LLM Embeddings for Deep Learning on Tabular Data

Tabular deep-learning methods require embedding numerical and categorical input features into high-dimensional spaces before processing them. Existing methods deal with this heterogeneous nature of tabular data by employing separate type-specific encoding approaches. This limits the cross-table transfer potential and the exploitation of pre-trained knowledge. We propose a novel approach that first transforms tabular data into text, and then leverages pre-trained representations from LLMs to encode this data, resulting in a plug-and-play solution to improv ing deep-learning tabular methods. We demonstrate that our approach improves accuracy over competitive models, such as MLP, ResNet and FT-Transformer, by validating on seven classification datasets.

Measuring Cross-Modal Interactions in Multimodal Models

Integrating AI in healthcare can greatly improve patient care and system efficiency. However, the lack of explainability in AI systems (XAI) hinders their clinical adoption, especially in multimodal settings that use increasingly complex model architectures. Most existing XAI methods focus on unimodal models, which fail to capture cross-modal interactions crucial for understanding the combined impact of multiple data sources. Existing methods for quantifying cross-modal interactions are limited to two modalities, rely on labelled data, and depend on model performance. This is problematic in healthcare, where XAI must handle multiple data sources and provide individualised explanations. This paper introduces InterSHAP, a cross-modal interaction score that addresses the limitations of existing approaches. InterSHAP uses the Shapley interaction index to precisely separate and quantify the contributions of the individual modalities and their interactions without approximations. By integrating an open-source implementation with the SHAP package, we enhance reproducibility and ease of use. We show that InterSHAP accurately measures the presence of cross-modal interactions, can handle multiple modalities, and provides detailed explanations at a local level for individual samples. Furthermore, we apply InterSHAP to multimodal medical datasets and demonstrate its applicability for individualised explanations.

PATHS: A Hierarchical Transformer for Efficient Whole Slide Image Analysis

Computational analysis of whole slide images (WSIs) has seen significant research progress in recent years, with applications ranging across important diagnostic and prognostic tasks such as survival or cancer subtype prediction. Many state-of-the-art models process the entire slide - which may be as large as $150,000 \times 150,000$ pixels - as a bag of many patches, the size of which necessitates computationally cheap feature aggregation methods. However, a large proportion of these patches are uninformative, such as those containing only healthy or adipose tissue, adding significant noise and size to the bag. We propose Pathology Transformer with Hierarchical Selection (PATHS), a novel top-down method for hierarchical weakly supervised representation learning on slide-level tasks in computational pathology. PATHS is inspired by the cross-magnification manner in which a human pathologist examines a slide, recursively filtering patches at each magnification level to a small subset relevant to the diagnosis. Our method overcomes the complications of processing the entire slide, enabling quadratic self-attention and providing a simple interpretable measure of region importance. We apply PATHS to five datasets of The Cancer Genome Atlas (TCGA), and achieve superior performance on slide-level prediction tasks when compared to previous methods, despite processing only a small proportion of the slide.

End-to-End Ontology Learning with Large Language Models

Ontologies are useful for automatic machine processing of domain knowledge as they represent it in a structured format. Yet, constructing ontologies requires substantial manual effort. To automate part of this process, large language models (LLMs) have been applied to solve various subtasks of ontology learning. However, this partial ontology learning does not capture the interactions between subtasks. We address this gap by introducing OLLM, a general and scalable method for building the taxonomic backbone of an ontology from scratch. Rather than focusing on subtasks, like individual relations between entities, we model entire subcomponents of the target ontology by finetuning an LLM with a custom regulariser that reduces overfitting on high-frequency concepts. We introduce a novel suite of metrics for evaluating the quality of the generated ontology by measuring its semantic and structural similarity to the ground truth. In contrast to standard metrics, our metrics use deep learning techniques to define more robust distance measures between graphs. Both our quantitative and qualitative results on Wikipedia show that OLLM outperforms subtask composition methods, producing more semantically accurate ontologies while maintaining structural integrity. We further demonstrate that our model can be effectively adapted to new domains, like arXiv, needing only a small number of training examples. Our source code and datasets are available at https://github.com/andylolu2/ollm.

Efficient Bias Mitigation Without Privileged Information

Deep neural networks trained via empirical risk minimisation often exhibit significant performance disparities across groups, particularly when group and task labels are spuriously correlated (e.g., "grassy background" and "cows"). Existing bias mitigation methods that aim to address this issue often either rely on group labels for training or validation, or require an extensive hyperparameter search. Such data and computational requirements hinder the practical deployment of these methods, especially when datasets are too large to be group-annotated, computational resources are limited, and models are trained through already complex pipelines. In this paper, we propose Targeted Augmentations for Bias Mitigation (TAB), a simple hyperparameter-free framework that leverages the entire training history of a helper model to identify spurious samples, and generate a group-balanced training set from which a robust model can be trained. We show that TAB improves worst-group performance without any group information or model selection, outperforming existing methods while maintaining overall accuracy.

