Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage, while recent cross-modal representation learning frameworks often encounter modality misalignment, resulting in suboptimal retrieval accuracy and generalization. To address these limitations, we propose GLMR, a Generative Language Model-based Retrieval framework that mitigates the cross-modal misalignment through a two-stage process. In the pre-retrieval stage, a contrastive learning-based model identifies top candidate molecules as contextual priors for the input mass spectrum. In the generative retrieval stage, these candidate molecules are integrated with the input mass spectrum to guide a generative model in producing refined molecular structures, which are then used to re-rank the candidates based on molecular similarity. Experiments on both MassSpecGym and the proposed MassRET-20k dataset demonstrate that GLMR significantly outperforms existing methods, achieving over 40% improvement in top-1 accuracy and exhibiting strong generalizability.

Kehua Feng, Keyan Ding, Tan Hongzhi, Kede Ma, Zhihua Wang, Shuangquan Guo, Cheng Yuzhou, Ge Sun, Guozhou Zheng, Qiang Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Yuhao Wang, Keyan Ding, Kehua Feng, Zeyuan Wang, Ming Qin, Xiaotong Li, Qiang Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Retrieval-augmented generation (RAG) systems often struggle with narrative-rich documents and event-centric reasoning, particularly when synthesizing information across multiple sources. We present EventRAG, a novel framework that enhances text generation through structured event representations. We first construct an Event Knowledge Graph by extracting events and merging semantically equivalent nodes across documents, while expanding under-connected relationships. We then employ an iterative retrieval and inference strategy that explicitly captures temporal dependencies and logical relationships across events. Experiments on UltraDomain and MultiHopRAG benchmarks show EventRAG’s superiority over baseline RAG systems, with substantial gains in generation effectiveness, logical consistency, and multi-hop reasoning accuracy. Our work advances RAG systems by integrating structured event semantics with iterative inference, particularly benefiting scenarios requiring temporal and logical reasoning across documents.

Xiang Zhuang, Bin Wu, Jiyu Cui, Kehua Feng, Xiaotong Li, Huabin Xing, Keyan Ding, Qiang Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

In the drug discovery process, the low success rate of drug candidate screening often leads to insufficient labeled data, causing the few-shot learning problem in molecular property prediction. Existing methods for few-shot molecular property prediction overlook the sample selection bias, which arises from non-random sample selection in chemical experiments. This bias in data representativeness leads to suboptimal performance. To overcome this challenge, we present a novel method named Contextual Representation Anchor Network (CRANet), where an anchor refers to a cluster center of the representations of molecules and serves as a bridge to transfer enriched contextual knowledge into molecular representations and enhance their expressiveness. CRANet introduces a dual-augmentation mechanism that includes context augmentation, which dynamically retrieves analogous unlabeled molecules and captures their task-specific contextual knowledge to enhance the anchors, and anchor augmentation, which leverages the anchors to augment the molecular representations. We evaluate our approach using the MoleculeNet and FS-Mol benchmarks, as well as through domain transfer experiments. The outcomes indicate that CRANet surpasses current state-of-the-art methods by 0.10% to 5.48% in AUC and 2.52% in ΔAUC-PR metrics, showcasing its exceptional generalization abilities.

Evaluating the response quality of large language models (LLMs) for open-ended questions poses a significant challenge, especially given the subjectivity and multi-dimensionality of "quality" in natural language generation. Existing LLM evaluators often neglect that different scenarios require distinct evaluation criteria. In this work, we propose **SaMer**, a scenario-aware multi-dimensional evaluator designed to provide both overall and fine-grained assessments of LLM-generated responses. Unlike fixed-dimension evaluation approaches, SaMer adapts to different scenarios by automatically identifying and prioritizing relevant evaluation dimensions tailored to the given query. To achieve this, we construct a large-scale fine-grained preference dataset spanning multiple real-world scenarios, each with distinct evaluation dimensions. We then leverage a text embedding model combined with three specialized heads to predict the appropriate evaluation dimensions and corresponding scores, as well as the respective weights that contribute to the overall score. The resulting model offers fine-grained and interpretable evaluations and shows robust adaptability across diverse scenarios. Extensive experiments on eight single rating and pairwise comparison datasets demonstrate that SaMer outperforms existing baselines in a variety of evaluation tasks, showcasing its robustness, versatility, and generalizability.

