Search

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.

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.

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., Comment: Accepted at the 18th European Conference on Computer Vision (ECCV 2024) as an Oral presentation

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., Comment: Accepted by the Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024)

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., Comment: NeurIPS 2024

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 an embedding space. TabMDA performs label-invariant transformations by encoding the data multiple times with varied contexts. This process explores the learned embedding space 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. Code is available at https://github.com/AdrianBZG/TabMDA., Comment: Presented at 1st ICML Workshop on In-Context Learning (ICL @ ICML 2024)

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.

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., Comment: Accepted at ICML 2024

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.

Concept-based methods explain model predictions using human-understandable concepts. These models require accurate concept predictors, yet the faithfulness of existing concept predictors to their underlying concepts is unclear. In this paper, we investigate the faithfulness of Concept Bottleneck Models (CBMs), a popular family of concept-based architectures, by looking at whether they respect "localities" in datasets. Localities involve using only relevant features when predicting a concept's value. When localities are not considered, concepts may be predicted based on spuriously correlated features, degrading performance and robustness. This work examines how CBM predictions change when perturbing model inputs, and reveals that CBMs may not capture localities, even when independent concepts are localised to non-overlapping feature subsets. Our empirical and theoretical results demonstrate that datasets with correlated concepts may lead to accurate but uninterpretable models that fail to learn localities. Overall, we find that CBM interpretability is fragile, as CBMs occasionally rely upon spurious features, necessitating further research into the robustness of concept predictors., Comment: Previous Version Accepted at NeurIPs 23 XAI in Action Workshop

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., Comment: NeurIPS 2024

Autoformalization is the task of translating natural language materials into machine-verifiable formalisations. Progress in autoformalization research is hindered by the lack of a sizeable dataset consisting of informal-formal pairs expressing the same essence. Existing methods tend to circumvent this challenge by manually curating small corpora or using few-shot learning with large language models. But these methods suffer from data scarcity and formal language acquisition difficulty. In this work, we create $\texttt{MMA}$, a large, flexible, multilingual, and multi-domain dataset of informal-formal pairs, by using a language model to translate in the reverse direction, that is, from formal mathematical statements into corresponding informal ones. Experiments show that language models fine-tuned on $\texttt{MMA}$ produce $16-18\%$ of statements acceptable with minimal corrections on the $\texttt{miniF2F}$ and $\texttt{ProofNet}$ benchmarks, up from $0\%$ with the base model. We demonstrate that fine-tuning on multilingual formal data results in more capable autoformalization models even when deployed on monolingual tasks.

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., Comment: Accepted as a spotlight at the Thirty-seventh Conference on Neural Information Processing Systems (NeurIPS 2023)

Variational Autoencoders and their many variants have displayed impressive ability to perform dimensionality reduction, often achieving state-of-the-art performance. Many current methods however, struggle to learn good representations in High Dimensional, Low Sample Size (HDLSS) tasks, which is an inherently challenging setting. We address this challenge by using an ensemble of lightweight VAEs to learn posteriors over subsets of the feature-space, which get aggregated into a joint posterior in a novel divide-and-conquer approach. Specifically, we present an alternative factorisation of the joint posterior that induces a form of implicit data augmentation that yields greater sample efficiency. Through a series of experiments on eight real-world datasets, we show that our method learns better latent representations in HDLSS settings, which leads to higher accuracy in a downstream classification task. Furthermore, we verify that our approach has a positive effect on disentanglement and achieves a lower estimated Total Correlation on learnt representations. Finally, we show that our approach is robust to partial features at inference, exhibiting little performance degradation even with most features missing.

Tabular biomedical data poses challenges in machine learning because it is often high-dimensional and typically low-sample-size (HDLSS). Previous research has attempted to address these challenges via local feature selection, but existing approaches often fail to achieve optimal performance due to their limitation in identifying globally important features and their susceptibility to the co-adaptation problem. In this paper, we propose ProtoGate, a prototype-based neural model for feature selection on HDLSS data. ProtoGate first selects instance-wise features via adaptively balancing global and local feature selection. Furthermore, ProtoGate employs a non-parametric prototype-based prediction mechanism to tackle the co-adaptation problem, ensuring the feature selection results and predictions are consistent with underlying data clusters. We conduct comprehensive experiments to evaluate the performance and interpretability of ProtoGate on synthetic and real-world datasets. The results show that ProtoGate generally outperforms state-of-the-art methods in prediction accuracy by a clear margin while providing high-fidelity feature selection and explainable predictions. Code is available at https://github.com/SilenceX12138/ProtoGate., Comment: Accepted by the Forty-first International Conference on Machine Learning (ICML2024)

