Weakly-Supervised Scientific Document Classification via Retrieval-Augmented Multi-Stage Training

Scientific document classification is a critical task for a wide range of applications, but the cost of obtaining massive amounts of human-labeled data can be prohibitive. To address this challenge, we propose a weakly-supervised approach for scientific document classification using label names only. In scientific domains, label names often include domain-specific concepts that may not appear in the document corpus, making it difficult to match labels and documents precisely. To tackle this issue, we propose WANDER, which leverages dense retrieval to perform matching in the embedding space to capture the semantics of label names. We further design the label name expansion module to enrich the label name representations. Lastly, a self-training step is used to refine the predictions. The experiments on three datasets show that WANDER outperforms the best baseline by 11.9% on average. Our code will be published at https://github.com/ritaranx/wander.

A Survey on Knowledge Graphs for Healthcare: Resources, Applications, and Promises

Healthcare knowledge graphs (HKGs) have emerged as a promising tool for organizing medical knowledge in a structured and interpretable way, which provides a comprehensive view of medical concepts and their relationships. However, challenges such as data heterogeneity and limited coverage remain, emphasizing the need for further research in the field of HKGs. This survey paper serves as the first comprehensive overview of HKGs. We summarize the pipeline and key techniques for HKG construction (i.e., from scratch and through integration), as well as the common utilization approaches (i.e., model-free and model-based). To provide researchers with valuable resources, we organize existing HKGs (The resource is available at https://github.com/lujiaying/Awesome-HealthCare-KnowledgeBase) based on the data types they capture and application domains, supplemented with pertinent statistical information. In the application section, we delve into the transformative impact of HKGs across various healthcare domains, spanning from fine-grained basic science research to high-level clinical decision support. Lastly, we shed light on the opportunities for creating comprehensive and accurate HKGs in the era of large language models, presenting the potential to revolutionize healthcare delivery and enhance the interpretability and reliability of clinical prediction.

GAD-NR: Graph Anomaly Detection via Neighborhood Reconstruction

Graph Anomaly Detection (GAD) is a technique used to identify abnormal nodes within graphs, finding applications in network security, fraud detection, social media spam detection, and various other domains. A common method for GAD is Graph Auto-Encoders (GAEs), which encode graph data into node representations and identify anomalies by assessing the reconstruction quality of the graphs based on these representations. However, existing GAE models are primarily optimized for direct link reconstruction, resulting in nodes connected in the graph being clustered in the latent space. As a result, they excel at detecting cluster-type structural anomalies but struggle with more complex structural anomalies that do not conform to clusters. To address this limitation, we propose a novel solution called GAD-NR, a new variant of GAE that incorporates neighborhood reconstruction for graph anomaly detection. GAD-NR aims to reconstruct the entire neighborhood of a node, encompassing the local structure, self-attributes, and neighbor attributes, based on the corresponding node representation. By comparing the neighborhood reconstruction loss between anomalous nodes and normal nodes, GAD-NR can effectively detect any anomalies. Extensive experimentation conducted on six real-world datasets validates the effectiveness of GAD-NR, showcasing significant improvements (by up to 30% in AUC) over state-of-the-art competitors. The source code for GAD-NR is openly available. Importantly, the comparative analysis reveals that the existing methods perform well only in detecting one or two types of anomalies out of the three types studied. In contrast, GAD-NR excels at detecting all three types of anomalies across the datasets, demonstrating its comprehensive anomaly detection capabilities.

Graph-Aware Language Model Pre-Training on a Large Graph Corpus Can Help Multiple Graph Applications

Model pre-training on large text corpora has been demonstrated effective for various downstream applications in the NLP domain. In the graph mining domain, a similar analogy can be drawn for pre-training graph models on large graphs in the hope of benefiting downstream graph applications, which has also been explored by several recent studies. However, no existing study has ever investigated the pre-training of text plus graph models on large heterogeneous graphs with abundant textual information (a.k.a. large graph corpora) and then fine-tuning the model on different related downstream applications with different graph schemas. To address this problem, we propose a framework of graph-aware language model pre-training (GALM) on a large graph corpus, which incorporates large language models and graph neural networks, and a variety of fine-tuning methods on downstream applications. We conduct extensive experiments on Amazon's real internal datasets and large public datasets. Comprehensive empirical results and in-depth analysis demonstrate the effectiveness of our proposed methods along with lessons learned.

R-Mixup: Riemannian Mixup for Biological Networks

Biological networks are commonly used in biomedical and healthcare domains to effectively model the structure of complex biological systems with interactions linking biological entities. However, due to their characteristics of high dimensionality and low sample size, directly applying deep learning models on biological networks usually faces severe overfitting. In this work, we propose R-MIXUP, a Mixup-based data augmentation technique that suits the symmetric positive definite (SPD) property of adjacency matrices from biological networks with optimized training efficiency. The interpolation process in R-MIXUP leverages the log-Euclidean distance metrics from the Riemannian manifold, effectively addressing the swelling effect and arbitrarily incorrect label issues of vanilla Mixup. We demonstrate the effectiveness of R-MIXUP with five real-world biological network datasets on both regression and classification tasks. Besides, we derive a commonly ignored necessary condition for identifying the SPD matrices of biological networks and empirically study its influence on the model performance. The code implementation can be found in Appendix E.