Drug discovery is crucial for identifying candidate drugs for various diseases. However, its low success rate often results in a scarcity of annotations, posing a few-shot learning problem. Existing methods primarily focus on single-scale features, overlooking the hierarchical molecular structures that determine different molecular properties. To address these issues, we introduce Universal Matching Networks (UniMatch), a dual matching framework that integrates explicit hierarchical molecular matching with implicit task-level matching via meta- learning, bridging multi-level molecular representations and task-level generalization. Specifically, our approach explicitly captures structural features across multiple levels—atoms, substructures, and molecules—via hierarchical pooling and matching, facilitating precise molecular representation and comparison. Additionally, we employ a meta-learning strategy for implicit task-level matching, allowing the model to capture shared patterns across tasks and quickly adapt to new ones. This unified matching framework ensures effective molecular alignment while leveraging shared meta-knowledge for fast adaptation. Our experimental results demonstrate that UniMatch outperforms state-of-the-art methods on the MoleculeNet and FS-Mol benchmarks, achieving improvements of 2.87% in AUROC and 6.52% in ∆AUPRC. UniMatch also shows excellent generalization ability on the Meta-MolNet benchmark.

The alignment of large language models (LLMs) with human preferences remains a key challenge. While post-training techniques like Reinforcement Learning from Human Feedback (RLHF) and Direct Preference Optimization (DPO) have achieved notable success, they often experience computational inefficiencies and training instability. In this paper, we propose Feature-level constrained Preference Optimization (FPO), a novel method designed to simplify the alignment process while ensuring stability. FPO leverages pre-trained Sparse Autoencoders (SAEs) and introduces feature-level constraints, allowing for efficient, sparsity-enforced alignment. Our approach enjoys efficiency by using sparse features activated in a well-trained sparse autoencoder and the quality of sequential KL divergence by using the feature-level offline reference. Experimental results on benchmark datasets demonstrate that FPO achieves an above 5% absolute improvement in win rate with much lower computational cost compared to state-of-the-art baselines, making it a promising solution for efficient and controllable LLM alignments.

Parameter-efficient fine-tuning (PEFT) methods, such as LoRA, have enabled the efficient adaptation of large language models (LLMs) by updating only a small subset of parameters. However, their robustness under out-of-distribution (OOD) conditions remains insufficiently studied. In this paper, we identify the limitations of conventional LoRA in handling distributional shifts and propose $\textbf{HiMoLE}$($\textbf{Hi}$erarchical $\textbf{M}$ixture of $\textbf{L}$oRA $\textbf{E}$xperts), a new framework designed to improve OOD generalization. HiMoLE integrates hierarchical expert modules and hierarchical routing strategies into the LoRA architecture and introduces a two-phase training procedure enhanced by a diversity-driven loss. This design mitigates negative transfer and promotes effective knowledge adaptation across diverse data distributions. We evaluate HiMoLE on three representative tasks in natural language processing. Experimental results evidence that HiMoLE consistently outperforms existing LoRA-based approaches, significantly reducing performance degradation on OOD data while improving in-distribution performance. Our work bridges the gap between parameter efficiency and distributional robustness, advancing the practical deployment of LLMs in real-world applications.

Zeyuan Wang, Qiang Zhang, Keyan Ding, Ming Qin, Xiang Zhuang, Xiaotong Li, Huajun Chen. Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2024.

Despite recent successes in natural language processing and computer vision, Transformer faces scalability issues when processing graphs, e.g., computing the full node-to-node attention on knowledge graphs (KGs) with million of entities is still infeasible. The existing methods mitigate this problem by considering only the local neighbors, sacrificing the Transformer’s ability to attend to elements at any distance. This paper proposes a new Transformer architecture called Dual-Encoding Transformer (DET). DET comprises a structural encoder to aggregate information from nearby neighbors, and a semantic encoder to seek for semantically relevant nodes. We adopt a semantic neighbor search approach inspired by multiple sequence alignment (MSA) algorithms used in biological sciences. By stacking the two encoders alternately, similar to the MSA Transformer for protein representation, our method achieves superior performance compared to state-of-the-art attention-based methods on complex relational graphs like KGs and citation networks. Additionally, DET remains competitive for smaller graphs such as molecules.

Directed evolution, a cornerstone of protein optimization, is to harness natural mutational processes to enhance protein functionality. Existing Machine Learning-assisted Directed Evolution (MLDE) methodologies typically rely on data-driven strategies and often overlook the profound domain knowledge in biochemical fields. In this paper, we introduce a novel Knowledge-aware Reinforced Language Model (KnowRLM) for MLDE. An Amino Acid Knowledge Graph (AAKG) is constructed to represent the intricate biochemical relationships among amino acids. We further propose a Protein Language Model (PLM)-based policy network that iteratively samples mutants through preferential random walks on the AAKG using a dynamic sliding window mechanism. The novel mutants are actively sampled to fine-tune a fitness predictor as the reward model, providing feedback to the knowledge-aware policy. Finally, we optimize the whole system in an active learning approach that mimics biological settings in practice.KnowRLM stands out for its ability to utilize contextual amino acid information from knowledge graphs, thus attaining advantages from both statistical patterns of protein sequences and biochemical properties of amino acids.Extensive experiments demonstrate the superior performance of KnowRLM in more efficiently identifying high-fitness mutants compared to existing methods.

