Qingyun Wang

Qingyun Wang, Manling Li, Hou Pong Chan et al.

Goal-oriented generative script learning aims to generate subsequent steps to reach a particular goal, which is an essential task to assist robots or humans in performing stereotypical activities. An important aspect of this process is the ability to capture historical states visually, which provides detailed information that is not covered by text and will guide subsequent steps. Therefore, we propose a new task, Multimedia Generative Script Learning, to generate subsequent steps by tracking historical states in both text and vision modalities, as well as presenting the first benchmark containing 5,652 tasks and 79,089 multimedia steps. This task is challenging in three aspects: the multimedia challenge of capturing the visual states in images, the induction challenge of performing unseen tasks, and the diversity challenge of covering different information in individual steps. We propose to encode visual state changes through a selective multimedia encoder to address the multimedia challenge, transfer knowledge from previously observed tasks using a retrieval-augmented decoder to overcome the induction challenge, and further present distinct information at each step by optimizing a diversity-oriented contrastive learning objective. We define metrics to evaluate both generation and inductive quality. Experiment results demonstrate that our approach significantly outperforms strong baselines.

Ruochen Li, Teerth Patel, Qingyun Wang et al.

Autonomous machine learning research has gained significant attention recently. We present MLR-COPILOT, an autonomous Machine Learning Research framework powered by large language model agents. The system is designed to enhance ML research productivity through automatic generation and implementation of research ideas within constraints. Our work was released in August 2024 (concurrent to AI-Scientist) and has gained notable recognition from leading projects. We further enhance our ideation with training afterwards. The framework consists of three stages: idea generation, experiment implementation, and code execution. First, existing research papers are used to generate feasible ideas and experiment plans with IdeaAgent, powered by an RL-tuned LLM. Next, ExperimentAgent leverages retrieved prototype code to convert plans into executable code with optionally retrieved candidate models and data from HuggingFace. In the final stage, ExperimentAgent runs experiments, and allows subsequent iterations of debugging and human feedback for a better chance of success with executable outcomes. We evaluate our framework on five machine learning research tasks. Experiment results demonstrate the potential of our framework to facilitate ML research progress and innovation.

Xuehang Guo, Zora Zhiruo Wang, Qingyun Wang et al.

Large language models (LLMs) have enabled powerful software engineering (SE) agents capable of navigating complex codebases and resolving real-world issues. However, these agents remain fundamentally episodic: they fail to retain, refine, and reuse experiences across tasks, repeatedly reconstructing context from scratch and reproducing similar mistakes. Even with memory support, they offer no remedy for the absence of a principled, task-agnostic \textit{memory utility}, making them difficult to evaluate rigorously or generalize across agents and settings. To tackle these limitations, we introduce \ours, a closed-loop framework for memory augmentation in SE agents. \ours grounds memory utility in \textit{validated downstream impact}, establishing utility as both a task-agnostic \textbf{evaluation benchmark} and an annotation-free \textbf{optimization signal}. Through complementary evaluation on \textit{single-episode} and \textit{cross-episode} memory augmentation, results demonstrate that \ours consistently improves SE agents across settings, achieving absolute gains of up to $\uparrow5.25\%$ in success rate and $\uparrow4.63\%$ in resolve efficiency, while substantially reducing computational cost by $\geq9.79\%$. Our project page: \href{https://xhguo7.github.io/MemOp/}{https://xhguo7.github.io/MemOp/}.

Yuting Hu, Dancheng Liu, Qingyun Wang et al.

Identifying effective interventions from the scientific literature is challenging due to the high volume of publications, specialized terminology, and inconsistent reporting formats, making manual curation laborious and prone to oversight. To address this challenge, this paper proposes a novel framework leveraging large language models (LLMs), which integrates a progressive ontology prompting (POP) algorithm with a dual-agent system, named LLM-Duo. On the one hand, the POP algorithm conducts a prioritized breadth-first search (BFS) across a predefined ontology, generating structured prompt templates and action sequences to guide the automatic annotation process. On the other hand, the LLM-Duo system features two specialized LLM agents, an explorer and an evaluator, working collaboratively and adversarially to continuously refine annotation quality. We showcase the real-world applicability of our framework through a case study focused on speech-language intervention discovery. Experimental results show that our approach surpasses advanced baselines, achieving more accurate and comprehensive annotations through a fully automated process. Our approach successfully identified 2,421 interventions from a corpus of 64,177 research articles in the speech-language pathology domain, culminating in the creation of a publicly accessible intervention knowledge base with great potential to benefit the speech-language pathology community.

Shuowen Liang, Sisi Li, Qingyun Wang et al.

Pose skeleton images are an important reference in pose-controllable image generation. In order to enrich the source of skeleton images, recent works have investigated the generation of pose skeletons based on natural language. These methods are based on GANs. However, it remains challenging to perform diverse, structurally correct and aesthetically pleasing human pose skeleton generation with various textual inputs. To address this problem, we propose a framework with GUNet as the main model, PoseDiffusion. It is the first generative framework based on a diffusion model and also contains a series of variants fine-tuned based on a stable diffusion model. PoseDiffusion demonstrates several desired properties that outperform existing methods. 1) Correct Skeletons. GUNet, a denoising model of PoseDiffusion, is designed to incorporate graphical convolutional neural networks. It is able to learn the spatial relationships of the human skeleton by introducing skeletal information during the training process. 2) Diversity. We decouple the key points of the skeleton and characterise them separately, and use cross-attention to introduce textual conditions. Experimental results show that PoseDiffusion outperforms existing SoTA algorithms in terms of stability and diversity of text-driven pose skeleton generation. Qualitative analyses further demonstrate its superiority for controllable generation in Stable Diffusion.

