Zipfian Whitening

The word embedding space in neural models is skewed, and correcting this can improve task performance. We point out that most approaches for modeling, correcting, and measuring the symmetry of an embedding space implicitly assume that the word frequencies are uniform; in reality, word frequencies follow a highly non-uniform distribution, known as Zipf's law. Surprisingly, simply performing PCA whitening weighted by the empirical word frequency that follows Zipf's law significantly improves task performance, surpassing established baselines. From a theoretical perspective, both our approach and existing methods can be clearly categorized: word representations are distributed according to an exponential family with either uniform or Zipfian base measures. By adopting the latter approach, we can naturally emphasize informative low-frequency words in terms of their vector norm, which becomes evident from the information-geometric perspective, and in terms of the loss functions for imbalanced classification. Additionally, our theory corroborates that popular natural language processing methods, such as skip-gram negative sampling, WhiteningBERT, and headless language models, work well just because their word embeddings encode the empirical word frequency into the underlying probabilistic model.

Understanding Higher-Order Correlations Among Semantic Components in Embeddings

Independent Component Analysis (ICA) is an effective method for interpreting the intrinsic geometric structure of embeddings as semantic components. While ICA theory assumes that embeddings can be linearly decomposed into independent components, real-world data often do not satisfy this assumption. Consequently, there are remaining non-independencies between the estimated components that ICA cannot eliminate. We quantified these non-independencies using higher-order correlations and demonstrated that when the higher-order correlation between two components is large, it indicates a strong semantic association between them. The entire structure was revealed through visualization using a maximum spanning tree of semantic components. These findings allow for further understanding of embeddings through ICA.

Norm of Mean Contextualized Embeddings Determines their Variance

Contextualized embeddings vary by context, even for the same token, and form a distribution in the embedding space. To analyze this distribution, we focus on the norm of the mean embedding and the variance of the embeddings. In this study, we first demonstrate that these values follow the well-known formula for variance in statistics and provide an efficient sequential computation method. Then, by observing embeddings from intermediate layers of several Transformer models, we found a strong trade-off relationship between the norm and the variance: as the mean embedding becomes closer to the origin, the variance increases. This trade-off is likely influenced by the layer normalization mechanism used in Transformer models. Furthermore, when the sets of token embeddings are treated as clusters, we show that the variance of the entire embedding set can theoretically be decomposed into the within-cluster variance and the between-cluster variance. We found experimentally that as the layers of Transformer models deepen, the embeddings move farther from the origin, the between-cluster variance relatively decreases, and the within-cluster variance relatively increases. These results are consistent with existing studies on the anisotropy of the embedding spaces across layers.

Shimo Lab at "Discharge Me!": Discharge Summarization by Prompt-Driven Concatenation of Electronic Health Record Sections

In this paper, we present our approach to the shared task "Discharge Me!" at the BioNLP Workshop 2024. The primary goal of this task is to reduce the time and effort clinicians spend on writing detailed notes in the electronic health record (EHR). Participants develop a pipeline to generate the "Brief Hospital Course" and "Discharge Instructions" sections from the EHR. Our approach involves a first step of extracting the relevant sections from the EHR. We then add explanatory prompts to these sections and concatenate them with separate tokens to create the input text. To train a text generation model, we perform LoRA fine-tuning on the ClinicalT5-large model. On the final test data, our approach achieved a ROUGE-1 score of $0.394$, which is comparable to the top solutions.

Revisiting Cosine Similarity via Normalized ICA-transformed Embeddings

Cosine similarity is widely used to measure the similarity between two embeddings, while interpretations based on angle and correlation coefficient are common. In this study, we focus on the interpretable axes of embeddings transformed by Independent Component Analysis (ICA), and propose a novel interpretation of cosine similarity as the sum of semantic similarities over axes. To investigate this, we first show experimentally that unnormalized embeddings contain norm-derived artifacts. We then demonstrate that normalized ICA-transformed embeddings exhibit sparsity, with a few large values in each axis and across embeddings, thereby enhancing interpretability by delineating clear semantic contributions. Finally, to validate our interpretation, we perform retrieval experiments using ideal embeddings with and without specific semantic components.