The decoder-only Transformer architecture with causal masking and relative position encoding (RPE) has become the de facto choice in language modeling. Despite its exceptional performance across various tasks, we have identified two limitations: First, it prevents all attended tokens from having zero weights during the softmax stage, even if the current embedding has sufficient self-contained information. This compels the model to assign disproportional excessive attention to specific tokens. Second, RPE-based Transformers are not universal approximators due to their limited capacity at encoding absolute positional information, which limits their application in position-critical tasks. In this work, we propose StableMask: a parameter-free method to address both limitations by refining the causal mask. It introduces pseudo-attention values to balance attention distributions and encodes absolute positional information via a progressively decreasing mask ratio. StableMask's effectiveness is validated both theoretically and empirically, showing significant enhancements in language models with parameter sizes ranging from 71M to 1.4B across diverse datasets and encoding methods. We further show that it supports integration with existing optimization techniques, making it easily usable in practical applications.

Large language models (LLMs) have significantly advanced performance across a spectrum of natural language processing (NLP) tasks. Yet, their application to knowledge graphs (KGs), which describe facts in the form of triplets and allow minimal hallucinations, remains an underexplored frontier. In this paper, we investigate the integration of LLMs with KGs by introducing a specialized KG Language (KGL), where a sentence precisely consists of an entity noun, a relation verb, and ends with another entity noun. Despite KGL's unfamiliar vocabulary to the LLM, we facilitate its learning through a tailored dictionary and illustrative sentences, and enhance context understanding via real-time KG context retrieval and KGL token embedding augmentation. Our results reveal that LLMs can achieve fluency in KGL, drastically reducing errors compared to conventional KG embedding methods on KG completion. Furthermore, our enhanced LLM shows exceptional competence in generating accurate three-word sentences from an initial entity and interpreting new unseen terms out of KGs.

Protein optimization is a fundamental biological task aimed at enhancing theperformance of proteins by modifying their sequences. Computational methodsprimarily rely on evolutionary information (EI) encoded by protein languagemodels (PLMs) to predict fitness landscape for optimization. However, thesemethods suffer from a few limitations. (1) Evolutionary processes involve thesimultaneous consideration of multiple functional properties, often overshadowingthe specific property of interest. (2) Measurements of these properties tend to betailored to experimental conditions, leading to reduced generalizability of trainedmodels to novel proteins. To address these limitations, we introduce DenoisingProtein Language Models (DePLM), a novel approach that refines the evolutionaryinformation embodied in PLMs for improved protein optimization. Specifically, weconceptualize EI as comprising both property-relevant and irrelevant information,with the latter acting as “noise” for the optimization task at hand. Our approachinvolves denoising this EI in PLMs through a diffusion process conducted in therank space of property values, thereby enhancing model generalization and ensuringdataset-agnostic learning. Extensive experimental results have demonstrated thatDePLM not only surpasses the state-of-the-art in mutation effect prediction butalso exhibits strong generalization capabilities for novel proteins.

Being the most cutting-edge generative methods, diffusion methods have shown great advances in wide generation tasks. Among them, graph generation attracts significant research attention for its broad application in real life. In our survey, we systematically and comprehensively review on diffusion-based graph generative methods. We first make a review on three mainstream paradigms of diffusion methods, which are denoising diffusion probabilistic models, score-based genrative models, and stochastic differential equations. Then we further categorize and introduce the latest applications of diffusion models on graphs. In the end, we point out some limitations of current studies and future directions of future explorations.

The ability to understand a user's underlying needs is critical for conversational systems, especially with limited input from users in a conversation.Thus, in such a domain, Asking Clarification Questions (ACQs) to reveal users' true intent from their queries or utterances arise as an essential task.However, it is noticeable that a key limitation of the existing ACQs studies is their incomparability, from inconsistent use of data, distinct experimental setups and evaluation strategies.Therefore, in this paper, to assist the development of ACQs techniques, we comprehensively analyse the current ACQs research status, which offers a detailed comparison of publicly available datasets, and discusses the applied evaluation metrics, joined with benchmarks for multiple ACQs-related tasks.In particular, given a thorough analysis of the ACQs task, we discuss a number of corresponding research directions for the investigation of ACQs as well as the development of conversational systems.