Kexuan Xin, Qingyun Wang, Junyu Chen et al.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Hongyi Liu, Qingyun Wang, Payam Karisani et al.

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a named entity recognition model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments, we observed that such a model is prone to mislabeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, but, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mislabeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We conduct our extensive experiments across three source and three target datasets, demonstrating that our method outperforms the baselines by up to 5% absolute value.

Qingyun Wang, Zixuan Zhang, Hongxiang Li et al.

Fine-grained few-shot entity extraction in the chemical domain faces two unique challenges. First, compared with entity extraction tasks in the general domain, sentences from chemical papers usually contain more entities. Moreover, entity extraction models usually have difficulty extracting entities of long-tailed types. In this paper, we propose Chem-FINESE, a novel sequence-to-sequence (seq2seq) based few-shot entity extraction approach, to address these two challenges. Our Chem-FINESE has two components: a seq2seq entity extractor to extract named entities from the input sentence and a seq2seq self-validation module to reconstruct the original input sentence from extracted entities. Inspired by the fact that a good entity extraction system needs to extract entities faithfully, our new self-validation module leverages entity extraction results to reconstruct the original input sentence. Besides, we design a new contrastive loss to reduce excessive copying during the extraction process. Finally, we release ChemNER+, a new fine-grained chemical entity extraction dataset that is annotated by domain experts with the ChemNER schema. Experiments in few-shot settings with both ChemNER+ and CHEMET datasets show that our newly proposed framework has contributed up to 8.26% and 6.84% absolute F1-score gains respectively.

Qingyun Wang, Doug Downey, Heng Ji et al.

We explore and enhance the ability of neural language models to generate novel scientific directions grounded in literature. Work on literature-based hypothesis generation has traditionally focused on binary link prediction--severely limiting the expressivity of hypotheses. This line of work also does not focus on optimizing novelty. We take a dramatic departure with a novel setting in which models use as input background contexts (e.g., problems, experimental settings, goals), and output natural language ideas grounded in literature. We present SciMON, a modeling framework that uses retrieval of "inspirations" from past scientific papers, and explicitly optimizes for novelty by iteratively comparing to prior papers and updating idea suggestions until sufficient novelty is achieved. Comprehensive evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our methods partially mitigate this issue. Our work represents a first step toward evaluating and developing language models that generate new ideas derived from the scientific literature

Qingyun Wang, Semih Yavuz, Victoria Lin et al.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Wenhao Yu, Chenguang Zhu, Zaitang Li et al.

The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.

Qingyun Wang, Manling Li, Xuan Wang et al.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Qingyun Wang, Lifu Huang, Zhiying Jiang et al.

We present a PaperRobot who performs as an automatic research assistant by (1) conducting deep understanding of a large collection of human-written papers in a target domain and constructing comprehensive background knowledge graphs (KGs); (2) creating new ideas by predicting links from the background KGs, by combining graph attention and contextual text attention; (3) incrementally writing some key elements of a new paper based on memory-attention networks: from the input title along with predicted related entities to generate a paper abstract, from the abstract to generate conclusion and future work, and finally from future work to generate a title for a follow-on paper. Turing Tests, where a biomedical domain expert is asked to compare a system output and a human-authored string, show PaperRobot generated abstracts, conclusion and future work sections, and new titles are chosen over human-written ones up to 30%, 24% and 12% of the time, respectively.

Qingyun Wang, Xiaoman Pan, Lifu Huang et al.

We aim to automatically generate natural language descriptions about an input structured knowledge base (KB). We build our generation framework based on a pointer network which can copy facts from the input KB, and add two attention mechanisms: (i) slot-aware attention to capture the association between a slot type and its corresponding slot value; and (ii) a new \emph{table position self-attention} to capture the inter-dependencies among related slots. For evaluation, besides standard metrics including BLEU, METEOR, and ROUGE, we propose a KB reconstruction based metric by extracting a KB from the generation output and comparing it with the input KB. We also create a new data set which includes 106,216 pairs of structured KBs and their corresponding natural language descriptions for two distinct entity types. Experiments show that our approach significantly outperforms state-of-the-art methods. The reconstructed KB achieves 68.8% - 72.6% F-score.

Qingyun Wang, Zhihao Zhou, Lifu Huang et al.

We present a paper abstract writing system based on an attentive neural sequence-to-sequence model that can take a title as input and automatically generate an abstract. We design a novel Writing-editing Network that can attend to both the title and the previously generated abstract drafts and then iteratively revise and polish the abstract. With two series of Turing tests, where the human judges are asked to distinguish the system-generated abstracts from human-written ones, our system passes Turing tests by junior domain experts at a rate up to 30% and by non-expert at a rate up to 80%.

Feifei Shen, Zhenjian Song, Congrui Wu et al.

Study of general purpose computation by GPU (Graphics Processing Unit) can improve the image processing capability of micro-computer system. This paper studies the parallelism of the different stages of decimation in time radix 2 FFT algorithm, designs the butterfly and scramble kernels and implements 2D FFT on GPU. The experiment result demonstrates the validity and advantage over general CPU, especially in the condition of large input size. The approach can also be generalized to other transforms alike.