Danqing Wang

Danqing Wang, Zeyu Wen, Fei Ye et al. · cmu

Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and do not consider crucial structure information. In this paper, we propose a latent sequence-structure model for designing AMPs (LSSAMP). LSSAMP exploits multi-scale vector quantization in the latent space to represent secondary structures (e.g. alpha helix and beta sheet). By sampling in the latent space, LSSAMP can simultaneously generate peptides with ideal sequence attributes and secondary structures. Experimental results show that the peptides generated by LSSAMP have a high probability of antimicrobial activity. Our wet laboratory experiments verified that two of the 21 candidates exhibit strong antimicrobial activity. The code is released at https://github.com/dqwang122/LSSAMP.

Danqing Wang, Kevin Yang, Hanlin Zhu et al. · cmu

Recent research has increasingly focused on evaluating large language models' (LLMs) alignment with diverse human values and preferences, particularly for open-ended tasks like story generation. Traditional evaluation metrics rely heavily on lexical similarity with human-written references, often showing poor correlation with human judgments and failing to account for alignment with the diversity of human preferences. To address these challenges, we introduce PerSE, an interpretable evaluation framework designed to assess alignment with specific human preferences. It is tuned to infer specific preferences from an in-context personal profile and evaluate the alignment between the generated content and personal preferences. PerSE enhances interpretability by providing detailed comments and fine-grained scoring, facilitating more personalized content generation. Our 13B LLaMA-2-based PerSE shows a 15.8% increase in Kendall correlation and a 13.7% rise in accuracy with zero-shot reviewers compared to GPT-4. It also outperforms GPT-4 by 46.01% in Kendall correlation on new domains, indicating its transferability.

Danqing Wang, Fei Ye, Hao Zhou

Antibodies are vital proteins offering robust protection for the human body from pathogens. The development of general protein and antibody-specific pre-trained language models both facilitate antibody prediction tasks. However, there have been limited studies that comprehensively explore the representation capability of distinct pre-trained language models on different antibody tasks. To investigate the problem, we aim to answer several key questions in this paper, such as how pre-trained language models perform in antibody tasks with different specificity and how introducing specific biological mechanisms to the pre-training process can benefit the model. Additionally, we evaluate if the learned antibody pre-trained representations can be applied to real-world antibody problems, like drug discovery and immune process understanding. Previously, no benchmark available largely hindered the study to answer these questions. To aid in our investigation, we provide an AnTibody Understanding Evaluation (ATUE) benchmark. We comprehensively evaluate the performance of protein pre-trained language models by empirical study along with conclusions and new insights. Our ATUE and code are released at https://github.com/dqwang122/EATLM.

Songwen Zhao, Danqing Wang, Kexun Zhang et al.

Vibe coding is a new programming paradigm in which human engineers instruct large language model (LLM) agents to complete complex coding tasks with little supervision. Although it is increasingly adopted, are vibe coding outputs really safe to deploy in production? To answer this question, we propose SU S VI B E S, a benchmark consisting of 200 feature-request software engineering tasks from real-world open-source projects, which, when given to human programmers, led to vulnerable implementations. We evaluate multiple widely used coding agents with frontier models on this benchmark. Disturbingly, all agents perform poorly in terms of software security. Although 61% of the solutions from SWE-Agent with Claude 4 Sonnet are functionally correct, only 10.5% are secure. Further experiments demonstrate that preliminary security strategies, such as augmenting the feature request with vulnerability hints, cannot mitigate these security issues. Our findings raise serious concerns about the widespread adoption of vibe-coding, particularly in security-sensitive applications.

Hanlin Zhu, Andrew Cohen, Danqing Wang et al.

