Anomaly detection on text-rich graphs is widely prevalent in real life, such as detecting incorrectly assigned academic papers to authors and detecting bots in social networks. The remarkable capabilities of large language models (LLMs) pave a new revenue by utilizing rich-text information for effective anomaly detection. However, simply introducing rich texts into LLMs can obscure essential detection cues and introduce high fine-tuning costs. Moreover, LLMs often overlook the intrinsic structural bias of graphs which is vital for distinguishing normal from abnormal node patterns. To this end, this paper introduces GuARD, a text-rich and graph-informed language model that combines key structural features from graph-based methods with fine-grained semantic attributes extracted via small language models for effective anomaly detection on text-rich graphs. GuARD is optimized with the progressive multimodal multi-turn instruction tuning framework in the task-guided instruction tuning regime tailed to incorporate both rich-text and structural modalities. Extensive experiments on four datasets reveal that GuARD outperforms graph-based and LLM-based anomaly detection methods, while offering up to 5× speedup in training and 10× speedup in inference over vanilla long-context LLMs on the large-scale WhoIsWho dataset.

MOTIVATION: As one of the recalcitrant challenges in life sciences and biomedicine, protein function prediction suffers from a deluge of AI-designed proteins, particularly having to face multi-modal information in the era of big data. Importing the high-throughput neural-network-based prediction framework to replace the low-throughput biological experiments, a universal multi-modal method is straightforward in addressing the growing gap between known sequences and predicting functions. RESULTS: To bridge the gap, we propose ProtGO, a three-step framework for predicting protein function, which leverages the credible Gene Ontology (GO) knowledge base and integrates four common modalities. Specifically, we first introduce frontier pre-trained protein language models (PLMs) for representation learning of mainstay functional protein sequences. For the remaining multi-modal data, we design a text alignment module for explainable text descriptions, a taxonomy encoding module for species-specific taxonomy, and a GO graph embedding module for biological GO relations. Each module is independent and adaptive for the referenced modalities. By harnessing these four knowledge representations, ProtGO maximizes the potential of GO resources, enhancing the performance of vanilla PLMs and biological language models (LMs) in downstream GO prediction tasks. Extensive experiments demonstrate that ProtGO significantly advances the abilities of state-of-the-art PLMs to predict protein functions: approximately 8% to 27% increase in the maximum F1 measure (Fmax) compared to base models. These comprehensive studies confirm ProtGO's capability to deliver outstanding performance in protein function prediction by utilizing a rich blend of functional and evolutionary knowledge. AVAILABILITY AND IMPLEMENTATION: Our source code and all the data are available at https://github.com/sunyatawang/ProtGO.

With the rapid proliferation of scientific literature, versatile academic knowledge services increasingly rely on comprehensive academic graph mining. Despite the availability of public academic graphs, benchmarks, and datasets, these resources often fall short in multi-aspect and fine-grained annotations, are constrained to specific task types and domains, or lack underlying real academic graphs. In this paper, we present OAG-Bench, a comprehensive, multi-aspect, and fine-grained human-curated benchmark based on the Open Academic Graph (OAG). OAG-Bench covers 10 tasks, 20 datasets, 70+ baselines, and 120+ experimental results to date. We propose new data annotation strategies for certain tasks and offer a suite of data pre-processing codes, algorithm implementations, and standardized evaluation protocols to facilitate academic graph mining. Extensive experiments reveal that even advanced algorithms like large language models (LLMs) encounter difficulties in addressing key challenges in certain tasks, such as paper source tracing and scholar profiling. We also introduce the Open Academic Graph Challenge (OAG-Challenge) to encourage community input and sharing. We envisage that OAG-Bench can serve as a common ground for the community to evaluate and compare algorithms in academic graph mining, thereby accelerating algorithm development and advancement in this field. OAG-Bench is accessible at https://www.aminer.cn/data/.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high-quality MSA. Although various methods have been proposed to generate high-quality MSA under these conditions, they fall short in comprehensively capturing the intricate co-evolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pre-training in a low-MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model the complex evolutionary patterns. Endowed by this, the flexible 1D MSA decoding framework facilitates zero- or few-shot learning. Moreover, we demonstrate leveraging the feedback from AlphaFold2 (AF2) can further enhance the model’s capacity via Rejective Fine-tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful and informative MSA (up to +8.5% TM-Score on few-shot scenarios). The transfer learning also demonstrates its great potential for the wide range of tasks resorting to the quality of MSA.

