Yanru Qu

Jianghao Lin, Yanru Qu, Wei Guo et al.

With the widespread application of personalized online services, click-through rate (CTR) prediction has received more and more attention and research. The most prominent features of CTR prediction are its multi-field categorical data format, and vast and daily-growing data volume. The large capacity of neural models helps digest such massive amounts of data under the supervised learning paradigm, yet they fail to utilize the substantial data to its full potential, since the 1-bit click signal is not sufficient to guide the model to learn capable representations of features and instances. The self-supervised learning paradigm provides a more promising pretrain-finetune solution to better exploit the large amount of user click logs, and learn more generalized and effective representations. However, self-supervised learning for CTR prediction is still an open question, since current works on this line are only preliminary and rudimentary. To this end, we propose a Model-agnostic pretraining (MAP) framework that applies feature corruption and recovery on multi-field categorical data, and more specifically, we derive two practical algorithms: masked feature prediction (MFP) and replaced feature detection (RFD). MFP digs into feature interactions within each instance through masking and predicting a small portion of input features, and introduces noise contrastive estimation (NCE) to handle large feature spaces. RFD further turns MFP into a binary classification mode through replacing and detecting changes in input features, making it even simpler and more effective for CTR pretraining. Our extensive experiments on two real-world large-scale datasets (i.e., Avazu, Criteo) demonstrate the advantages of these two methods on several strong backbones (e.g., DCNv2, DeepFM), and achieve new state-of-the-art performance in terms of both effectiveness and efficiency for CTR prediction.

Jianghao Lin, Bo Chen, Hangyu Wang et al.

Click-through rate (CTR) prediction has become increasingly indispensable for various Internet applications. Traditional CTR models convert the multi-field categorical data into ID features via one-hot encoding, and extract the collaborative signals among features. Such a paradigm suffers from the problem of semantic information loss. Another line of research explores the potential of pretrained language models (PLMs) for CTR prediction by converting input data into textual sentences through hard prompt templates. Although semantic signals are preserved, they generally fail to capture the collaborative information (e.g., feature interactions, pure ID features), not to mention the unacceptable inference overhead brought by the huge model size. In this paper, we aim to model both the semantic knowledge and collaborative knowledge for accurate CTR estimation, and meanwhile address the inference inefficiency issue. To benefit from both worlds and close their gaps, we propose a novel model-agnostic framework (i.e., ClickPrompt), where we incorporate CTR models to generate interaction-aware soft prompts for PLMs. We design a prompt-augmented masked language modeling (PA-MLM) pretraining task, where PLM has to recover the masked tokens based on the language context, as well as the soft prompts generated by CTR model. The collaborative and semantic knowledge from ID and textual features would be explicitly aligned and interacted via the prompt interface. Then, we can either tune the CTR model with PLM for superior performance, or solely tune the CTR model without PLM for inference efficiency. Experiments on four real-world datasets validate the effectiveness of ClickPrompt compared with existing baselines.

Yanru Qu, Keyue Qiu, Yuxuan Song et al.

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Yanru Qu, Cheng-Yen Hsieh, Zaixiang Zheng et al.

We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and refining structural details over scales. To achieve this, PAR consists of three key components: (i) multi-scale downsampling operations that represent protein structures across multiple scales during training; (ii) an autoregressive transformer that encodes multi-scale information and produces conditional embeddings to guide structure generation; (iii) a flow-based backbone decoder that generates backbone atoms conditioned on these embeddings. Moreover, autoregressive models suffer from exposure bias, caused by the training and the generation procedure mismatch, and substantially degrades structure generation quality. We effectively alleviate this issue by adopting noisy context learning and scheduled sampling, enabling robust backbone generation. Notably, PAR exhibits strong zero-shot generalization, supporting flexible human-prompted conditional generation and motif scaffolding without requiring fine-tuning. On the unconditional generation benchmark, PAR effectively learns protein distributions and produces backbones of high design quality, and exhibits favorable scaling behavior. Together, these properties establish PAR as a promising framework for protein structure generation.

Zihao Li, Zhichen Zeng, Xiao Lin et al.

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

Yuxuan Song, Jingjing Gong, Yanru Qu et al.

Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance).

Luran Wang, Chaoran Cheng, Yizhen Liao et al.