Predicting Drug-Gene Relations via Analogy Tasks with Word Embeddings

Natural language processing (NLP) is utilized in a wide range of fields, where words in text are typically transformed into feature vectors called embeddings. BioConceptVec is a specific example of embeddings tailored for biology, trained on approximately 30 million PubMed abstracts using models such as skip-gram. Generally, word embeddings are known to solve analogy tasks through simple vector arithmetic. For instance, $\mathrm{\textit{king}} - \mathrm{\textit{man}} + \mathrm{\textit{woman}}$ predicts $\mathrm{\textit{queen}}$. In this study, we demonstrate that BioConceptVec embeddings, along with our own embeddings trained on PubMed abstracts, contain information about drug-gene relations and can predict target genes from a given drug through analogy computations. We also show that categorizing drugs and genes using biological pathways improves performance. Furthermore, we illustrate that vectors derived from known relations in the past can predict unknown future relations in datasets divided by year.

Block-Diagonal Orthogonal Relation and Matrix Entity for Knowledge Graph Embedding

The primary aim of Knowledge Graph embeddings (KGE) is to learn low-dimensional representations of entities and relations for predicting missing facts. While rotation-based methods like RotatE and QuatE perform well in KGE, they face two challenges: limited model flexibility requiring proportional increases in relation size with entity dimension, and difficulties in generalizing the model for higher-dimensional rotations. To address these issues, we introduce OrthogonalE, a novel KGE model employing matrices for entities and block-diagonal orthogonal matrices with Riemannian optimization for relations. This approach enhances the generality and flexibility of KGE models. The experimental results indicate that our new KGE model, OrthogonalE, is both general and flexible, significantly outperforming state-of-the-art KGE models while substantially reducing the number of relation parameters.

Axis Tour: Word Tour Determines the Order of Axes in ICA-transformed Embeddings

Word embedding is one of the most important components in natural language processing, but interpreting high-dimensional embeddings remains a challenging problem. To address this problem, Independent Component Analysis (ICA) is identified as an effective solution. ICA-transformed word embeddings reveal interpretable semantic axes; however, the order of these axes are arbitrary. In this study, we focus on this property and propose a novel method, Axis Tour, which optimizes the order of the axes. Inspired by Word Tour, a one-dimensional word embedding method, we aim to improve the clarity of the word embedding space by maximizing the semantic continuity of the axes. Furthermore, we show through experiments on downstream tasks that Axis Tour constructs better low-dimensional embeddings compared to both PCA and ICA.

Knowledge Sanitization of Large Language Models

We explore a knowledge sanitization approach to mitigate the privacy concerns associated with large language models (LLMs). LLMs trained on a large corpus of Web data can memorize and potentially reveal sensitive or confidential information, raising critical security concerns. Our technique fine-tunes these models, prompting them to generate harmless responses such as ``I don't know'' when queried about specific information. Experimental results in a closed-book question-answering task show that our straightforward method not only minimizes particular knowledge leakage but also preserves the overall performance of LLM. These two advantages strengthen the defense against extraction attacks and reduces the emission of harmful content such as hallucinations.

3D Rotation and Translation for Hyperbolic Knowledge Graph Embedding

The main objective of Knowledge Graph (KG) embeddings is to learn low-dimensional representations of entities and relations, enabling the prediction of missing facts. A significant challenge in achieving better KG embeddings lies in capturing relation patterns, including symmetry, antisymmetry, inversion, commutative composition, non-commutative composition, hierarchy, and multiplicity. This study introduces a novel model called 3H-TH (3D Rotation and Translation in Hyperbolic space) that captures these relation patterns simultaneously. In contrast, previous attempts have not achieved satisfactory performance across all the mentioned properties at the same time. The experimental results demonstrate that the new model outperforms existing state-of-the-art models in terms of accuracy, hierarchy property, and other relation patterns in low-dimensional space, meanwhile performing similarly in high-dimensional space.