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for Masked Language Model (MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.

From-scratch name disambiguation is an essential task for establishing a reliable foundation for academic platforms.It involves partitioning documents authored by identically named individuals into groups representing distinct real-life experts.Canonically, the process is divided into two decoupled tasks: locally estimating the pairwise similarities between documents followed by globally grouping these documents into appropriate clusters.However, such a decoupled approach often inhibits optimal information exchange between these intertwined tasks.Therefore, we present BOND, which bootstraps the local and global informative signals to promote each other in an end-to-end regime.Specifically, BOND harnesses local pairwise similarities to drive global clustering, subsequently generating pseudo-clustering labels.These global signals further refine local pairwise characterizations.The experimental results establish BOND's superiority, outperforming other advanced baselines by a substantial margin.Moreover, an enhanced version, BOND+, incorporating ensemble and post-match techniques, rivals the top methods in the WhoIsWho competition 1 .

Name disambiguation---a fundamental problem in online academic systems--is now facing greater challenges with the increasing growth of research papers. For example, on AMiner, an online academic search platform, about 10% of names own more than 100 authors. Such real-world challenging cases have not been effectively addressed by existing researches due to the small-scale or low-quality datasets that they have used. The development of effective algorithms is further hampered by a variety of tasks and evaluation protocols designed on top of diverse datasets. To this end, we present Who Is Who owning, a large-scale benchmark with over 1,000,000 papers built using an interactive annotation process, a regular leaderboard with comprehensive tasks, and an easy-to-use toolkit encapsulating the entire pipeline as well as the most powerful features and baseline models for tackling the tasks. Our developed strong baseline has already been deployed online in the AMiner system to enable daily arXiv paper assignments.

AlphaFold-Multimer has greatly improved the protein complex structure prediction, but its accuracy also depends on the quality of the multiple sequence alignment (MSA) formed by the interacting homologs (i.e. interologs) of the complex under prediction. Here we propose a novel method, ESMPair, that can identify interologs of a complex using protein language models. We show that ESMPair can generate better interologs than the default MSA generation method in AlphaFold-Multimer. Our method results in better complex structure prediction than AlphaFold-Multimer by a large margin (+10.7% in terms of the Top-5 best DockQ), especially when the predicted complex structures have low confidence. We further show that by combining several MSA generation methods, we may yield even better complex structure prediction accuracy than Alphafold-Multimer (+22% in terms of the Top-5 best DockQ). By systematically analyzing the impact factors of our algorithm we find that the diversity of MSA of interologs significantly affects the prediction accuracy. Moreover, we show that ESMPair performs particularly well on complexes in eucaryotes.

Graph-based anomaly detection has been widely used for detecting malicious activities in real-world applications. Existing attempts to address this problem have thus far focused on structural feature engineering or learning in the binary classification regime. In this work, we propose to leverage graph contrastive learning and present the supervised GCCAD model for contrasting abnormal nodes with normal ones in terms of their distances to the global context (e.g., the average of all nodes). To handle scenarios with scarce labels, we further enable GCCAD as a self-supervised framework by designing a graph corrupting strategy for generating synthetic node labels. To achieve the contrastive objective, we design a graph neural network encoder that can infer and further remove suspicious links during message passing, as well as learn the global context of the input graph. We conduct extensive experiments on four public datasets, demonstrating that 1) GCCAD significantly and consistently outperforms various advanced baselines and 2) its self-supervised version without fine-tuning can achieve comparable performance with its fully supervised version.

Expert finding, a popular service provided by many online websites such as Expertise Finder, LinkedIn, and AMiner, is beneficial to seeking candidate qualifications, consultants, and collaborators. However, its quality is suffered from lack of ample sources of expert information. This paper employs AMiner as the basis with an aim at linking any external experts to the counterparts on AMiner. As it is infeasible to acquire sufficient linkages from arbitrary external sources, we explore the problem of zero-shot expert linking. In this paper, we propose CODE, which first pre-trains an expert linking model by contrastive learning on AMiner such that it can capture the representation and matching patterns of experts without supervised signals, then it is fine-tuned between AMinerand external sources to enhance the model’s transferability in an adversarial manner. For evaluation, we first design two intrinsic tasks, author identification and paper clustering, to validate the representation and matching capability endowed by contrastive learning. Then the final external expert linking performance on two genres of external sources also implies the superiority of adversarial fine-tuning method. Additionally, we show the online deployment of CODE, and continuously improve its online performance via active learning.