Controlled generation with pre-trained Diffusion and Flow Matching models has vast applications. One strategy for guiding ODE-based generative models is through optimizing a target loss $R(x_1)$ while staying close to the prior distribution. Along this line, some recent work showed the effectiveness of guiding flow model by differentiating through its ODE sampling process. Despite the superior performance, the theoretical understanding of this line of methods is still preliminary, leaving space for algorithm improvement. Moreover, existing methods predominately focus on Euclidean data manifold, and there is a compelling need for guided flow methods on complex geometries such as SO(3), which prevails in high-stake scientific applications like protein design. We present OC-Flow, a general and theoretically grounded training-free framework for guided flow matching using optimal control. Building upon advances in optimal control theory, we develop effective and practical algorithms for solving optimal control in guided ODE-based generation and provide a systematic theoretical analysis of the convergence guarantee in both Euclidean and SO(3). We show that existing backprop-through-ODE methods can be interpreted as special cases of Euclidean OC-Flow. OC-Flow achieved superior performance in extensive experiments on text-guided image manipulation, conditional molecule generation, and all-atom peptide design.

Yanru Qu, Yijie Zhang, Wenjuan Tan et al.

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking, occur only under specific local conditions. Most existing approaches represent molecules as atom-level graphs; however, atom-level representations can hardly express higher-order chemical context (e.g., stereochemistry, lone pairs, conjugation). Fragment-based methods (e.g., principal subgraph, predefined functional groups) fail to preserve essential information such as chirality, aromaticity, and ionic states. This work addresses these limitations from two aspects. (i) OverlapBPE tokenization. We propose a novel data-driven molecule tokenization method. Unlike existing approaches, our method allows overlapping fragments, reflecting the inherently fuzzy boundaries of small-molecule substructures and, together with enriched chemical information at the token level, thereby preserving a more complete chemical context. (ii) h-MINT model. OverlapBPE induces many-to-many atom-fragment mappings, which necessitate a new hierarchical architecture. We therefore develop a hierarchical molecular interaction network capable of jointly modeling interactions at both atom and fragment levels. By supporting fragment overlaps, the model naturally accommodates the many-to-many atom-fragment mappings introduced by the OverlapBPE scheme. Extensive evaluation against state-of-the-art methods shows our method improves binding affinity prediction by 2-4% Pearson/Spearman correlation on PDBBind and LBA, enhances virtual screening by 1-3% in key metrics on DUD-E and LIT-PCBA, and achieves the best overall HTS performance on PubChem assays. Further analysis demonstrates that our method effectively captures interactive information while maintaining good generalization.

Mingcheng Chen, Zhenghui Wang, Zhiyun Zhao et al.

Diabetes prediction is an important data science application in the social healthcare domain. There exist two main challenges in the diabetes prediction task: data heterogeneity since demographic and metabolic data are of different types, data insufficiency since the number of diabetes cases in a single medical center is usually limited. To tackle the above challenges, we employ gradient boosting decision trees (GBDT) to handle data heterogeneity and introduce multi-task learning (MTL) to solve data insufficiency. To this end, Task-wise Split Gradient Boosting Trees (TSGB) is proposed for the multi-center diabetes prediction task. Specifically, we firstly introduce task gain to evaluate each task separately during tree construction, with a theoretical analysis of GBDT's learning objective. Secondly, we reveal a problem when directly applying GBDT in MTL, i.e., the negative task gain problem. Finally, we propose a novel split method for GBDT in MTL based on the task gain statistics, named task-wise split, as an alternative to standard feature-wise split to overcome the mentioned negative task gain problem. Extensive experiments on a large-scale real-world diabetes dataset and a commonly used benchmark dataset demonstrate TSGB achieves superior performance against several state-of-the-art methods. Detailed case studies further support our analysis of negative task gain problems and provide insightful findings. The proposed TSGB method has been deployed as an online diabetes risk assessment software for early diagnosis.

Yanru Qu, Dinghan Shen, Yelong Shen et al.