PV2TEA: Patching Visual Modality to Textual-Established Information Extraction

Information extraction, e.g., attribute value extraction, has been extensively studied and formulated based only on text. However, many attributes can benefit from image-based extraction, like color, shape, pattern, among others. The visual modality has long been underutilized, mainly due to multimodal annotation difficulty. In this paper, we aim to patch the visual modality to the textual-established attribute information extractor. The cross-modality integration faces several unique challenges: (C1) images and textual descriptions are loosely paired intra-sample and inter-samples; (C2) images usually contain rich backgrounds that can mislead the prediction; (C3) weakly supervised labels from textual-established extractors are biased for multimodal training. We present PV2TEA, an encoder-decoder architecture equipped with three bias reduction schemes: (S1) Augmented label-smoothed contrast to improve the cross-modality alignment for loosely-paired image and text; (S2) Attention-pruning that adaptively distinguishes the visual foreground; (S3) Two-level neighborhood regularization that mitigates the label textual bias via reliability estimation. Empirical results on real-world e-Commerce datasets demonstrate up to 11.74% absolute (20.97% relatively) F1 increase over unimodal baselines.

Beyond One-Model-Fits-All: A Survey of Domain Specialization for Large Language Models

Large language models (LLMs) have significantly advanced the field of natural language processing (NLP), providing a highly useful, task-agnostic foundation for a wide range of applications. The great promise of LLMs as general task solvers motivated people to extend their functionality largely beyond just a ``chatbot'', and use it as an assistant or even replacement for domain experts and tools in specific domains such as healthcare, finance, and education. However, directly applying LLMs to solve sophisticated problems in specific domains meets many hurdles, caused by the heterogeneity of domain data, the sophistication of domain knowledge, the uniqueness of domain objectives, and the diversity of the constraints (e.g., various social norms, cultural conformity, religious beliefs, and ethical standards in the domain applications). To fill such a gap, explosively-increase research, and practices have been conducted in very recent years on the domain specialization of LLMs, which, however, calls for a comprehensive and systematic review to better summarizes and guide this promising domain. In this survey paper, first, we propose a systematic taxonomy that categorizes the LLM domain-specialization techniques based on the accessibility to LLMs and summarizes the framework for all the subcategories as well as their relations and differences to each other. We also present a comprehensive taxonomy of critical application domains that can benefit from specialized LLMs, discussing their practical significance and open challenges. Furthermore, we offer insights into the current research status and future trends in this area.

PTGB: Pre-Train Graph Neural Networks for Brain Network Analysis

The human brain is the central hub of the neurobiological system, controlling behavior and cognition in complex ways. Recent advances in neuroscience and neuroimaging analysis have shown a growing interest in the interactions between brain regions of interest (ROIs) and their impact on neural development and disorder diagnosis. As a powerful deep model for analyzing graph-structured data, Graph Neural Networks (GNNs) have been applied for brain network analysis. However, training deep models requires large amounts of labeled data, which is often scarce in brain network datasets due to the complexities of data acquisition and sharing restrictions. To make the most out of available training data, we propose PTGB, a GNN pre-training framework that captures intrinsic brain network structures, regardless of clinical outcomes, and is easily adaptable to various downstream tasks. PTGB comprises two key components: (1) an unsupervised pre-training technique designed specifically for brain networks, which enables learning from large-scale datasets without task-specific labels; (2) a data-driven parcellation atlas mapping pipeline that facilitates knowledge transfer across datasets with different ROI systems. Extensive evaluations using various GNN models have demonstrated the robust and superior performance of PTGB compared to baseline methods.

GNNs,You can be Stronger,Deeper and Faster

Graph neural networks (GNNs), a type of neural network that can learn from graph-structured data and learn the representation of nodes by aggregating their neighbors, have shown excellent performance in downstream tasks.However, it is known that the performance of graph neural networks (GNNs) degrades gradually as the number of layers increases. Based on k-hop subgraph aggregation, which is a new concept, we propose a new perspective to understand the expressive power of GNN.From this perspective, we reveal the potential causes of the performance degradation of the deep traditional GNN - aggregated subgraph overlap, and the fact that the residual-based graph neural networks in fact exploit the aggregation results of 1 to k hop subgraphs to improve the effectiveness.Further, we propose a new sampling-based node-level residual module named SDF, which is shown by theoretical derivation to obtain a superior expressive power compared to previous residual methods by using information from 1 to k hop subgraphs more flexibly. Extensive experiments show that the performance and efficiency of GNN with the SDF module outperform other methods.

Transformer-Based Hierarchical Clustering for Brain Network Analysis

Brain networks, graphical models such as those constructed from MRI, have been widely used in pathological prediction and analysis of brain functions. Within the complex brain system, differences in neuronal connection strengths parcellate the brain into various functional modules (network communities), which are critical for brain analysis. However, identifying such communities within the brain has been a nontrivial issue due to the complexity of neuronal interactions. In this work, we propose a novel interpretable transformer-based model for joint hierarchical cluster identification and brain network classification. Extensive experimental results on real-world brain network datasets show that with the help of hierarchical clustering, the model achieves increased accuracy and reduced runtime complexity while providing plausible insight into the functional organization of brain regions. The implementation is available at https://github.com/DDVD233/THC.