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Mateja Jamnik

Publications and source records attributed to Mateja Jamnik.

At least 37 records · Page 2Linked to original sources
arXiv2025

Oruga: An Avatar of Representational Systems Theory

Humans use representations flexibly. We draw diagrams, change representations and exploit creative analogies across different domains. We want to harness this kind of power and endow machines with it to make them more compatible with human use. Previously we developed Representational Systems Theory (RST) to study the structure and transformations of representations. In this paper we present Oruga (caterpillar in Spanish; a symbol of transformation), an implementation of various aspects of RST. Oruga consists of a core of data structures corresponding to concepts in RST, a language for communicating with the core, and an engine for producing transformations using a method we call structure transfer. In this paper we present an overview of the core and language of Oruga, with a brief example of the kind of transformation that structure transfer can execute.

cs.AI↗
arXiv2025

Avoiding Leakage Poisoning: Concept Interventions Under Distribution Shifts

In this paper, we investigate how concept-based models (CMs) respond to out-of-distribution (OOD) inputs. CMs are interpretable neural architectures that first predict a set of high-level concepts (e.g., stripes, black) and then predict a task label from those concepts. In particular, we study the impact of concept interventions (i.e., operations where a human expert corrects a CM's mispredicted concepts at test time) on CMs' task predictions when inputs are OOD. Our analysis reveals a weakness in current state-of-the-art CMs, which we term leakage poisoning, that prevents them from properly improving their accuracy when intervened on for OOD inputs. To address this, we introduce MixCEM, a new CM that learns to dynamically exploit leaked information missing from its concepts only when this information is in-distribution. Our results across tasks with and without complete sets of concept annotations demonstrate that MixCEMs outperform strong baselines by significantly improving their accuracy for both in-distribution and OOD samples in the presence and absence of concept interventions.

cs.LG↗
arXiv2025

Foundations of Interpretable Models

We argue that existing definitions of interpretability are not actionable in that they fail to inform users about general, sound, and robust interpretable model design. This makes current interpretability research fundamentally ill-posed. To address this issue, we propose a definition of interpretability that is general, simple, and subsumes existing informal notions within the interpretable AI community. We show that our definition is actionable, as it directly reveals the foundational properties, underlying assumptions, principles, data structures, and architectural features necessary for designing interpretable models. Building on this, we propose a general blueprint for designing interpretable models and introduce the first open-sourced library with native support for interpretable data structures and processes.

cs.LG↗
arXiv2025

Do Concept Bottleneck Models Respect Localities?

Concept-based explainability methods use human-understandable intermediaries to produce explanations for machine learning models. These methods assume concept predictions can help understand a model's internal reasoning. In this work, we assess the degree to which such an assumption is true by analyzing whether concept predictors leverage "relevant" features to make predictions, a term we call locality. Concept-based models that fail to respect localities also fail to be explainable because concept predictions are based on spurious features, making the interpretation of the concept predictions vacuous. To assess whether concept-based models respect localities, we construct and use three metrics to characterize when models respect localities, complementing our analysis with theoretical results. Each of our metrics captures a different notion of perturbation and assess whether perturbing "irrelevant" features impacts the predictions made by a concept predictors. We find that many concept-based models used in practice fail to respect localities because concept predictors cannot always clearly distinguish distinct concepts. Based on these findings, we propose suggestions for alleviating this issue.

cs.LG↗
arXiv2025

Multimodal Lego: Model Merging and Fine-Tuning Across Topologies and Modalities in Biomedicine

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 general-purpose fusion 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 any unimodal encoder that enforces shape consistency between modality representations. It harmonises these 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, surpasses all benchmarks in five out of seven datasets.

cs.LG↗
arXiv2025

RO-FIGS: Efficient and Expressive Tree-Based Ensembles for Tabular Data

Tree-based models are often robust to uninformative features and can accurately capture non-smooth, complex decision boundaries. Consequently, they often outperform neural network-based models on tabular datasets at a significantly lower computational cost. Nevertheless, the capability of traditional tree-based ensembles to express complex relationships efficiently is limited by using a single feature to make splits. To improve the efficiency and expressiveness of tree-based methods, we propose Random Oblique Fast Interpretable Greedy-Tree Sums (RO-FIGS). RO-FIGS builds on Fast Interpretable Greedy-Tree Sums, and extends it by learning trees with oblique or multivariate splits, where each split consists of a linear combination learnt from random subsets of features. This helps uncover interactions between features and improves performance. The proposed method is suitable for tabular datasets with both numerical and categorical features. We evaluate RO-FIGS on 22 real-world tabular datasets, demonstrating superior performance and much smaller models over other tree- and neural network-based methods. Additionally, we analyse their splits to reveal valuable insights into feature interactions, enriching the information learnt from SHAP summary plots, and thereby demonstrating the enhanced interpretability of RO-FIGS models. The proposed method is well-suited for applications, where balance between accuracy and interpretability is essential.

cs.LG↗
arXiv2025

How Well Does Your Tabular Generator Learn the Structure of Tabular Data?