Directed evolution is a widely-used strategy of protein engineering to improve protein function via mimicking natural mutation and selection. Machine learning-assisted directed evolution (MLDE) approaches aim to learn a fitness predictor, thereby efficiently searching for optimal mutants within the vast combinatorial mutation space. Since annotating mutants is both costly and labor-intensive, how to efficiently sample and utilize informative protein mutants to train the predictor is a critical problem in MLDE. Previous MLDE works just simply utilized pre-trained protein language models (PPLMs) for sampling without tailoring to the specific target protein of interest, which has not fully exploited the potential of PPLMs. In this work, we propose a novel method, the Actively-Finetuned Protein language model for Directed Evolution(AFP-DE), which leverages PPLMs to actively sample and fine-tune themselves, continuously improving the model’s sampling and overall performance through iterations, to achieve efficient directed protein evolution. Extensive experiments have shown the effectiveness of our method in generating optimal mutants with minimal annotation effort, outperforming previous works even with fewer annotated mutants, making it budget-friendly for biological experiments.

This paper focuses on continual meta-learning, where few-shot tasks are heterogeneous and sequentially available. Recent works use a mixture model for meta-knowledge to deal with the heterogeneity. However, these methods suffer from parameter inefficiency caused by two reasons: (1) the underlying assumption of mutual exclusiveness among mixture components hinders sharing meta-knowledge across heterogeneous tasks. (2) they only allow increasing mixture components and cannot adaptively filter out redundant components. In this paper, we propose an Adaptive Compositional Continual Meta-Learning (ACML) algorithm, which employs a compositional premise to associate a task with a subset of mixture components, allowing meta-knowledge sharing among heterogeneous tasks. Moreover, to adaptively adjust the number of mixture components, we propose a component sparsification method based on evidential theory to filter out redundant components. Experimental results show ACML outperforms strong baselines, showing the effectiveness of our compositional meta-knowledge, and confirming that ACML can adaptively learn meta-knowledge.

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effectively utilize many-to-many correlations of molecules and properties, we propose a Graph Sampling-based Meta-learning (GS-Meta) framework for few-shot molecular property prediction. First, we construct a Molecule-Property relation Graph (MPG): molecule and properties are nodes, while property labels decide edges. Then, to utilize the topological information of MPG, we reformulate an episode in meta-learning as a subgraph of the MPG, containing a target property node, molecule nodes, and auxiliary property nodes. Third, as episodes in the form of subgraphs are no longer independent of each other, we propose to schedule the subgraph sampling process with a contrastive loss function, which considers the consistency and discrimination of subgraphs. Extensive experiments on 5 commonly-used benchmarks show GS-Meta consistently outperforms state-of-the-art methods by 5.71%-6.93% in ROC-AUC and verify the effectiveness of each proposed module. Our code is available at https://github.com/HICAI-ZJU/GS-Meta.

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton–Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different environments. To address this issue, we propose a new framework for learning molecular representations that exhibit invariance and robustness against distribution shifts. Specifically, we propose a strategy called ``first-encoding-then-separation'' to identify invariant molecule features in the latent space, which deviates from conventional practices. Prior to the separation step, we introduce a residual vector quantization module that mitigates the over-fitting to training data distributions while preserving the expressivity of encoders. Furthermore, we design a task-agnostic self-supervised learning objective to encourage precise invariance identification, which enables our method widely applicable to a variety of tasks, such as regression and multi-label classification. Extensive experiments on 18 real-world molecular datasets demonstrate that our model achieves stronger generalization against state-of-the-art baselines in the presence of various distribution shifts. Our code is available at https://github.com/HICAI-ZJU/iMoLD.

In this paper, we study the task of cross-temporal snapshot alignment for dynamic networks. The goal of this task is to match equivalent nodes across temporal snapshots of a given dynamic network. Previous static network alignment methods ignore the non-stationary nature of networks, while existing dynamic counterparts focusing on two separate evolving networks lose sight of the problem of aligning two snapshots of the same dynamic network. To alleviate these issues, we propose a Cross-Temporal Snapshot Alignment model (CTSA), which maps nodes from different snapshots into the same semantic space and makes the equivalent nodes in the source and target snapshots to be aligned locate as closely as possible. Our CTSA model utilizes graph neural networks to embed nodes for each snapshot by aggregating the local structural information, and integrates the self-attention based encoders to model the dependencies in different snapshots over time. Additionally, to improve the alignment performance of the model, we contrive a novel positional embedding learning method, which takes into account both the ordering information of input representation sequences at each time step and the graph information of each network snapshot. Experimental results on real-world dynamic networks demonstrate that our model outperforms the state-of-the-art baselines.