Name disambiguation is a key and also a very tough problem in many online systems such as social search and academic search. Despite considerable research, a critical issue that has not been systematically studied isdisambiguation on the fly— to complete the disambiguation in the real-time. This is very challenging, as the disambiguation algorithm must be accurate, efficient, and error tolerance. In this paper, we propose a novel framework — CONNA — to train a matching component and a decision component jointly via reinforcement learning. The matching component is responsible for finding the top matched candidate for the given paper, and the decision component is responsible for deciding on assigning the top matched person or creating a new person. The two components are intertwined and can be bootstrapped via jointly training. Empirically, we evaluate CONNA on two name disambiguation datasets. Experimental results show that the proposed framework can achieve a 1.21-19.84 percent improvement on F1-score using joint training of the matching and the decision components. The proposed CONNA has been successfully deployed on AMiner — a large online academic search system.

Knowledge graph alignment aims to link equivalent entities across different knowledge graphs. To utilize both the graph structures and the side information such as name, description and attributes, most of the works propagate the side information especially names through linked entities by graph neural networks. However, due to the heterogeneity of different knowledge graphs, the alignment accuracy will be suffered from aggregating different neighbors. This work presents an interaction model to only leverage the side information. Instead of aggregating neighbors, we compute the interactions between neighbors which can capture fine-grained matches of neighbors. Similarly, the interactions of attributes are also modeled. Experimental results show that our model significantly outperforms the best state-of-the-art methods by 1.9-9.7% in terms of HitRatio@1 on the dataset DBP15K.

The proliferation of massive open online courses (MOOCs) demands an effective way of personalized course recommendation. The recent attention-based recommendation models can distinguish the effects of different historical courses when recommending different target courses. However, when a user has interests in many different courses, the attention mechanism will perform poorly as the effects of the contributing courses are diluted by diverse historical courses. To address such a challenge, we propose a hierarchical reinforcement learning algorithm to revise the user profiles and tune the course recommendation model on the revised profiles.Systematically, we evaluate the proposed model on a real dataset consisting of 1,302 courses, 82,535 users and 458,454 user enrolled behaviors, which were collected from XuetangX—one of the largest MOOCs in China. Experimental results show that the proposed model significantly outperforms the state-of-the-art recommendation models (improving 5.02% to 18.95% in terms of HR@10).

Aligning users across multiple heterogeneous social networks is a fundamental issue in many data mining applications. Methods that incorporate user attributes and network structure have received much attention. However, most of them suffer from error propagation or the noise from diverse neighbors in the network. To effectively model the influence from neighbors, we propose a graph neural network to directly represent the ego networks of two users to be aligned into an embedding, based on which we predict the alignment label. Three major mechanisms in the model are designed to unitedly represent different attributes, distinguish different neighbors and capture the structure information of the ego networks respectively.

Social instant messaging services are emerging as a transformative form with which people connect, communicate with friends in their daily life they catalyze the formation of social groups, and they bring people stronger sense of community and connection. However, research community still knows little about the formation and evolution of groups in the context of social messaging their lifecycles, the change in their underlying structures over time, and the diffusion processes by which they develop new members. In this paper, we analyze the daily usage logs from WeChat group messaging platform the largest standalone messaging communication service in China with the goal of understanding the processes by which social messaging groups come together, grow new members, and evolve over time. Specifically, we discover a strong dichotomy among groups in terms of their lifecycle, and develop a separability model by taking into account a broad range of group-level features, showing that long-term and short-term groups are inherently distinct. We also found that the lifecycle of messaging groups is largely dependent on their social roles and functions in users' daily social experiences and specific purposes. Given the strong separability between the long-term and short-term groups, we further address the problem concerning the early prediction of successful communities. In addition to modeling the growth and evolution from group-level perspective, we investigate the individual-level attributes of group members and study the diffusion process by which groups gain new members. By considering members' historical engagement behavior as well as the local social network structure that they embedded in, we develop a membership cascade model and demonstrate the effectiveness by achieving AUC of 95.31% in predicting inviter, and an AUC of 98.66% in predicting invitee.