TabEBM: A Tabular Data Augmentation Method with Distinct Class-Specific Energy-Based Models

Data collection is often difficult in critical fields such as medicine, physics, and chemistry. As a result, classification methods usually perform poorly with these small datasets, leading to weak predictive performance. Increasing the training set with additional synthetic data, similar to data augmentation in images, is commonly believed to improve downstream classification performance. However, current tabular generative methods that learn either the joint distribution $ p(\mathbf{x}, y) $ or the class-conditional distribution $ p(\mathbf{x} \mid y) $ often overfit on small datasets, resulting in poor-quality synthetic data, usually worsening classification performance compared to using real data alone. To solve these challenges, we introduce TabEBM, a novel class-conditional generative method using Energy-Based Models (EBMs). Unlike existing methods that use a shared model to approximate all class-conditional densities, our key innovation is to create distinct EBM generative models for each class, each modelling its class-specific data distribution individually. This approach creates robust energy landscapes, even in ambiguous class distributions. Our experiments show that TabEBM generates synthetic data with higher quality and better statistical fidelity than existing methods. When used for data augmentation, our synthetic data consistently improves the classification performance across diverse datasets of various sizes, especially small ones.

Repurposing Language Models into Embedding Models: Finding the Compute-Optimal Recipe

Text embeddings are essential for many tasks, such as document retrieval, clustering, and semantic similarity assessment. In this paper, we study how to contrastively train text embedding models in a compute-optimal fashion, given a suite of pre-trained decoder-only language models. Our innovation is an algorithm that produces optimal configurations of model sizes, data quantities, and fine-tuning methods for text-embedding models at different computational budget levels. The resulting recipe, which we obtain through extensive experiments, can be used by practitioners to make informed design choices for their embedding models. Specifically, our findings suggest that full fine-tuning and low-rank adaptation fine-tuning produce optimal models at lower and higher computational budgets respectively.

TabMDA: Tabular Manifold Data Augmentation for Any Classifier using Transformers with In-context Subsetting

Tabular data is prevalent in many critical domains, yet it is often challenging to acquire in large quantities. This scarcity usually results in poor performance of machine learning models on such data. Data augmentation, a common strategy for performance improvement in vision and language tasks, typically underperforms for tabular data due to the lack of explicit symmetries in the input space. To overcome this challenge, we introduce TabMDA, a novel method for manifold data augmentation on tabular data. This method utilises a pre-trained in-context model, such as TabPFN, to map the data into a manifold space. TabMDA performs label-invariant transformations by encoding the data multiple times with varied contexts. This process explores the manifold of the underlying in-context models, thereby enlarging the training dataset. TabMDA is a training-free method, making it applicable to any classifier. We evaluate TabMDA on five standard classifiers and observe significant performance improvements across various tabular datasets. Our results demonstrate that TabMDA provides an effective way to leverage information from pre-trained in-context models to enhance the performance of downstream classifiers.

MM-Lego: Modular Biomedical Multimodal Models with Minimal Fine-Tuning

Learning holistic computational representations in physical, chemical or biological systems requires the ability to process information from different distributions and modalities within the same model. Thus, the demand for multimodal machine learning models has sharply risen for modalities that go beyond vision and language, such as sequences, graphs, time series, or tabular data. While there are many available multimodal fusion and alignment approaches, most of them require end-to-end training, scale quadratically with the number of modalities, cannot handle cases of high modality imbalance in the training set, or are highly topology-specific, making them too restrictive for many biomedical learning tasks. This paper presents Multimodal Lego (MM-Lego), a modular and general-purpose fusion and model merging framework to turn any set of encoders into a competitive multimodal model with no or minimal fine-tuning. We achieve this by introducing a wrapper for unimodal encoders that enforces lightweight dimensionality assumptions between modalities and harmonises their representations by learning features in the frequency domain to enable model merging with little signal interference. We show that MM-Lego 1) can be used as a model merging method which achieves competitive performance with end-to-end fusion models without any fine-tuning, 2) can operate on any unimodal encoder, and 3) is a model fusion method that, with minimal fine-tuning, achieves state-of-the-art results on six benchmarked multimodal biomedical tasks.

Understanding Inter-Concept Relationships in Concept-Based Models

Concept-based explainability methods provide insight into deep learning systems by constructing explanations using human-understandable concepts. While the literature on human reasoning demonstrates that we exploit relationships between concepts when solving tasks, it is unclear whether concept-based methods incorporate the rich structure of inter-concept relationships. We analyse the concept representations learnt by concept-based models to understand whether these models correctly capture inter-concept relationships. First, we empirically demonstrate that state-of-the-art concept-based models produce representations that lack stability and robustness, and such methods fail to capture inter-concept relationships. Then, we develop a novel algorithm which leverages inter-concept relationships to improve concept intervention accuracy, demonstrating how correctly capturing inter-concept relationships can improve downstream tasks.