a voting ensemble method. Experimental results demonstrate that BioT5+ achieves superior performance on L+M-24 dataset. On the final leaderboard, our method (team name: qizhipei) ranks first in the text-based molecule generation task and second in the molecule captioning task, highlighting its efficacy and robustness in translating between molecules and natural language. The pre-trained BioT5+ models are available at https://github.com/QizhiPei/BioT5.

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.

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.

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.

Neural machine translation, which achieves near human-level performance in some languages, strongly relies on the large amounts of parallel sentences, which hinders its applicability to low-resource language pairs. Recent works explore the possibility of unsupervised machine translation with monolingual data only, leading to much lower accuracy compared with the supervised one. Observing that weakly paired bilingual documents are much easier to collect than bilingual sentences, e.g., from Wikipedia, news websites or books, in this paper, we investigate training translation models with weakly paired bilingual documents. Our approach contains two components. 1) We provide a simple approach to mine implicitly bilingual sentence pairs from document pairs which can then be used as supervised training signals. 2) We leverage the topic consistency of two weakly paired documents and learn the sentence translation model by constraining the word distribution-level alignments. We evaluate our method on weakly paired documents from Wikipedia on six tasks, the widely used WMT16 German↔English, WMT13 Spanish↔English and WMT16 Romanian↔English translation tasks. We obtain 24.1/30.3, 28.1/27.6 and 30.1/27.6 BLEU points separately, outperforming previous results by more than 5 BLEU points in each direction and reducing the gap between unsupervised translation and supervised translation up to 50%.

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).