Solving the Right Problem is Key for Translational NLP: A Case Study in UMLS Vocabulary Insertion

As the immense opportunities enabled by large language models become more apparent, NLP systems will be increasingly expected to excel in real-world settings. However, in many instances, powerful models alone will not yield translational NLP solutions, especially if the formulated problem is not well aligned with the real-world task. In this work, we study the case of UMLS vocabulary insertion, an important real-world task in which hundreds of thousands of new terms, referred to as atoms, are added to the UMLS, one of the most comprehensive open-source biomedical knowledge bases. Previous work aimed to develop an automated NLP system to make this time-consuming, costly, and error-prone task more efficient. Nevertheless, practical progress in this direction has been difficult to achieve due to a problem formulation and evaluation gap between research output and the real-world task. In order to address this gap, we introduce a new formulation for UMLS vocabulary insertion which mirrors the real-world task, datasets which faithfully represent it and several strong baselines we developed through re-purposing existing solutions. Additionally, we propose an effective rule-enhanced biomedical language model which enables important new model behavior, outperforms all strong baselines and provides measurable qualitative improvements to editors who carry out the UVI task. We hope this case study provides insight into the considerable importance of problem formulation for the success of translational NLP solutions.

From Coupled Oscillators to Graph Neural Networks: Reducing Over-smoothing via a Kuramoto Model-based Approach

We propose the Kuramoto Graph Neural Network (KuramotoGNN), a novel class of continuous-depth graph neural networks (GNNs) that employs the Kuramoto model to mitigate the over-smoothing phenomenon, in which node features in GNNs become indistinguishable as the number of layers increases. The Kuramoto model captures the synchronization behavior of non-linear coupled oscillators. Under the view of coupled oscillators, we first show the connection between Kuramoto model and basic GNN and then over-smoothing phenomenon in GNNs can be interpreted as phase synchronization in Kuramoto model. The KuramotoGNN replaces this phase synchronization with frequency synchronization to prevent the node features from converging into each other while allowing the system to reach a stable synchronized state. We experimentally verify the advantages of the KuramotoGNN over the baseline GNNs and existing methods in reducing over-smoothing on various graph deep learning benchmark tasks.

p-Laplacian Transformer

$p$-Laplacian regularization, rooted in graph and image signal processing, introduces a parameter $p$ to control the regularization effect on these data. Smaller values of $p$ promote sparsity and interpretability, while larger values encourage smoother solutions. In this paper, we first show that the self-attention mechanism obtains the minimal Laplacian regularization ($p=2$) and encourages the smoothness in the architecture. However, the smoothness is not suitable for the heterophilic structure of self-attention in transformers where attention weights between tokens that are in close proximity and non-close ones are assigned indistinguishably. From that insight, we then propose a novel class of transformers, namely the $p$-Laplacian Transformer (p-LaT), which leverages $p$-Laplacian regularization framework to harness the heterophilic features within self-attention layers. In particular, low $p$ values will effectively assign higher attention weights to tokens that are in close proximity to the current token being processed. We empirically demonstrate the advantages of p-LaT over the baseline transformers on a wide range of benchmark datasets.

Revisiting Over-smoothing and Over-squashing using Ollivier's Ricci Curvature

Graph Neural Networks (GNNs) had been demonstrated to be inherently susceptible to the problems of over-smoothing and over-squashing. These issues prohibit the ability of GNNs to model complex graph interactions by limiting their effectiveness at taking into account distant information. Our study reveals the key connection between the local graph geometry and the occurrence of both of these issues, thereby providing a unified framework for studying them at a local scale using the Ollivier's Ricci curvature. Based on our theory, a number of principled methods are proposed to alleviate the over-smoothing and over-squashing issues.

VidConv: A modernized 2D ConvNet for Efficient Video Recognition

Since being introduced in 2020, Vision Transformers (ViT) has been steadily breaking the record for many vision tasks and are often described as ``all-you-need" to replace ConvNet. Despite that, ViTs are generally computational, memory-consuming, and unfriendly for embedded devices. In addition, recent research shows that standard ConvNet if redesigned and trained appropriately can compete favorably with ViT in terms of accuracy and scalability. In this paper, we adopt the modernized structure of ConvNet to design a new backbone for action recognition. Particularly, our main target is to serve for industrial product deployment, such as FPGA boards in which only standard operations are supported. Therefore, our network simply consists of 2D convolutions, without using any 3D convolution, long-range attention plugin, or Transformer blocks. While being trained with much fewer epochs (5x-10x), our backbone surpasses the methods using (2+1)D and 3D convolution, and achieve comparable results with ViT on two benchmark datasets.

UVA Resources for the Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus

The construction and maintenance process of the UMLS (Unified Medical Language System) Metathesaurus is time-consuming, costly, and error-prone as it relies on (1) the lexical and semantic processing for suggesting synonymous terms, and (2) the expertise of UMLS editors for curating the suggestions. For improving the UMLS Metathesaurus construction process, our research group has defined a new task called UVA (UMLS Vocabulary Alignment) and generated a dataset for evaluating the task. Our group has also developed different baselines for this task using logical rules (RBA), and neural networks (LexLM and ConLM). In this paper, we present a set of reusable and reproducible resources including (1) a dataset generator, (2) three datasets generated by using the generator, and (3) three baseline approaches. We describe the UVA dataset generator and its implementation generalized for any given UMLS release. We demonstrate the use of the dataset generator by generating datasets corresponding to three UMLS releases, 2020AA, 2021AA, and 2021AB. We provide three UVA baselines using the three existing approaches (LexLM, ConLM, and RBA). The code, the datasets, and the experiments are publicly available, reusable, and reproducible with any UMLS release (a no-cost license agreement is required for downloading the UMLS).