Data augmentation has been demonstrated as an effective strategy for improving model generalization and data efficiency. However, due to the discrete nature of natural language, designing label-preserving transformations for text data tends to be more challenging. In this paper, we propose a novel data augmentation framework dubbed CoDA, which synthesizes diverse and informative augmented examples by integrating multiple transformations organically. Moreover, a contrastive regularization objective is introduced to capture the global relationship among all the data samples. A momentum encoder along with a memory bank is further leveraged to better estimate the contrastive loss. To verify the effectiveness of the proposed framework, we apply CoDA to Transformer-based models on a wide range of natural language understanding tasks. On the GLUE benchmark, CoDA gives rise to an average improvement of 2.2% while applied to the RoBERTa-large model. More importantly, it consistently exhibits stronger results relative to several competitive data augmentation and adversarial training base-lines (including the low-resource settings). Extensive experiments show that the proposed contrastive objective can be flexibly combined with various data augmentation approaches to further boost their performance, highlighting the wide applicability of the CoDA framework.

Yuning Mao, Yanru Qu, Yiqing Xie et al.

While neural sequence learning methods have made significant progress in single-document summarization (SDS), they produce unsatisfactory results on multi-document summarization (MDS). We observe two major challenges when adapting SDS advances to MDS: (1) MDS involves larger search space and yet more limited training data, setting obstacles for neural methods to learn adequate representations; (2) MDS needs to resolve higher information redundancy among the source documents, which SDS methods are less effective to handle. To close the gap, we present RL-MMR, Maximal Margin Relevance-guided Reinforcement Learning for MDS, which unifies advanced neural SDS methods and statistical measures used in classical MDS. RL-MMR casts MMR guidance on fewer promising candidates, which restrains the search space and thus leads to better representation learning. Additionally, the explicit redundancy measure in MMR helps the neural representation of the summary to better capture redundancy. Extensive experiments demonstrate that RL-MMR achieves state-of-the-art performance on benchmark MDS datasets. In particular, we show the benefits of incorporating MMR into end-to-end learning when adapting SDS to MDS in terms of both learning effectiveness and efficiency.

Dinghan Shen, Mingzhi Zheng, Yelong Shen et al.

Adversarial training has been shown effective at endowing the learned representations with stronger generalization ability. However, it typically requires expensive computation to determine the direction of the injected perturbations. In this paper, we introduce a set of simple yet effective data augmentation strategies dubbed cutoff, where part of the information within an input sentence is erased to yield its restricted views (during the fine-tuning stage). Notably, this process relies merely on stochastic sampling and thus adds little computational overhead. A Jensen-Shannon Divergence consistency loss is further utilized to incorporate these augmented samples into the training objective in a principled manner. To verify the effectiveness of the proposed strategies, we apply cutoff to both natural language understanding and generation problems. On the GLUE benchmark, it is demonstrated that cutoff, in spite of its simplicity, performs on par or better than several competitive adversarial-based approaches. We further extend cutoff to machine translation and observe significant gains in BLEU scores (based upon the Transformer Base model). Moreover, cutoff consistently outperforms adversarial training and achieves state-of-the-art results on the IWSLT2014 German-English dataset.

Yang Yang, Jian Shen, Yanru Qu et al.

With the rapid development in online education, knowledge tracing (KT) has become a fundamental problem which traces students' knowledge status and predicts their performance on new questions. Questions are often numerous in online education systems, and are always associated with much fewer skills. However, the previous literature fails to involve question information together with high-order question-skill correlations, which is mostly limited by data sparsity and multi-skill problems. From the model perspective, previous models can hardly capture the long-term dependency of student exercise history, and cannot model the interactions between student-questions, and student-skills in a consistent way. In this paper, we propose a Graph-based Interaction model for Knowledge Tracing (GIKT) to tackle the above probems. More specifically, GIKT utilizes graph convolutional network (GCN) to substantially incorporate question-skill correlations via embedding propagation. Besides, considering that relevant questions are usually scattered throughout the exercise history, and that question and skill are just different instantiations of knowledge, GIKT generalizes the degree of students' master of the question to the interactions between the student's current state, the student's history related exercises, the target question, and related skills. Experiments on three datasets demonstrate that GIKT achieves the new state-of-the-art performance, with at least 1% absolute AUC improvement.

Yanru Qu, Ting Bai, Weinan Zhang et al.

