By focusing the pre-training process on domain-specific corpora, some domain-specific pre-trained language models (PLMs) have achieved state-of-the-art results. However, it is under-investigated to design a unified paradigm to inject domain knowledge in the PLM fine-tuning stage. We propose KnowledgeDA, a unified domain language model development service to enhance the task-specific training procedure with domain knowledge graphs. Given domain-specific task texts input, KnowledgeDA can automatically generate a domain-specific language model following three steps: (i) localize domain knowledge entities in texts via an embedding-similarity approach; (ii) generate augmented samples by retrieving replaceable domain entity pairs from two views of both knowledge graph and training data; (iii) select high-quality augmented samples for fine-tuning via confidence-based assessment. We implement a prototype of KnowledgeDA to learn language models for two domains, healthcare and software development. Experiments on domain-specific text classification and QA tasks verify the effectiveness and generalizability of KnowledgeDA.

In this paper, we present the ``joint pre-training and local re-training'' framework for learning and applying multi-source knowledge graph (KG) embeddings. We are motivated by the fact that different KGs contain complementary information to improve KG embeddings and downstream tasks. We pre-train a large teacher KG embedding model over linked multi-source KGs and distill knowledge to train a student model for a task-specific KG. To enable knowledge transfer across different KGs, we use entity alignment to build a linked subgraph for connecting the pre-trained KGs and the target KG. The linked subgraph is re-trained for three-level knowledge distillation from the teacher to the student, i.e., feature knowledge distillation, network knowledge distillation, and prediction knowledge distillation, to generate more expressive embeddings. The teacher model can be reused for different target KGs and tasks without having to train from scratch. We conduct extensive experiments to demonstrate the effectiveness and efficiency of our framework.

Joint representation learning over multi-sourced knowledge graphs (KGs) yields transferable and expressive embeddings that improve downstream tasks. Entity alignment (EA) is a critical step in this process. Despite recent considerable research progress in embedding-based EA, how it works remains to be explored. In this paper, we provide a similarity flooding perspective to explain existing translation-based and aggregation-based EA models. We prove that the embedding learning process of these models actually seeks a fixpoint of pairwise similarities between entities. We also provide experimental evidence to support our theoretical analysis. We propose two simple but effective methods inspired by the fixpoint computation in similarity flooding, and demonstrate their effectiveness on benchmark datasets. Our work bridges the gap between recent embedding-based models and the conventional similarity flooding algorithm. It would improve our understanding of and increase our faith in embedding-based EA.

This project demonstrates how medical corpus hypothesis generation, a knowledge discovery field of AI, can be used to derive new research angles for landscape and urban planners. The hypothesis generation approach herein consists of a combination of deep learning with topic modeling, a probabilistic approach to natural language analysis that scans aggregated research databases for words that can be grouped together based on their subject matter commonalities; the word groups accordingly form topics that can provide implicit connections between two general research terms. The hypothesis generation system AGATHA was used to identify likely conceptual relationships between emerging infectious diseases (EIDs) and deforestation, with the objective of providing landscape planners guidelines for productive research directions to help them formulate research hypotheses centered on deforestation and EIDs that will contribute to the broader health field that asserts causal roles of landscape-level issues. This research also serves as a partial proof-of-concept for the application of medical database hypothesis generation to medicine-adjacent hypothesis discovery. Keywords deforestation, emerging infectious disease, hypothesis generation, landscape planning, topic modeling Funding This research was funded by National Science Foundation grant numbers 1633608 and 2027864. The authors express their gratitude to the NSF for its generous support of their research. Introduction The recent COVID-19 crisis has put the issue of emerging infectious diseases (EIDs) back in the global spotlight. Addressing EIDs going forward will require widespread interdisciplinary cooperation, as discouraging them is a multifaceted and omnipresent endeavor. Biologists and health experts have frequently asserted that landscape-level issues drive EIDs (e.g.

Link prediction on knowledge graphs (KGs) has been extensively studied on binary relational KGs, wherein each fact is represented by a triple. A significant amount of important knowledge, however, is represented by hyper-relational facts where each fact is composed of a primal triple and a set of qualifiers comprising a key-value pair that allows for expressing more complicated semantics. Although some recent works have proposed to embed hyper-relational KGs, these methods fail to capture essential inference patterns of hyper-relational facts such as qualifier monotonicity, qualifier implication, and qualifier mutual exclusion, limiting their generalization capability. To unlock this, we present \emph{ShrinkE}, a geometric hyper-relational KG embedding method aiming to explicitly model these patterns. ShrinkE models the primal triple as a spatial-functional transformation from the head into a relation-specific box. Each qualifier ``shrinks'' the box to narrow down the possible answer set and, thus, realizes qualifier monotonicity. The spatial relationships between the qualifier boxes allow for modeling core inference patterns of qualifiers such as implication and mutual exclusion. Experimental results demonstrate ShrinkE's superiority on three benchmarks of hyper-relational KGs.