Story plots, while short, carry most of the essential information of a full story that may contain tens of thousands of words. We study the problem of automatic generation of story plots, which includes story premise, character descriptions, plot outlines, etc. To generate a single engaging plot, existing plot generators (e.g., DOC (Yang et al., 2022a)) require hundreds to thousands of calls to LLMs (e.g., OpenAI API) in the planning stage of the story plot, which is costly and takes at least several minutes. Moreover, the hard-wired nature of the method makes the pipeline non-differentiable, blocking fast specialization and personalization of the plot generator. In this paper, we propose three models, $\texttt{OpenPlot}$, $\texttt{E2EPlot}$ and $\texttt{RLPlot}$, to address these challenges. $\texttt{OpenPlot}$ replaces expensive OpenAI API calls with LLaMA2 (Touvron et al., 2023) calls via careful prompt designs, which leads to inexpensive generation of high-quality training datasets of story plots. We then train an end-to-end story plot generator, $\texttt{E2EPlot}$, by supervised fine-tuning (SFT) using approximately 13000 story plots generated by $\texttt{OpenPlot}$. $\texttt{E2EPlot}$ generates story plots of comparable quality to $\texttt{OpenPlot}$, and is > 10$\times$ faster (1k tokens in only 30 seconds on average). Finally, we obtain $\texttt{RLPlot}$ that is further fine-tuned with RLHF on several different reward models for different aspects of story quality, which yields 60.0$\%$ winning rate against $\texttt{E2EPlot}$ along the aspect of suspense and surprise.

Danqing Wang, Antonis Antoniades, Kha-Dinh Luong et al.

Counterfactual explanations of Graph Neural Networks (GNNs) offer a powerful way to understand data that can naturally be represented by a graph structure. Furthermore, in many domains, it is highly desirable to derive data-driven global explanations or rules that can better explain the high-level properties of the models and data in question. However, evaluating global counterfactual explanations is hard in real-world datasets due to a lack of human-annotated ground truth, which limits their use in areas like molecular sciences. Additionally, the increasing scale of these datasets provides a challenge for random search-based methods. In this paper, we develop a novel global explanation model RLHEX for molecular property prediction. It aligns the counterfactual explanations with human-defined principles, making the explanations more interpretable and easy for experts to evaluate. RLHEX includes a VAE-based graph generator to generate global explanations and an adapter to adjust the latent representation space to human-defined principles. Optimized by Proximal Policy Optimization (PPO), the global explanations produced by RLHEX cover 4.12% more input graphs and reduce the distance between the counterfactual explanation set and the input set by 0.47% on average across three molecular datasets. RLHEX provides a flexible framework to incorporate different human-designed principles into the counterfactual explanation generation process, aligning these explanations with domain expertise. The code and data are released at https://github.com/dqwang122/RLHEX.

Yiran Chen, Zhenqiao Song, Xianze Wu et al.

We introduce MTG, a new benchmark suite for training and evaluating multilingual text generation. It is the first-proposed multilingual multiway text generation dataset with the largest human-annotated data (400k). It includes four generation tasks (story generation, question generation, title generation and text summarization) across five languages (English, German, French, Spanish and Chinese). The multiway setup enables testing knowledge transfer capabilities for a model across languages and tasks. Using MTG, we train and analyze several popular multilingual generation models from different aspects. Our benchmark suite fosters model performance enhancement with more human-annotated parallel data. It provides comprehensive evaluations with diverse generation scenarios. Code and data are available at \url{https://github.com/zide05/MTG}.

Yiran Chen, Pengfei Liu, Ming Zhong et al.

Neural network-based models augmented with unsupervised pre-trained knowledge have achieved impressive performance on text summarization. However, most existing evaluation methods are limited to an in-domain setting, where summarizers are trained and evaluated on the same dataset. We argue that this approach can narrow our understanding of the generalization ability for different summarization systems. In this paper, we perform an in-depth analysis of characteristics of different datasets and investigate the performance of different summarization models under a cross-dataset setting, in which a summarizer trained on one corpus will be evaluated on a range of out-of-domain corpora. A comprehensive study of 11 representative summarization systems on 5 datasets from different domains reveals the effect of model architectures and generation ways (i.e. abstractive and extractive) on model generalization ability. Further, experimental results shed light on the limitations of existing summarizers. Brief introduction and supplementary code can be found in https://github.com/zide05/CDEvalSumm.