This paper studies graph-based recommendation, where an interaction graph is constructed from historical records and is lever-aged to alleviate data sparsity and cold start problems. We reveal an early summarization problem in existing graph-based models, and propose Neighborhood Interaction (NI) model to capture each neighbor pair (between user-side and item-side) distinctively. NI model is more expressive and can capture more complicated structural patterns behind user-item interactions. To further enrich node connectivity and utilize high-order structural information, we incorporate extra knowledge graphs (KGs) and adopt graph neural networks (GNNs) in NI, called Knowledge-enhanced NeighborhoodInteraction (KNI). Compared with the state-of-the-art recommendation methods,e.g., feature-based, meta path-based, and KG-based models, our KNI achieves superior performance in click-through rate prediction (1.1%-8.4% absolute AUC improvements) and out-performs by a wide margin in top-N recommendation on 4 real-world datasets.

Yunxuan Xiao, Yanru Qu, Lin Qiu et al.

Text-based question answering (TBQA) has been studied extensively in recent years. Most existing approaches focus on finding the answer to a question within a single paragraph. However, many difficult questions require multiple supporting evidence from scattered text among two or more documents. In this paper, we propose Dynamically Fused Graph Network(DFGN), a novel method to answer those questions requiring multiple scattered evidence and reasoning over them. Inspired by human's step-by-step reasoning behavior, DFGN includes a dynamic fusion layer that starts from the entities mentioned in the given query, explores along the entity graph dynamically built from the text, and gradually finds relevant supporting entities from the given documents. We evaluate DFGN on HotpotQA, a public TBQA dataset requiring multi-hop reasoning. DFGN achieves competitive results on the public board. Furthermore, our analysis shows DFGN produces interpretable reasoning chains.

Liheng Chen, Yanru Qu, Zhenghui Wang et al.

In graphs with rich texts, incorporating textual information with structural information would benefit constructing expressive graph embeddings. Among various graph embedding models, random walk (RW)-based is one of the most popular and successful groups. However, it is challenged by two issues when applied on graphs with rich texts: (i) sampling efficiency: deriving from the training objective of RW-based models (e.g., DeepWalk and node2vec), we show that RW-based models are likely to generate large amounts of redundant training samples due to three main drawbacks. (ii) text utilization: these models have difficulty in dealing with zero-shot scenarios where graph embedding models have to infer graph structures directly from texts. To solve these problems, we propose a novel framework, namely Text-driven Graph Embedding with Pairs Sampling (TGE-PS). TGE-PS uses Pairs Sampling (PS) to improve the sampling strategy of RW, being able to reduce ~99% training samples while preserving competitive performance. TGE-PS uses Text-driven Graph Embedding (TGE), an inductive graph embedding approach, to generate node embeddings from texts. Since each node contains rich texts, TGE is able to generate high-quality embeddings and provide reasonable predictions on existence of links to unseen nodes. We evaluate TGE-PS on several real-world datasets, and experiment results demonstrate that TGE-PS produces state-of-the-art results on both traditional and zero-shot link prediction tasks.

Yanru Qu, Bohui Fang, Weinan Zhang et al.

User response prediction is a crucial component for personalized information retrieval and filtering scenarios, such as recommender system and web search. The data in user response prediction is mostly in a multi-field categorical format and transformed into sparse representations via one-hot encoding. Due to the sparsity problems in representation and optimization, most research focuses on feature engineering and shallow modeling. Recently, deep neural networks have attracted research attention on such a problem for their high capacity and end-to-end training scheme. In this paper, we study user response prediction in the scenario of click prediction. We first analyze a coupled gradient issue in latent vector-based models and propose kernel product to learn field-aware feature interactions. Then we discuss an insensitive gradient issue in DNN-based models and propose Product-based Neural Network (PNN) which adopts a feature extractor to explore feature interactions. Generalizing the kernel product to a net-in-net architecture, we further propose Product-network In Network (PIN) which can generalize previous models. Extensive experiments on 4 industrial datasets and 1 contest dataset demonstrate that our models consistently outperform 8 baselines on both AUC and log loss. Besides, PIN makes great CTR improvement (relatively 34.67%) in online A/B test.

Zhenghui Wang, Yanru Qu, Liheng Chen et al.