\textit{Metric Differential Privacy} enables text-to-text privatization by adding calibrated noise to the vector of a word derived from an embedding space and projecting this noisy vector back to a discrete vocabulary using a nearest neighbor search. Since words are substituted without context, this mechanism is expected to fall short at finding substitutes for words with ambiguous meanings, such as \textit{'bank'}. To account for these ambiguous words, we leverage a sense embedding and incorporate a sense disambiguation step prior to noise injection. We encompass our modification to the privatization mechanism with an estimation of privacy and utility. For word sense disambiguation on the \textit{Words in Context} dataset, we demonstrate a substantial increase in classification accuracy by $6.05\%$.

A complex logic query in a knowledge graph refers to a query expressed in logic form that conveys a complex meaning, such as where did the Canadian Turing award winner graduate from? Knowledge graph reasoning-based applications, such as dialogue systems and interactive search engines, rely on the ability to answer complex logic queries as a fundamental task. In most knowledge graphs, edges are typically used to either describe the relationships between entities or their associated attribute values. An attribute value can be in categorical or numerical format, such as dates, years, sizes, etc. However, existing complex query answering (CQA) methods simply treat numerical values in the same way as they treat entities. This can lead to difficulties in answering certain queries, such as which Australian Pulitzer award winner is born before 1927, and which drug is a pain reliever and has fewer side effects than Paracetamol. In this work, inspired by the recent advances in numerical encoding and knowledge graph reasoning, we propose numerical complex query answering. In this task, we introduce new numerical variables and operations to describe queries involving numerical attribute values. To address the difference between entities and numerical values, we also propose the framework of Number Reasoning Network (NRN) for alternatively encoding entities and numerical values into separate encoding structures. During the numerical encoding process, NRN employs a parameterized density function to encode the distribution of numerical values. During the entity encoding process, NRN uses established query encoding methods for the original CQA problem. Experimental results show that NRN consistently improves various query encoding methods on three different knowledge graphs and achieves state-of-the-art results.

It is crucial to automatically construct knowledge graphs (KGs) of diverse new relations to support knowledge discovery and broad applications. Previous KG construction methods, based on either crowdsourcing or text mining, are often limited to a small predefined set of relations due to manual cost or restrictions in text corpus. Recent research proposed to use pretrained language models (LMs) as implicit knowledge bases that accept knowledge queries with prompts. Yet, the implicit knowledge lacks many desirable properties of a full-scale symbolic KG, such as easy access, navigation, editing, and quality assurance. In this paper, we propose a new approach of harvesting massive KGs of arbitrary relations from pretrained LMs. With minimal input of a relation definition (a prompt and a few shot of example entity pairs), the approach efficiently searches in the vast entity pair space to extract diverse accurate knowledge of the desired relation. We develop an effective search-and-rescore mechanism for improved efficiency and accuracy. We deploy the approach to harvest KGs of over 400 new relations from different LMs. Extensive human and automatic evaluations show our approach manages to extract diverse accurate knowledge, including tuples of complex relations (e.g., "A is capable of but not good at B"). The resulting KGs as a symbolic interpretation of the source LMs also reveal new insights into the LMs' knowledge capacities.

Due to the increasing adoption of electronic health records (EHR), large scale EHRs have become another rich data source for translational clinical research. Despite its potential, deriving generalizable knowledge from EHR data remains challenging. First, EHR data are generated as part of clinical care with data elements too detailed and fragmented for research. Despite recent progress in mapping EHR data to common ontology with hierarchical structures, much development is still needed to enable automatic grouping of local EHR codes to meaningful clinical concepts at a large scale. Second, the total number of unique EHR features is large, imposing methodological challenges to derive reproducible knowledge graph, especially when interest lies in conditional dependency structure. Third, the detailed EHR data on a very large patient cohort imposes additional computational challenge to deriving a knowledge network. To overcome these challenges, we propose to infer the conditional dependency structure among EHR features via a latent graphical block model (LGBM). The LGBM has a two layer structure with the first providing semantic embedding vector (SEV) representation for the EHR features and the second overlaying a graphical block model on the latent SEVs. The block structures on the graphical model also allows us to cluster synonymous features in EHR. We propose to learn the LGBM efficiently, in both statistical and computational sense, based on the empirical point mutual information matrix. We establish the statistical rates of the proposed estimators and show the perfect recovery of the block structure. Numerical results from simulation studies and real EHR data analyses suggest that the proposed LGBM estimator performs well in finite sample.

Sense embedding learning methods learn multiple vectors for a given ambiguous word, corresponding to its different word senses. For this purpose, different methods have been proposed in prior work on sense embedding learning that use different sense inventories, sense-tagged corpora and learning methods. However, not all existing sense embeddings cover all senses of ambiguous words equally well due to the discrepancies in their training resources. To address this problem, we propose the first-ever meta-sense embedding method -- Neighbour Preserving Meta-Sense Embeddings, which learns meta-sense embeddings by combining multiple independently trained source sense embeddings such that the sense neighbourhoods computed from the source embeddings are preserved in the meta-embedding space. Our proposed method can combine source sense embeddings that cover different sets of word senses. Experimental results on Word Sense Disambiguation (WSD) and Word-in-Context (WiC) tasks show that the proposed meta-sense embedding method consistently outperforms several competitive baselines.