Ming Zhong, Pengfei Liu, Yiran Chen et al.

This paper creates a paradigm shift with regard to the way we build neural extractive summarization systems. Instead of following the commonly used framework of extracting sentences individually and modeling the relationship between sentences, we formulate the extractive summarization task as a semantic text matching problem, in which a source document and candidate summaries will be (extracted from the original text) matched in a semantic space. Notably, this paradigm shift to semantic matching framework is well-grounded in our comprehensive analysis of the inherent gap between sentence-level and summary-level extractors based on the property of the dataset. Besides, even instantiating the framework with a simple form of a matching model, we have driven the state-of-the-art extractive result on CNN/DailyMail to a new level (44.41 in ROUGE-1). Experiments on the other five datasets also show the effectiveness of the matching framework. We believe the power of this matching-based summarization framework has not been fully exploited. To encourage more instantiations in the future, we have released our codes, processed dataset, as well as generated summaries in https://github.com/maszhongming/MatchSum.

Wenda Xu, Danqing Wang, Liangming Pan et al.

Automatically evaluating the quality of language generation is critical. Although recent learned metrics show high correlation with human judgement, these metrics can not explain their verdict or associate the scores with defects in generated text. To address this limitation, we present InstructScore, an explainable evaluation metric for text generation. By harnessing both explicit human instruction and the implicit knowledge of GPT-4, we fine-tune a text evaluation metric based on LLaMA, producing both a score for generated text and a human readable diagnostic report. We evaluate InstructScore on a variety of generation tasks, including translation, captioning, data-to-text and commonsense generation. Experiments show that our 7B model surpasses all other unsupervised metrics, including those based on 175B GPT-3 and GPT-4. Surprisingly, our InstructScore, even without direct supervision from human-rated data, achieves performance levels on par with state-of-the-art metrics like COMET22, which were fine-tuned on human ratings.

Danqing Wang, Lei Li

Large language models (LLMs) have demonstrated their potential to refine their generation based on their own feedback. However, the feedback from LLM itself is often inaccurate, thereby limiting its benefits. In this paper, we propose Study Assistant for Large LAnguage Model (SALAM), a novel framework with an auxiliary agent to assist the main LLM in learning from mistakes through interactive cooperation. In the gathering phase, the student assistant agent probes the main LLM, analyzes its errors, and collects the interaction in a mistake memory. During the examination phase, the study assistant provides guidelines by retrieving relevant cases to help the main LLM anticipate and avoid similar errors. We first investigate the effectiveness of a general study assistant and then customize it to provide LLM-specific guidance through imitation learning from successful guidance experiences. Our experiments on three LLMs using two challenging frameworks demonstrate that SALAM can significantly boost LLMs by an accuracy margin of up to 6.6 on BBH and 12.6 on BBQ.

Danqing Wang, Jiaze Chen, Xianze Wu et al.

Automatic text summarization aims to produce a brief but crucial summary for the input documents. Both extractive and abstractive methods have witnessed great success in English datasets in recent years. However, there has been a minimal exploration of text summarization in Chinese, limited by the lack of large-scale datasets. In this paper, we present a large-scale Chinese news summarization dataset CNewSum, which consists of 304,307 documents and human-written summaries for the news feed. It has long documents with high-abstractive summaries, which can encourage document-level understanding and generation for current summarization models. An additional distinguishing feature of CNewSum is that its test set contains adequacy and deducibility annotations for the summaries. The adequacy level measures the degree of summary information covered by the document, and the deducibility indicates the reasoning ability the model needs to generate the summary. These annotations can help researchers analyze and target their model performance bottleneck. We examine recent methods on CNewSum and release our dataset to provide a solid testbed for automatic Chinese summarization research.

