Jinhua Zhu

Qizhi Pei, Lijun Wu, Zhenyu He et al.

Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain suboptimal. In this work, inspired by the recent success of retrieval methods, we propose $k$NN-DTA, a non-parametric embedding-based retrieval method adopted on a pre-trained DTA prediction model, which can extend the power of the DTA model with no or negligible cost. Different from existing methods, we introduce two neighbor aggregation ways from both embedding space and label space that are integrated into a unified framework. Specifically, we propose a \emph{label aggregation} with \emph{pair-wise retrieval} and a \emph{representation aggregation} with \emph{point-wise retrieval} of the nearest neighbors. This method executes in the inference phase and can efficiently boost the DTA prediction performance with no training cost. In addition, we propose an extension, Ada-$k$NN-DTA, an instance-wise and adaptive aggregation with lightweight learning. Results on four benchmark datasets show that $k$NN-DTA brings significant improvements, outperforming previous state-of-the-art (SOTA) results, e.g, on BindingDB IC$_{50}$ and $K_i$ testbeds, $k$NN-DTA obtains new records of RMSE $\bf{0.684}$ and $\bf{0.750}$. The extended Ada-$k$NN-DTA further improves the performance to be $\bf{0.675}$ and $\bf{0.735}$ RMSE. These results strongly prove the effectiveness of our method. Results in other settings and comprehensive studies/analyses also show the great potential of our $k$NN-DTA approach.

Qizhi Pei, Lijun Wu, Kaiyuan Gao et al.

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 \emph{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 \url{https://github.com/QizhiPei/BioT5}.

Jinhua Zhu, Yingce Xia, Lijun Wu et al.

The recently proposed BERT has shown great power on a variety of natural language understanding tasks, such as text classification, reading comprehension, etc. However, how to effectively apply BERT to neural machine translation (NMT) lacks enough exploration. While BERT is more commonly used as fine-tuning instead of contextual embedding for downstream language understanding tasks, in NMT, our preliminary exploration of using BERT as contextual embedding is better than using for fine-tuning. This motivates us to think how to better leverage BERT for NMT along this direction. We propose a new algorithm named BERT-fused model, in which we first use BERT to extract representations for an input sequence, and then the representations are fused with each layer of the encoder and decoder of the NMT model through attention mechanisms. We conduct experiments on supervised (including sentence-level and document-level translations), semi-supervised and unsupervised machine translation, and achieve state-of-the-art results on seven benchmark datasets. Our code is available at \url{https://github.com/bert-nmt/bert-nmt}.

Ruopei Sun, Jianfeng Cai, Jinhua Zhu et al.

RLHF has emerged as a predominant approach for aligning artificial intelligence systems with human preferences, demonstrating exceptional and measurable efficacy in instruction following tasks; however, it exhibits insufficient compliance capabilities when confronted with complex multi-instruction tasks. Conventional approaches rely heavily on human annotation or more sophisticated large language models, thereby introducing substantial resource expenditure or potential bias concerns. Meanwhile, alternative synthetic methods that augment standard preference datasets often compromise the model's semantic quality. Our research identifies a critical oversight in existing techniques, which predominantly focus on comparing responses while neglecting valuable latent signals embedded within prompt inputs, and which only focus on preference disparities at the intra-sample level, while neglecting to account for the inter-sample level preference differentials that exist among preference data. To leverage these previously neglected indicators, we propose a novel Multi-level Aware Preference Learning (MAPL) framework, capable of enhancing multi-instruction capabilities. Specifically, for any given response in original preference data pairs, we construct varied prompts with a preference relation under different conditions, in order to learn intra-sample level preference disparities. Furthermore, for any given original preference pair, we synthesize multi-instruction preference pairs to capture preference discrepancies at the inter-sample level. Building on the two datasets constructed above, we consequently devise two sophisticated training objective functions. Subsequently, our framework integrates seamlessly into both Reward Modeling and Direct Preference Optimization paradigms. Through rigorous evaluation across multiple benchmarks, we empirically validate the efficacy of our framework.

Jinhua Zhu, Javier Conde, Zhen Gao et al.