Learning effective representations of entities and relations for knowledge graphs (KGs) is critical to the success of many multi-relational learning tasks. Existing methods based on graph neural networks learn a deterministic embedding function, which lacks sufficient flexibility to explore better choices when dealing with the imperfect and noisy KGs such as the scarce labeled nodes and noisy graph structure. To this end, we propose a novel multi-relational graph Gaussian Process network (GGPN), which aims to improve the flexibility of deterministic methods by simultaneously learning a family of embedding functions, i.e., a stochastic embedding function. Specifically, a Bayesian Gaussian Process (GP) is proposed to model the distribution of this stochastic function and the resulting representations are obtained by aggregating stochastic function values, i.e., messages, from neighboring entities. The two problems incurred when leveraging GP in GGPN are the proper choice of kernel function and the cubic computational complexity. To address the first problem, we further propose a novel kernel function that can explicitly take the diverse relations between each pair of entities into account and be adaptively learned in a data-driven way. We address the second problem by reformulating GP as a Bayesian linear model, resulting in a linear computational complexity. With these two solutions, our GGPN can be efficiently trained in an end-to-end manner. We evaluate our GGPN in link prediction and entity classification tasks, and the experimental results demonstrate the superiority of our method. Our code is available at https://github.com/sysu-gzchen/GGPN.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs.

Inferring spatial relations in natural language is a crucial ability an intelligent system should possess. The bAbI dataset tries to capture tasks relevant to this domain (task 17 and 19). However, these tasks have several limitations. Most importantly, they are limited to fixed expressions, they are limited in the number of reasoning steps required to solve them, and they fail to test the robustness of models to input that contains irrelevant or redundant information. In this paper, we present a new Question-Answering dataset called StepGame for robust multi-step spatial reasoning in texts. Our experiments demonstrate that state-of-the-art models on the bAbI dataset struggle on the StepGame dataset. Moreover, we propose a Tensor-Product based Memory-Augmented Neural Network (TP-MANN) specialized for spatial reasoning tasks. Experimental results on both datasets show that our model outperforms all the baselines with superior generalization and robustness performance.

Dialogue State Tracking (DST) aims to keep track of users' intentions during the course of a conversation.In DST, modelling the relations among domains and slots is still an under-studied problem.Existing approaches that have considered such relations generally fall short in: (1) fusing prior slot-domain membership relations and dialogue-aware dynamic slot relations explicitly, and (2) generalizing to unseen domains.To address these issues, we propose a novel Dynamic Schema Graph Fusion Network (DSGFNet), which generates a dynamic schema graph to explicitly fuse the prior slot-domain membership relations and dialogue-aware dynamic slot relations.It also uses the schemata to facilitate knowledge transfer to new domains.DSGFNet consists of a dialogue utterance encoder, a schema graph encoder, a dialogue-aware schema graph evolving network, and a schema graph enhanced dialogue state decoder.Empirical results on benchmark datasets (i.e., SGD, MultiWOZ2.1,and MultiWOZ2.2),show that DSGFNet outperforms existing methods.

Embedding-based entity alignment (EEA) has recently received great attention. Despite significant performance improvement, few efforts have been paid to facilitate understanding of EEA methods. Most existing studies rest on the assumption that a small number of pre-aligned entities can serve as anchors connecting the embedding spaces of two KGs. Nevertheless, no one has investigated the rationality of such an assumption. To fill the research gap, we define a typical paradigm abstracted from existing EEA methods and analyze how the embedding discrepancy between two potentially aligned entities is implicitly bounded by a predefined margin in the score function. Further, we find that such a bound cannot guarantee to be tight enough for alignment learning. We mitigate this problem by proposing a new approach, named NeoEA, to explicitly learn KG-invariant and principled entity embeddings. In this sense, an EEA model not only pursues the closeness of aligned entities based on geometric distance, but also aligns the neural ontologies of two KGs by eliminating the discrepancy in embedding distribution and underlying ontology knowledge. Our experiments demonstrate consistent and significant performance improvement against the best-performing EEA methods.

Personalized product search that provides users with customized search services is an important task for e-commerce platforms. This task remains a challenge when inferring users’ preferences from few records or even no records, which is also known as the few-shot or zero-shot learning problem. In this paper, we propose a Bayesian Online Meta-Learning Model (BOML), which transfers meta-knowledge, from the inference for other users’ preferences, to help to infer the current user’s interest behind her/his few or even no historical records. To extract meta-knowledge from various inference patterns, our model constructs a mixture of meta-knowledge and transfers the corresponding meta-knowledge to the specific user according to her/his records. Based on the meta-knowledge learned from other similar inferences, our proposed model searches a ranked list of products to meet users’ personalized query intents for those with few search records (i.e., few-shot learning problem) or even no search records (i.e., zero-shot learning problem). Under the records arriving sequentially setting, we propose an online variational inference algorithm to update meta-knowledge over time. Experimental results demonstrate that our proposed BOML outperforms state-of-the-art algorithms.