Chenxin An, Ming Zhong, Yiran Chen et al.

Previous work for text summarization in scientific domain mainly focused on the content of the input document, but seldom considering its citation network. However, scientific papers are full of uncommon domain-specific terms, making it almost impossible for the model to understand its true meaning without the help of the relevant research community. In this paper, we redefine the task of scientific papers summarization by utilizing their citation graph and propose a citation graph-based summarization model CGSum which can incorporate the information of both the source paper and its references. In addition, we construct a novel scientific papers summarization dataset Semantic Scholar Network (SSN) which contains 141K research papers in different domains and 661K citation relationships. The entire dataset constitutes a large connected citation graph. Extensive experiments show that our model can achieve competitive performance when compared with the pretrained models even with a simple architecture. The results also indicates the citation graph is crucial to better understand the content of papers and generate high-quality summaries.

Danqing Wang, Pengfei Liu, Yining Zheng et al.

As a crucial step in extractive document summarization, learning cross-sentence relations has been explored by a plethora of approaches. An intuitive way is to put them in the graph-based neural network, which has a more complex structure for capturing inter-sentence relationships. In this paper, we present a heterogeneous graph-based neural network for extractive summarization (HeterSumGraph), which contains semantic nodes of different granularity levels apart from sentences. These additional nodes act as the intermediary between sentences and enrich the cross-sentence relations. Besides, our graph structure is flexible in natural extension from a single-document setting to multi-document via introducing document nodes. To our knowledge, we are the first one to introduce different types of nodes into graph-based neural networks for extractive document summarization and perform a comprehensive qualitative analysis to investigate their benefits. The code will be released on Github

Ming Zhong, Danqing Wang, Pengfei Liu et al.

In this paper, we take stock of the current state of summarization datasets and explore how different factors of datasets influence the generalization behaviour of neural extractive summarization models. Specifically, we first propose several properties of datasets, which matter for the generalization of summarization models. Then we build the connection between priors residing in datasets and model designs, analyzing how different properties of datasets influence the choices of model structure design and training methods. Finally, by taking a typical dataset as an example, we rethink the process of the model design based on the experience of the above analysis. We demonstrate that when we have a deep understanding of the characteristics of datasets, a simple approach can bring significant improvements to the existing state-of-the-art model.A

Danqing Wang, Pengfei Liu, Ming Zhong et al.

Although domain shift has been well explored in many NLP applications, it still has received little attention in the domain of extractive text summarization. As a result, the model is under-utilizing the nature of the training data due to ignoring the difference in the distribution of training sets and shows poor generalization on the unseen domain. With the above limitation in mind, in this paper, we first extend the conventional definition of the domain from categories into data sources for the text summarization task. Then we re-purpose a multi-domain summarization dataset and verify how the gap between different domains influences the performance of neural summarization models. Furthermore, we investigate four learning strategies and examine their abilities to deal with the domain shift problem. Experimental results on three different settings show their different characteristics in our new testbed. Our source code including \textit{BERT-based}, \textit{meta-learning} methods for multi-domain summarization learning and the re-purposed dataset \textsc{Multi-SUM} will be available on our project: \url{http://pfliu.com/TransferSum/}.

Ming Zhong, Pengfei Liu, Danqing Wang et al.

The recent years have seen remarkable success in the use of deep neural networks on text summarization. However, there is no clear understanding of \textit{why} they perform so well, or \textit{how} they might be improved. In this paper, we seek to better understand how neural extractive summarization systems could benefit from different types of model architectures, transferable knowledge and learning schemas. Additionally, we find an effective way to improve current frameworks and achieve the state-of-the-art result on CNN/DailyMail by a large margin based on our observations and analyses. Hopefully, our work could provide more clues for future research on extractive summarization.