arXiv subjects

Yushi Bai

Publications and source records attributed to Yushi Bai.

41 records · Page 3Linked to original sources

arXiv2023

Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.

cs.LG↗

arXiv2023

Answering Complex Logical Queries on Knowledge Graphs via Query Computation Tree Optimization

Answering complex logical queries on incomplete knowledge graphs is a challenging task, and has been widely studied. Embedding-based methods require training on complex queries, and cannot generalize well to out-of-distribution query structures. Recent work frames this task as an end-to-end optimization problem, and it only requires a pretrained link predictor. However, due to the exponentially large combinatorial search space, the optimal solution can only be approximated, limiting the final accuracy. In this work, we propose QTO (Query Computation Tree Optimization) that can efficiently find the exact optimal solution. QTO finds the optimal solution by a forward-backward propagation on the tree-like computation graph, i.e., query computation tree. In particular, QTO utilizes the independence encoded in the query computation tree to reduce the search space, where only local computations are involved during the optimization procedure. Experiments on 3 datasets show that QTO obtains state-of-the-art performance on complex query answering, outperforming previous best results by an average of 22%. Moreover, QTO can interpret the intermediate solutions for each of the one-hop atoms in the query with over 90% accuracy. The code of our paper is at https://github.com/bys0318/QTO.

cs.LG↗

arXiv2022

SQUIRE: A Sequence-to-sequence Framework for Multi-hop Knowledge Graph Reasoning

Multi-hop knowledge graph (KG) reasoning has been widely studied in recent years to provide interpretable predictions on missing links with evidential paths. Most previous works use reinforcement learning (RL) based methods that learn to navigate the path towards the target entity. However, these methods suffer from slow and poor convergence, and they may fail to infer a certain path when there is a missing edge along the path. Here we present SQUIRE, the first Sequence-to-sequence based multi-hop reasoning framework, which utilizes an encoder-decoder Transformer structure to translate the query to a path. Our framework brings about two benefits: (1) It can learn and predict in an end-to-end fashion, which gives better and faster convergence; (2) Our Transformer model does not rely on existing edges to generate the path, and has the flexibility to complete missing edges along the path, especially in sparse KGs. Experiments on standard and sparse KGs show that our approach yields significant improvement over prior methods, while converging 4x-7x faster.

cs.CL↗

arXiv2022

Envy-Free and Pareto-Optimal Allocations for Agents with Asymmetric Random Valuations

We study the problem of allocating $m$ indivisible items to $n$ agents with additive utilities. It is desirable for the allocation to be both fair and efficient, which we formalize through the notions of envy-freeness and Pareto-optimality. While envy-free and Pareto-optimal allocations may not exist for arbitrary utility profiles, previous work has shown that such allocations exist with high probability assuming that all agents' values for all items are independently drawn from a common distribution. In this paper, we consider a generalization of this model where each agent's utilities are drawn independently from a distribution specific to the agent. We show that envy-free and Pareto-optimal allocations are likely to exist in this asymmetric model when $m=Ω\left(n\log n\right)$, which is tight up to a log log gap that also remains open in the symmetric subsetting. Furthermore, these guarantees can be achieved by a polynomial-time algorithm.

cs.GT↗

arXiv2021

Modeling Heterogeneous Hierarchies with Relation-specific Hyperbolic Cones

Hierarchical relations are prevalent and indispensable for organizing human knowledge captured by a knowledge graph (KG). The key property of hierarchical relations is that they induce a partial ordering over the entities, which needs to be modeled in order to allow for hierarchical reasoning. However, current KG embeddings can model only a single global hierarchy (single global partial ordering) and fail to model multiple heterogeneous hierarchies that exist in a single KG. Here we present ConE (Cone Embedding), a KG embedding model that is able to simultaneously model multiple hierarchical as well as non-hierarchical relations in a knowledge graph. ConE embeds entities into hyperbolic cones and models relations as transformations between the cones. In particular, ConE uses cone containment constraints in different subspaces of the hyperbolic embedding space to capture multiple heterogeneous hierarchies. Experiments on standard knowledge graph benchmarks show that ConE obtains state-of-the-art performance on hierarchical reasoning tasks as well as knowledge graph completion task on hierarchical graphs. In particular, our approach yields new state-of-the-art Hits@1 of 45.3% on WN18RR and 16.1% on DDB14 (0.231 MRR). As for hierarchical reasoning task, our approach outperforms previous best results by an average of 20% across the three datasets.

cs.LG↗