Spatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facilitate inference of spatially resolved cell-cell communications, we here present SpaTalk, which relies on a graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data. The benchmarked performance of SpaTalk on public single-cell spatial transcriptomic datasets is superior to that of existing inference methods. Then we apply SpaTalk to STARmap, Slide-seq, and 10X Visium data, revealing the in-depth communicative mechanisms underlying normal and disease tissues with spatial structure. SpaTalk can uncover spatially resolved cell-cell communications for single-cell and spot-based spatially resolved transcriptomic data universally, providing valuable insights into spatial inter-cellular tissue dynamics.
Knowledge Graph Completion (KGC) has been proposed to improve Knowledge Graphs by filling in missing connections via link prediction or relation extraction. One of the main difficulties for KGC is a low resource problem. Previous approaches assume sufficient training triples to learn versatile vectors for entities and relations, or a satisfactory number of labeled sentences to train a competent relation extraction model. However, low resource relations are very common in KGs, and those newly added relations often do not have many known samples for training. In this work, we aim at predicting new facts under a challenging setting where only limited training instances are available. We propose a general framework called Weighted Relation Adversarial Network, which utilizes an adversarial procedure to help adapt knowledge/features learned from high resource relations to different but related low resource relations. Specifically, the framework takes advantage of a relation discriminator to distinguish between samples from different relations, and help learn relation-invariant features more transferable from source relations to target relations. Experimental results show that the proposed approach outperforms previous methods regarding low resource settings for both link prediction and relation extraction.
Zero-shot learning has been a tough problem since no labeled data is available for unseen classes during training, especially for classes with low similarity. In this situation, transferring from seen classes to unseen classes is extremely hard. To tackle this problem, in this paper we propose a self-training based method to efficiently leverage unlabeled data. Traditional self-training methods use fixed heuristics to select instances from unlabeled data, whose performance varies among different datasets. We propose a reinforcement learning framework to learn data selection strategy automatically and provide more reliable selection. Experimental results on both benchmarks and a real-world e-commerce dataset show that our approach significantly outperforms previous methods in zero-shot text classification.
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.
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