UBERT: A Novel Language Model for Synonymy Prediction at Scale in the UMLS Metathesaurus

The UMLS Metathesaurus integrates more than 200 biomedical source vocabularies. During the Metathesaurus construction process, synonymous terms are clustered into concepts by human editors, assisted by lexical similarity algorithms. This process is error-prone and time-consuming. Recently, a deep learning model (LexLM) has been developed for the UMLS Vocabulary Alignment (UVA) task. This work introduces UBERT, a BERT-based language model, pretrained on UMLS terms via a supervised Synonymy Prediction (SP) task replacing the original Next Sentence Prediction (NSP) task. The effectiveness of UBERT for UMLS Metathesaurus construction process is evaluated using the UMLS Vocabulary Alignment (UVA) task. We show that UBERT outperforms the LexLM, as well as biomedical BERT-based models. Key to the performance of UBERT are the synonymy prediction task specifically developed for UBERT, the tight alignment of training data to the UVA task, and the similarity of the models used for pretrained UBERT.

Evaluating Biomedical BERT Models for Vocabulary Alignment at Scale in the UMLS Metathesaurus

The current UMLS (Unified Medical Language System) Metathesaurus construction process for integrating over 200 biomedical source vocabularies is expensive and error-prone as it relies on the lexical algorithms and human editors for deciding if the two biomedical terms are synonymous. Recent advances in Natural Language Processing such as Transformer models like BERT and its biomedical variants with contextualized word embeddings have achieved state-of-the-art (SOTA) performance on downstream tasks. We aim to validate if these approaches using the BERT models can actually outperform the existing approaches for predicting synonymy in the UMLS Metathesaurus. In the existing Siamese Networks with LSTM and BioWordVec embeddings, we replace the BioWordVec embeddings with the biomedical BERT embeddings extracted from each BERT model using different ways of extraction. In the Transformer architecture, we evaluate the use of the different biomedical BERT models that have been pre-trained using different datasets and tasks. Given the SOTA performance of these BERT models for other downstream tasks, our experiments yield surprisingly interesting results: (1) in both model architectures, the approaches employing these biomedical BERT-based models do not outperform the existing approaches using Siamese Network with BioWordVec embeddings for the UMLS synonymy prediction task, (2) the original BioBERT large model that has not been pre-trained with the UMLS outperforms the SapBERT models that have been pre-trained with the UMLS, and (3) using the Siamese Networks yields better performance for synonymy prediction when compared to using the biomedical BERT models.

Alternative Blockmodelling

Many approaches have been proposed to discover clusters within networks. Community finding field encompasses approaches which try to discover clusters where nodes are tightly related within them but loosely related with nodes of other clusters. However, a community network configuration is not the only possible latent structure in a graph. Core-periphery and hierarchical network configurations are valid structures to discover in a relational dataset. On the other hand, a network is not completely explained by only knowing the membership of each node. A high level view of the inter-cluster relationships is needed. Blockmodelling techniques deal with these two issues. Firstly, blockmodelling allows finding any network configuration besides to the well-known community structure. Secondly, blockmodelling is a summary representation of a network which regards not only membership of nodes but also relations between clusters. Finally, a unique summary representation of a network is unlikely. Networks might hide more than one blockmodel. Therefore, our proposed problem aims to discover a secondary blockmodel representation of a network that is of good quality and dissimilar with respect to a given blockmodel. Our methodology is presented through two approaches, (a) inclusion of cannot-link constraints and (b) dissimilarity between image matrices. Both approaches are based on non-negative matrix factorisation NMF which fits the blockmodelling representation. The evaluation of these two approaches regards quality and dissimilarity of the discovered alternative blockmodel as these are the requirements of the problem.

Logical Inferences with Contexts of RDF Triples

Logical inference, an integral feature of the Semantic Web, is the process of deriving new triples by applying entailment rules on knowledge bases. The entailment rules are determined by the model-theoretic semantics. Incorporating context of an RDF triple (e.g., provenance, time, and location) into the inferencing process requires the formal semantics to be capable of describing the context of RDF triples also in the form of triples, or in other words, RDF contextual triples about triples. The formal semantics should also provide the rules that could entail new contextual triples about triples. In this paper, we propose the first inferencing mechanism that allows context of RDF triples, represented in the form of RDF triples about triples, to be the first-class citizens in the model-theoretic semantics and in the logical rules. Our inference mechanism is well-formalized with all new concepts being captured in the model-theoretic semantics. This formal semantics also allows us to derive a new set of entailment rules that could entail new contextual triples about triples. To demonstrate the feasibility and the scalability of the proposed mechanism, we implement a new tool in which we transform the existing knowledge bases to our representation of RDF triples about triples and provide the option for this tool to compute the inferred triples for the proposed rules. We evaluate the computation of the proposed rules on a large scale using various real-world knowledge bases such as Bio2RDF NCBI Genes and DBpedia. The results show that the computation of the inferred triples can be highly scalable. On average, one billion inferred triples adds 5-6 minutes to the overall transformation process. NCBI Genes, with 20 billion triples in total, took only 232 minutes for the transformation of 12 billion triples and added 42 minutes for inferring 8 billion triples to the overall process.