We study the problem of named entity recognition (NER) from electronic medical records, which is one of the most fundamental and critical problems for medical text mining. Medical records which are written by clinicians from different specialties usually contain quite different terminologies and writing styles. The difference of specialties and the cost of human annotation makes it particularly difficult to train a universal medical NER system. In this paper, we propose a label-aware double transfer learning framework (La-DTL) for cross-specialty NER, so that a medical NER system designed for one specialty could be conveniently applied to another one with minimal annotation efforts. The transferability is guaranteed by two components: (i) we propose label-aware MMD for feature representation transfer, and (ii) we perform parameter transfer with a theoretical upper bound which is also label aware. We conduct extensive experiments on 12 cross-specialty NER tasks. The experimental results demonstrate that La-DTL provides consistent accuracy improvement over strong baselines. Besides, the promising experimental results on non-medical NER scenarios indicate that La-DTL is potential to be seamlessly adapted to a wide range of NER tasks.

Lin Qiu, Hao Zhou, Yanru Qu et al.

Information Extraction (IE) refers to automatically extracting structured relation tuples from unstructured texts. Common IE solutions, including Relation Extraction (RE) and open IE systems, can hardly handle cross-sentence tuples, and are severely restricted by limited relation types as well as informal relation specifications (e.g., free-text based relation tuples). In order to overcome these weaknesses, we propose a novel IE framework named QA4IE, which leverages the flexible question answering (QA) approaches to produce high quality relation triples across sentences. Based on the framework, we develop a large IE benchmark with high quality human evaluation. This benchmark contains 293K documents, 2M golden relation triples, and 636 relation types. We compare our system with some IE baselines on our benchmark and the results show that our system achieves great improvements.

Minzhe Niu, Weinan Zhang, Yanru Qu et al.

Introducing consumed items as users' implicit feedback in matrix factorization (MF) method, SVD++ is one of the most effective collaborative filtering methods for personalized recommender systems. Though powerful, SVD++ has two limitations: (i). only user-side implicit feedback is utilized, whereas item-side implicit feedback, which can also enrich item representations, is not leveraged;(ii). in SVD++, the interacted items are equally weighted when combining the implicit feedback, which can not reflect user's true preferences accurately. To tackle the above limitations, in this paper we propose Graph-based collaborative filtering (GCF) model, Weighted Graph-based collaborative filtering (W-GCF) model and Attentive Graph-based collaborative filtering (A-GCF) model, which (i). generalize the implicit feedback to item side based on the user-item bipartite graph; (ii). flexibly learn the weights of individuals in the implicit feedback hence improve the model's capacity. Comprehensive experiments show that our proposed models outperform state-of-the-art models.For sparse implicit feedback scenarios, additional improvement is further achieved by leveraging the step-two implicit feedback information.

Jian Shen, Yanru Qu, Weinan Zhang et al.

Domain adaptation aims at generalizing a high-performance learner on a target domain via utilizing the knowledge distilled from a source domain which has a different but related data distribution. One solution to domain adaptation is to learn domain invariant feature representations while the learned representations should also be discriminative in prediction. To learn such representations, domain adaptation frameworks usually include a domain invariant representation learning approach to measure and reduce the domain discrepancy, as well as a discriminator for classification. Inspired by Wasserstein GAN, in this paper we propose a novel approach to learn domain invariant feature representations, namely Wasserstein Distance Guided Representation Learning (WDGRL). WDGRL utilizes a neural network, denoted by the domain critic, to estimate empirical Wasserstein distance between the source and target samples and optimizes the feature extractor network to minimize the estimated Wasserstein distance in an adversarial manner. The theoretical advantages of Wasserstein distance for domain adaptation lie in its gradient property and promising generalization bound. Empirical studies on common sentiment and image classification adaptation datasets demonstrate that our proposed WDGRL outperforms the state-of-the-art domain invariant representation learning approaches.

Yanru Qu, Han Cai, Kan Ren et al.

Predicting user responses, such as clicks and conversions, is of great importance and has found its usage in many Web applications including recommender systems, web search and online advertising. The data in those applications is mostly categorical and contains multiple fields; a typical representation is to transform it into a high-dimensional sparse binary feature representation via one-hot encoding. Facing with the extreme sparsity, traditional models may limit their capacity of mining shallow patterns from the data, i.e. low-order feature combinations. Deep models like deep neural networks, on the other hand, cannot be directly applied for the high-dimensional input because of the huge feature space. In this paper, we propose a Product-based Neural Networks (PNN) with an embedding layer to learn a distributed representation of the categorical data, a product layer to capture interactive patterns between inter-field categories, and further fully connected layers to explore high-order feature interactions. Our experimental results on two large-scale real-world ad click datasets demonstrate that PNNs consistently outperform the state-of-the-art models on various metrics.