There is much excitement about the opportunity to harness the power of large language models (LLMs) when building problem-solving assistants. However, the standard methodology of evaluating LLMs relies on static pairs of inputs and outputs, and is insufficient for making an informed decision about which LLMs and under which assistive settings can they be sensibly used. Static assessment fails to account for the essential interactive element in LLM deployment, and therefore limits how we understand language model capabilities. We introduce CheckMate, an adaptable prototype platform for humans to interact with and evaluate LLMs. We conduct a study with CheckMate to evaluate three language models (InstructGPT, ChatGPT, and GPT-4) as assistants in proving undergraduate-level mathematics, with a mixed cohort of participants from undergraduate students to professors of mathematics. We release the resulting interaction and rating dataset, MathConverse. By analysing MathConverse, we derive a taxonomy of human behaviours and uncover that despite a generally positive correlation, there are notable instances of divergence between correctness and perceived helpfulness in LLM generations, amongst other findings. Further, we garner a more granular understanding of GPT-4 mathematical problem-solving through a series of case studies, contributed by expert mathematicians. We conclude with actionable takeaways for ML practitioners and mathematicians: models that communicate uncertainty respond well to user corrections, and are more interpretable and concise may constitute better assistants. Interactive evaluation is a promising way to navigate the capability of these models; humans should be aware of language models' algebraic fallibility and discern where they are appropriate to use.

Deep learning methods are highly accurate, yet their opaque decision process prevents them from earning full human trust. Concept-based models aim to address this issue by learning tasks based on a set of human-understandable concepts. However, state-of-the-art concept-based models rely on high-dimensional concept embedding representations which lack a clear semantic meaning, thus questioning the interpretability of their decision process. To overcome this limitation, we propose the Deep Concept Reasoner (DCR), the first interpretable concept-based model that builds upon concept embeddings. In DCR, neural networks do not make task predictions directly, but they build syntactic rule structures using concept embeddings. DCR then executes these rules on meaningful concept truth degrees to provide a final interpretable and semantically-consistent prediction in a differentiable manner. Our experiments show that DCR: (i) improves up to +25% w.r.t. state-of-the-art interpretable concept-based models on challenging benchmarks (ii) discovers meaningful logic rules matching known ground truths even in the absence of concept supervision during training, and (iii), facilitates the generation of counterfactual examples providing the learnt rules as guidance.

Rule-based surrogate models are an effective and interpretable way to approximate a Deep Neural Network's (DNN) decision boundaries, allowing humans to easily understand deep learning models. Current state-of-the-art decompositional methods, which are those that consider the DNN's latent space to extract more exact rule sets, manage to derive rule sets at high accuracy. However, they a) do not guarantee that the surrogate model has learned from the same variables as the DNN (alignment), b) only allow to optimise for a single objective, such as accuracy, which can result in excessively large rule sets (complexity), and c) use decision tree algorithms as intermediate models, which can result in different explanations for the same DNN (stability). This paper introduces the CGX (Column Generation eXplainer) to address these limitations - a decompositional method using dual linear programming to extract rules from the hidden representations of the DNN. This approach allows to optimise for any number of objectives and empowers users to tweak the explanation model to their needs. We evaluate our results on a wide variety of tasks and show that CGX meets all three criteria, by having exact reproducibility of the explanation model that guarantees stability and reduces the rule set size by >80% (complexity) at equivalent or improved accuracy and fidelity across tasks (alignment)., Comment: Accepted at ICLR 2023 Workshop on Trustworthy Machine Learning for Healthcare

Placing a human in the loop may abate the risks of deploying AI systems in safety-critical settings (e.g., a clinician working with a medical AI system). However, mitigating risks arising from human error and uncertainty within such human-AI interactions is an important and understudied issue. In this work, we study human uncertainty in the context of concept-based models, a family of AI systems that enable human feedback via concept interventions where an expert intervenes on human-interpretable concepts relevant to the task. Prior work in this space often assumes that humans are oracles who are always certain and correct. Yet, real-world decision-making by humans is prone to occasional mistakes and uncertainty. We study how existing concept-based models deal with uncertain interventions from humans using two novel datasets: UMNIST, a visual dataset with controlled simulated uncertainty based on the MNIST dataset, and CUB-S, a relabeling of the popular CUB concept dataset with rich, densely-annotated soft labels from humans. We show that training with uncertain concept labels may help mitigate weaknesses of concept-based systems when handling uncertain interventions. These results allow us to identify several open challenges, which we argue can be tackled through future multidisciplinary research on building interactive uncertainty-aware systems. To facilitate further research, we release a new elicitation platform, UElic, to collect uncertain feedback from humans in collaborative prediction tasks.