Posttranslational modification of lysine residues, K-PTM, is one of the most popular PTMs. Some lysine residues in proteins can be continuously or cascaded covalently modified, such as acetylation, crotonylation, methylation and succinylation modification. The covalent modification of lysine residues may have some special functions in basic research and drug development. Although many computational methods have been developed to predict lysine PTMs, up to now, the K-PTM prediction methods have been modeled and learned a single class of K-PTM modification. In view of this, this study aims to fill this gap by building a multi-label computational model that can be directly used to predict multiple K-PTMs in proteins. In this study, a multi-label prediction model, MLysPRED, is proposed to identify multiple lysine sites using features generated from human protein sequences. In MLysPRED, three kinds of multi-label sequence encoding algorithms (MLDBPB, MLPSDAAP, MLPSTAAP) are proposed and combined with three encoding strategies (CHHAA, DR and Kmer) to convert preprocessed lysine sequences into effective numerical features. A multidimensional normal distribution oversampling technique and graph-based multi-view clustering under-sampling algorithm were first proposed and incorporated to reduce the proportion of the original training samples, and multi-label nearest neighbor algorithm is used for classification. It is observed that MLysPRED achieved an Aiming of 92.21%, Coverage of 94.98%, Accuracy of 89.63%, Absolute-True of 81.46% and Absolute-False of 0.0682 on the independent datasets. Additionally, comparison of results with five existing predictors also indicated that MLysPRED is very promising and encouraging to predict multiple K-PTMs in proteins. For the convenience of the experimental scientists, 'MLysPRED' has been deployed as a user-friendly web-server at http://47.100.136.41:8181.

The task of personalized product search aims at retrieving a ranked list of products given a user’s input query and his/her purchase history. To address this task, we propose the PSAM model, a Personalized, Sequential, Attentive and Metric-aware (PSAM) model, that learns the semantic representations of three different categories of entities, i.e., users, queries, and products, based on user sequential purchase historical data and the corresponding sequential queries. Specifically, a query-based attentive LSTM (QA-LSTM) model and an attention mechanism are designed to infer users dynamic embeddings, which is able to capture their short-term and long-term preferences. To obtain more fine-grained embeddings of the three categories of entities, a metric-aware objective is deployed in our model to force the inferred embeddings subject to the triangle inequality, which is a more realistic distance measurement for product search. Experiments conducted on four benchmark datasets show that our PSAM model significantly outperforms the state-of-the-art product search baselines in terms of effectiveness by up to 50.9% improvement under NDCG@20. Our visualization experiments further illustrate that the learned product embeddings are able to distinguish different types of products.

Deep quantization methods have shown high efficiency on large-scale image retrieval. However, current models heavily rely on ground-truth information, hindering the application of quantization in label-hungry scenarios. A more realistic demand is to learn from inexhaustible uploaded images that are associated with informal tags provided by amateur users. Though such sketchy tags do not obviously reveal the labels, they actually contain useful semantic information for supervising deep quantization. To this end, we propose Weakly-Supervised Deep Hyperspherical Quantization (WSDHQ), which is the first work to learn deep quantization from weakly tagged images. Specifically, 1) we use word embeddings to represent the tags and enhance their semantic information based on a tag correlation graph. 2) To better preserve semantic information in quantization codes and reduce quantization error, we jointly learn semantics-preserving embeddings and supervised quantizer on hypersphere by employing a well-designed fusion layer and tailor-made loss functions. Extensive experiments show that WSDHQ can achieve state-of-art performance in weakly-supervised compact coding.

Gaussian Process (GP) offers a principled non-parametric framework for learning stochastic functions. The generalization capability of GPs depends heavily on the kernel function, which implicitly imposes the smoothness assumptions of the data. However, common feature-based kernel functions are inefficient to model the relational data, where the smoothness assumptions implied by the kernels are violated. To model the complex and non-differentiable functions over relational data, we propose a novel Graph Convolutional Kernel, which enables to incorporate relational structures to feature-based kernels to capture the statistical structure of data. To validate the effectiveness of proposed kernel function in modeling relational data, we introduce GP models with Graph Convolutional Kernel in two relational learning settings, i.e., unsupervised settings of link prediction and semi-supervised settings of object classification. The parameters of our GP models are optimized through the scalable variational inducing point method. However, the highly structured likelihood objective requires densely sampling from variational distributions, which is costly and makes its optimization challenging in the unsupervised settings. To tackle this challenge, we propose a Local Neighbor Sampling technique with a provable more efficient computational complexity. Experimental results on real-world datasets demonstrate that our model achieves state-of-the-art performance in two relational learning tasks.

