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.

In this paper, we define a widely neglected property in dialogue text, duality, which is a hierarchical property that is reflected in human behaviours in daily conversations: Based on the logic in a conversation (or a sentence), people can infer follow-up utterances (or tokens) based on the previous text, and vice versa. We propose a hierarchical duality learning for dialogue (HDLD) to simulate this human cognitive ability, for generating high quality responses that connect both previous and follow-up dialogues. HDLD utilizes hierarchical dualities at token hierarchy and utterance hierarchy. HDLD maximizes the mutual information between past and future utterances. Thus, even if future text is invisible during inference, HDLD is capable of estimating future information implicitly based on dialogue history and generates both coherent and informative responses. In contrast to previous approaches that solely utilize future text as auxiliary information to encode during training, HDLD leverages duality to enable interaction between dialogue history and the future. This enhances the utilization of dialogue data, leading to the improvement in both automatic and human evaluation.

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.

While Neural Machine Translation (NMT) has achieved great progress in recent years, it still suffers from inaccurate translation of entities (e.g., person/organization name, location), due to the lack of entity training instances. When we humans encounter an unknown entity during translation, we usually first look up in a dictionary and then organize the entity translation together with the translations of other parts to form a smooth target sentence. Inspired by this translation process, we propose an Extract-and-Attend approach to enhance entity translation in NMT, where the translation candidates of source entities are first extracted from a dictionary and then attended to by the NMT model to generate the target sentence. Specifically, the translation candidates are extracted by first detecting the entities in a source sentence and then translating the entities through looking up in a dictionary. Then, the extracted candidates are added as a prefix of the decoder input to be attended to by the decoder when generating the target sentence through self-attention. Experiments conducted on En-Zh and En-Ru demonstrate that the proposed method is effective on improving both the translation accuracy of entities and the overall translation quality, with up to 35% reduction on entity error rate and 0.85 gain on BLEU and 13.8 gain on COMET.

Multilingual Neural Machine Translation (MNMT) enables one system to translate sentences from multiple source languages to multiple target languages, greatly reducing deployment costs compared with conventional bilingual systems. The MNMT training benefit, however, is often limited to many-to-one directions. The model suffers from poor performance in one-to-many and many-to-many with zero-shot setup. To address this issue, this paper discusses how to practically build MNMT systems that serve arbitrary X-Y translation directions while leveraging multilinguality with a two-stage training strategy of pretraining and finetuning. Experimenting with the WMT’21 multilingual translation task, we demonstrate that our systems outperform the conventional baselines of direct bilingual models and pivot translation models for most directions, averagely giving +6.0 and +4.1 BLEU, without the need for architecture change or extra data collection. Moreover, we also examine our proposed approach in an extremely large-scale data setting to accommodate practical deployment scenarios.

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.

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.