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce $\textbf{TabStruct}$, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

cs.LG↗
arXiv2025

Sphere Neural-Networks for Rational Reasoning

The success of Large Language Models (LLMs), e.g., ChatGPT, is witnessed by their planetary popularity, their capability of human-like communication, and also by their steadily improved reasoning performance. However, it remains unclear whether LLMs reason. It is an open problem how traditional neural networks can be qualitatively extended to go beyond the statistic paradigm and achieve high-level cognition. Here, we present a novel qualitative extension by generalising computational building blocks from vectors to spheres. We propose Sphere Neural Networks (SphNNs) for human-like reasoning through model construction and inspection, and develop SphNN for syllogistic reasoning, a microcosm of human rationality. SphNN is a hierarchical neuro-symbolic Kolmogorov-Arnold geometric GNN, and uses a neuro-symbolic transition map of neighbourhood spatial relations to transform the current sphere configuration towards the target. SphNN is the first neural model that can determine the validity of long-chained syllogistic reasoning in one epoch without training data, with the worst computational complexity of O(N). SphNN can evolve into various types of reasoning, such as spatio-temporal reasoning, logical reasoning with negation and disjunction, event reasoning, neuro-symbolic unification, and humour understanding (the highest level of cognition). All these suggest a new kind of Herbert A. Simon's scissors with two neural blades. SphNNs will tremendously enhance interdisciplinary collaborations to develop the two neural blades and realise deterministic neural reasoning and human-bounded rationality and elevate LLMs to reliable psychological AI. This work suggests that the non-zero radii of spheres are the missing components that prevent traditional deep-learning systems from reaching the realm of rational reasoning and cause LLMs to be trapped in the swamp of hallucination.

cs.AI↗
arXiv2025

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.

cs.LG↗
arXiv2025

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.

cs.LG↗
arXiv2025

Discrete Lagrangian Neural Networks with Automatic Symmetry Discovery

By one of the most fundamental principles in physics, a dynamical system will exhibit those motions which extremise an action functional. This leads to the formation of the Euler-Lagrange equations, which serve as a model of how the system will behave in time. If the dynamics exhibit additional symmetries, then the motion fulfils additional conservation laws, such as conservation of energy (time invariance), momentum (translation invariance), or angular momentum (rotational invariance). To learn a system representation, one could learn the discrete Euler-Lagrange equations, or alternatively, learn the discrete Lagrangian function $\mathcal{L}_d$ which defines them. Based on ideas from Lie group theory, in this work we introduce a framework to learn a discrete Lagrangian along with its symmetry group from discrete observations of motions and, therefore, identify conserved quantities. The learning process does not restrict the form of the Lagrangian, does not require velocity or momentum observations or predictions and incorporates a cost term which safeguards against unwanted solutions and against potential numerical issues in forward simulations. The learnt discrete quantities are related to their continuous analogues using variational backward error analysis and numerical results demonstrate the improvement such models can have both qualitatively and quantitatively even in the presence of noise.

cs.LG↗
arXiv2024

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.

cs.CV↗
arXiv2024

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.

cs.LG↗
arXiv2024

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. Code is available at https://github.com/andreimargeloiu/TabEBM.

cs.LG↗
arXiv2024

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.

cs.LG↗
arXiv2024

HEALNet: Multimodal Fusion for Heterogeneous Biomedical Data

Technological advances in medical data collection, such as high-throughput genomic sequencing and digital high-resolution histopathology, have contributed to the rising requirement for multimodal biomedical modelling, specifically for image, tabular and graph data. Most multimodal deep learning approaches use modality-specific architectures that are often trained separately and cannot capture the crucial cross-modal information that motivates the integration of different data sources. This paper presents the Hybrid Early-fusion Attention Learning Network (HEALNet): a flexible multimodal fusion architecture, which a) preserves modality-specific structural information, b) captures the cross-modal interactions and structural information in a shared latent space, c) can effectively handle missing modalities during training and inference, and d) enables intuitive model inspection by learning on the raw data input instead of opaque embeddings. We conduct multimodal survival analysis on Whole Slide Images and Multi-omic data on four cancer datasets from The Cancer Genome Atlas (TCGA). HEALNet achieves state-of-the-art performance compared to other end-to-end trained fusion models, substantially improving over unimodal and multimodal baselines whilst being robust in scenarios with missing modalities.

cs.LG↗
arXiv2024

Learning to Receive Help: Intervention-Aware Concept Embedding Models

Concept Bottleneck Models (CBMs) tackle the opacity of neural architectures by constructing and explaining their predictions using a set of high-level concepts. A special property of these models is that they permit concept interventions, wherein users can correct mispredicted concepts and thus improve the model's performance. Recent work, however, has shown that intervention efficacy can be highly dependent on the order in which concepts are intervened on and on the model's architecture and training hyperparameters. We argue that this is rooted in a CBM's lack of train-time incentives for the model to be appropriately receptive to concept interventions. To address this, we propose Intervention-aware Concept Embedding models (IntCEMs), a novel CBM-based architecture and training paradigm that improves a model's receptiveness to test-time interventions. Our model learns a concept intervention policy in an end-to-end fashion from where it can sample meaningful intervention trajectories at train-time. This conditions IntCEMs to effectively select and receive concept interventions when deployed at test-time. Our experiments show that IntCEMs significantly outperform state-of-the-art concept-interpretable models when provided with test-time concept interventions, demonstrating the effectiveness of our approach.

cs.LG↗
arXiv2024

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.

cs.LG↗