The wide adoption of Large language models (LLMs) makes their dependability a pressing concern. Detection of errors is the first step to mitigating their impact on a system and thus, efficient error detection for LLMs is an important issue. In many settings, the LLM is considered as a black box with no access to the internal nodes; this prevents the use of many error detection schemes that need access to the model's internal nodes. An interesting observation is that the output of LLMs in error-free operation should be valid and normal text. Therefore, when the text is not valid or differs significantly from normal text, it is likely that there is an error. Based on this observation we propose to perform Concurrent Linguistic Error Detection (CLED); this scheme extracts some linguistic features of the text generated by the LLM and feeds them to a concurrent classifier that detects errors. Since the proposed error detection mechanism only relies on the outputs of the model, then it can be used on LLMs in which there is no access to the internal nodes. The proposed CLED scheme has been evaluated on the T5 model when used for news summarization and on the OPUS-MT model when used for translation. In both cases, the same set of linguistic features has been used for error detection to illustrate the applicability of the proposed scheme beyond a specific case. The results show that CLED can detect most of the errors at a low overhead penalty. The use of the concurrent classifier also enables a trade-off between error detection effectiveness and its associated overhead, so providing flexibility to a designer.

Jinhua Zhu, Yingce Xia, Tao Qin et al.

Inspired by its success in natural language processing and computer vision, pre-training has attracted substantial attention in cheminformatics and bioinformatics, especially for molecule based tasks. A molecule can be represented by either a graph (where atoms are connected by bonds) or a SMILES sequence (where depth-first-search is applied to the molecular graph with specific rules). Existing works on molecule pre-training use either graph representations only or SMILES representations only. In this work, we propose to leverage both the representations and design a new pre-training algorithm, dual-view molecule pre-training (briefly, DMP), that can effectively combine the strengths of both types of molecule representations. The model of DMP consists of two branches: a Transformer branch that takes the SMILES sequence of a molecule as input, and a GNN branch that takes a molecular graph as input. The training of DMP contains three tasks: (1) predicting masked tokens in a SMILES sequence by the Transformer branch, (2) predicting masked atoms in a molecular graph by the GNN branch, and (3) maximizing the consistency between the two high-level representations output by the Transformer and GNN branches separately. After pre-training, we can use either the Transformer branch (this one is recommended according to empirical results), the GNN branch, or both for downstream tasks. DMP is tested on nine molecular property prediction tasks and achieves state-of-the-art performances on seven of them. Furthermore, we test DMP on three retrosynthesis tasks and achieve state-of-the-art results on them.

Jinhua Zhu, Lijun Wu, Yingce Xia et al.

With sequentially stacked self-attention, (optional) encoder-decoder attention, and feed-forward layers, Transformer achieves big success in natural language processing (NLP), and many variants have been proposed. Currently, almost all these models assume that the layer order is fixed and kept the same across data samples. We observe that different data samples actually favor different orders of the layers. Based on this observation, in this work, we break the assumption of the fixed layer order in the Transformer and introduce instance-wise layer reordering into the model structure. Our Instance-wise Ordered Transformer (IOT) can model variant functions by reordered layers, which enables each sample to select the better one to improve the model performance under the constraint of almost the same number of parameters. To achieve this, we introduce a light predictor with negligible parameter and inference cost to decide the most capable and favorable layer order for any input sequence. Experiments on 3 tasks (neural machine translation, abstractive summarization, and code generation) and 9 datasets demonstrate consistent improvements of our method. We further show that our method can also be applied to other architectures beyond Transformer. Our code is released at Github.

Guoqing Liu, Chuheng Zhang, Li Zhao et al.

Recently, various auxiliary tasks have been proposed to accelerate representation learning and improve sample efficiency in deep reinforcement learning (RL). However, existing auxiliary tasks do not take the characteristics of RL problems into consideration and are unsupervised. By leveraging returns, the most important feedback signals in RL, we propose a novel auxiliary task that forces the learnt representations to discriminate state-action pairs with different returns. Our auxiliary loss is theoretically justified to learn representations that capture the structure of a new form of state-action abstraction, under which state-action pairs with similar return distributions are aggregated together. In low data regime, our algorithm outperforms strong baselines on complex tasks in Atari games and DeepMind Control suite, and achieves even better performance when combined with existing auxiliary tasks.

Yingce Xia, Xu Tan, Fei Tian et al.

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).

Jinhua Zhu, Fei Gao, Lijun Wu et al.

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 datasets demonstrate the superiority of our method over strong baselines.