Gaussian Processes (GPs) define distributions over functions and their generalization capabilities depend heavily on the choice of kernels. In this paper, we propose a novel structure-aware random Fourier (SRF) kernel for GPs that brings several benefits when modeling graph-structured data. First, SRF kernel is defined with a spectral distribution based on the Fourier duality given by the Bochner's theorem, transforming the kernel learning problem to a distribution inference problem. Second, SRF kernel admits a random Fourier feature formulation that makes the kernel scalable for optimization. Third, SRF kernel enables to leverage geometric structures by taking subgraphs as inputs. To effectively optimize GPs with SRF kernel, we develop a variational EM algorithm, which alternates between an inference procedure (E-step) and a learning procedure (M-step). Experimental results on five real-world datasets show that our model can achieve state-of-the-art performance in two typical graph learning tasks, i.e., object classification and link prediction.

Conventional meta-learning considers a set of tasks from a stationary distribution. In contrast, this paper focuses on a more complex online setting, where tasks arrive sequentially and follow a non-stationary distribution. Accordingly, we propose a Variational Continual Bayesian Meta-Learning (VC-BML) algorithm. VC-BML maintains a Dynamic Gaussian Mixture Model for meta-parameters, with the number of component distributions determined by a Chinese Restaurant Process. Dynamic mixtures at the meta-parameter level increase the capability to adapt to diverse tasks due to a larger parameter space, alleviating the negative knowledge transfer problem. To infer posteriors of model parameters, compared to the previously used point estimation method, we develop a more robust posterior approximation method -- structured variational inference for the sake of avoiding forgetting knowledge. Experiments on tasks from non-stationary distributions show that VC-BML is superior in transferring knowledge among diverse tasks and alleviating catastrophic forgetting in an online setting.

Representation learning for temporal knowledge graphs has attracted increasing attention in recent years. In this paper, we study the problem of learning dynamic embeddings for temporal knowledge graphs. We address this problem by proposing a Dynamic Bayesian Knowledge Graphs Embedding model (DBKGE), which is able to dynamically track the semantic representations of entities over time in a joint metric space and make predictions for the future. Unlike other temporal knowledge graph embedding methods, DBKGE is a novel probabilistic representation learning method that aims at inferring dynamic embeddings of entities in a streaming scenario. To obtain high-quality embeddings and model their uncertainty, our DBKGE embeds entities with means and variances of Gaussian distributions. Based on amortized inference, an online inference algorithm is proposed to jointly learn the latent representations of entities and smooth their changes across time. Experiments on Yago and Wiki datasets demonstrate that our proposed algorithm outperforms the state-of-the-art static and temporal knowledge graph embedding models.

An indispensable component in task-oriented dialogue systems is the dialogue state tracker, which keeps track of users’ intentions in the course of conversation. The typical approach towards this goal is to fill in multiple pre-defined slots that are essential to complete the task. Although various dialogue state tracking methods have been proposed in recent years, most of them predict the value of each slot separately and fail to consider the correlations among slots. In this paper, we propose a slot self-attention mechanism that can learn the slot correlations automatically. Specifically, a slot-token attention is first utilized to obtain slot-specific features from the dialogue context. Then a stacked slot self-attention is applied on these features to learn the correlations among slots. We conduct comprehensive experiments on two multi-domain task-oriented dialogue datasets, including MultiWOZ 2.0 and MultiWOZ 2.1. The experimental results demonstrate that our approach achieves state-of-the-art performance on both datasets, verifying the necessity and effectiveness of taking slot correlations into consideration.

Neural point processes (NPPs) employ neural networks to capture complicated dynamics of asynchronous event sequences. Existing NPPs feed all history events into neural networks, assuming that all event types contribute to the prediction of the target type. However, this assumption can be problematic because in reality some event types do not contribute to the predictions of another type. To correct this defect, we learn to omit those types of events that do not contribute to the prediction of one target type during the formulation of NPPs. Towards this end, we simultaneously consider the tasks of (1) finding event types that contribute to predictions of the target types and (2) learning a NPP model from event sequences. For the former, we formulate a latent graph, with event types being vertices and non-zero contributing relationships being directed edges; then we propose a probabilistic graph generator, from which we sample a latent graph. For the latter, the sampled graph can be readily used as a plug-in to modify an existing NPP model. Because these two tasks are nested, we propose to optimize the model parameters through bilevel programming, and develop an efficient solution based on truncated gradient back-propagation. Experimental results on both synthetic and real-world datasets show the improved performance against state-of-the-art baselines. This work removes disturbance of non-contributing event types with the aid of a validation procedure, similar to the practice to mitigate overfitting used when training machine learning models.

Capturing the occurrence dynamics is crucial to predicting which type of events will happen next and when. A common method to do this is through Hawkes processes. To enhance their capacity, recurrent neural networks (RNNs) have been incorporated due to RNNs’ successes in processing sequential data such as languages. Recent evidence suggests that self-attention is more competent than RNNs in dealing with languages. However, we are unaware of the effectiveness of self-attention in the context of Hawkes processes. This study aims to fill the gap by designing a self-attentive Hawkes process (SAHP). SAHP employs self-attention to summarise the influence of history events and compute the probability of the next event. One deficit of the conventional self-attention when applied to event sequences is that its positional encoding only considers the order of a sequence ignoring the time intervals between events. To overcome this deficit, we modify its encoding by translating time intervals into phase shifts of sinusoidal functions. Experiments on goodness-of-fit and prediction tasks show the improved capability of SAHP. Furthermore, SAHP is more interpretable than RNN-based counterparts because the learnt attention weights reveal contributions of one event type to the happening of another type. To the best of our knowledge, this is the first work that studies the effectiveness of self-attention in Hawkes processes.

The field of recommender systems has rapidly evolved over the last few years, with significant advances made due to the in-flux of deep learning techniques. However, as a result of this rapid progress, escalating barriers-to-entry for new researchers is emerging. In particular, state-of-the-art approaches have fragmented into a large number of code-bases, often requiring different input formats, pre-processing stages and evaluating with different metric packages. Hence, it is time-consuming for new researchers to reach the point of having both an effective baseline set and a sound comparative environment. As a step towards elevating this problem, we have developed BETA-Rec, an open source project for Building, Evaluating and Tuning Automated Recommender Systems. BETA-Rec aims to provide a practical data toolkit for building end-to-end recommendation systems in a standardized way. It provides means for dataset preparation and splitting using common strategies, a generalized model engine for implementing recommender models using Pytorch with 9 models available out-of-the-box, as well as a unified training, validation, tuning and testing pipeline. Furthermore, BETA-Rec is designed to be both modular and extensible, enabling new models to be quickly added to the framework. It is deployable in a wide range of environments via pre-built docker containers and supports distributed parameter tuning using Ray. In this demo, we will illustrate the deployment and use of BETA-Rec for researchers and practitioners on a number of standard recommendation datasets. The source code of the project is available at github: https://github.com/beta-team/beta-recsys.

The quality of digital information on the web has been disquieting due to the absence of careful checking. Consequently, a large volume of false textual information is being produced and disseminated. The focus of this doctoral study is to work towards evaluating veracity of textual statements on the web. The major contributions to this growing area of research will be made from the following aspects: (1) improve stance detection and incorporate it to misinformation detection; (2) effectively utilize noisy, unstructured user engagements on social media platforms; (3) design a general framework for the early misinformation detection. Findings of this research will provide a deeper understanding of how machine learning can be leveraged to automatically detect misinformation.

Stance detection has gained increasing interest from the research community due to its importance for fake news detection. The goal of stance detection is to categorize an overall position of a subject towards an object into one of the four classes: agree, disagree, discuss, and unrelated. One of the major problems faced by current machine learning models used for stance detection is caused by a severe class imbalance among these classes. Hence, most models fail to correctly classify instances that fall into minority classes. In this paper, we address this problem by proposing a hierarchical representation of these classes, which combines the agree, disagree, and discuss classes under a new related class. Further, we propose a two-layer neural network that learns from this hierarchical representation and controls the error propagation between the two layers using the Maximum Mean Discrepancy regularizer. Compared with conventional four-way classifiers, this model has two advantages: (1) the hierarchical architecture mitigates the class imbalance problem; (2) the regularization makes the model to better discern between the related and unrelated stances. An extensive experimentation demonstrates state-of-the-art accuracy performance of the proposed model for stance detection.

Social media platforms are a plethora of misinformation and its potential negative influence on the public is a growing concern. This concern has drawn the attention of the research community on developing mechanisms to detect misinformation. The task of misinformation detection consists of classifying whether a claim is True or False. Most research concentrates on developing machine learning models, such as neural networks, that outputs a single value in order to predict the veracity of a claim. One of the major problem faced by these models is the inability of representing the uncertainty of the prediction, which is due incomplete or finite available information about the claim being examined. We address this problem by proposing a Bayesian deep learning model. The Bayesian model outputs a distribution used to represent both the prediction and its uncertainty. In addition to the claim content, we also encode auxiliary information given by people's replies to the claim. First, the model encodes a claim to be verified, and generate a prior belief distribution from which we sample a latent variable. Second, the model encodes all the people's replies to the claim in a temporal order through a Long Short Term Memory network in order to summarize their content. This summary is then used to update the prior belief generating the posterior belief. Moreover, in order to train this model, we develop a Stochastic Gradient Variational Bayes algorithm to approximate the analytically intractable posterior distribution. Experiments conducted on two public datasets demonstrate that our model outperforms the state-of-the-art detection models.