Explainable AI (XAI) underwent a recent surge in research on concept extraction, focusing on extracting human-interpretable concepts from Deep Neural Networks. An important challenge facing concept extraction approaches is the difficulty of interpreting and evaluating discovered concepts, especially for complex tasks such as molecular property prediction. We address this challenge by presenting GCI: a (G)raph (C)oncept (I)nterpretation framework, used for quantitatively measuring alignment between concepts discovered from Graph Neural Networks (GNNs) and their corresponding human interpretations. GCI encodes concept interpretations as functions, which can be used to quantitatively measure the alignment between a given interpretation and concept definition. We demonstrate four applications of GCI: (i) quantitatively evaluating concept extractors, (ii) measuring alignment between concept extractors and human interpretations, (iii) measuring the completeness of interpretations with respect to an end task and (iv) a practical application of GCI to molecular property prediction, in which we demonstrate how to use chemical functional groups to explain GNNs trained on molecular property prediction tasks, and implement interpretations with a 0.76 AUCROC completeness score.

Recent work on interpretability has focused on concept-based explanations, where deep learning models are explained in terms of high-level units of information, referred to as concepts. Concept learning models, however, have been shown to be prone to encoding impurities in their representations, failing to fully capture meaningful features of their inputs. While concept learning lacks metrics to measure such phenomena, the field of disentanglement learning has explored the related notion of underlying factors of variation in the data, with plenty of metrics to measure the purity of such factors. In this paper, we show that such metrics are not appropriate for concept learning and propose novel metrics for evaluating the purity of concept representations in both approaches. We show the advantage of these metrics over existing ones and demonstrate their utility in evaluating the robustness of concept representations and interventions performed on them. In addition, we show their utility for benchmarking state-of-the-art methods from both families and find that, contrary to common assumptions, supervision alone may not be sufficient for pure concept representations., Comment: To appear at AAAI 2023

Tabular biomedical data is often high-dimensional but with a very small number of samples. Although recent work showed that well-regularised simple neural networks could outperform more sophisticated architectures on tabular data, they are still prone to overfitting on tiny datasets with many potentially irrelevant features. To combat these issues, we propose Weight Predictor Network with Feature Selection (WPFS) for learning neural networks from high-dimensional and small sample data by reducing the number of learnable parameters and simultaneously performing feature selection. In addition to the classification network, WPFS uses two small auxiliary networks that together output the weights of the first layer of the classification model. We evaluate on nine real-world biomedical datasets and demonstrate that WPFS outperforms other standard as well as more recent methods typically applied to tabular data. Furthermore, we investigate the proposed feature selection mechanism and show that it improves performance while providing useful insights into the learning task., Comment: Accepted to AAAI-2023

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.

Recent work has suggested post-hoc explainers might be ineffective for detecting spurious correlations in Deep Neural Networks (DNNs). However, we show there are serious weaknesses with the existing evaluation frameworks for this setting. Previously proposed metrics are extremely difficult to interpret and are not directly comparable between explainer methods. To alleviate these constraints, we propose a new evaluation methodology, Explainer Divergence Scores (EDS), grounded in an information theory approach to evaluate explainers. EDS is easy to interpret and naturally comparable across explainers. We use our methodology to compare the detection performance of three different explainers - feature attribution methods, influential examples and concept extraction, on two different image datasets. We discover post-hoc explainers often contain substantial information about a DNN's dependence on spurious artifacts, but in ways often imperceptible to human users. This suggests the need for new techniques that can use this information to better detect a DNN's reliance on spurious correlations., Comment: Presented at the AIMLAI workshop at the 31st ACM International Conference on Information and Knowledge Management (CIKM 2022)

Neural networks often struggle with high-dimensional but small sample-size tabular datasets. One reason is that current weight initialisation methods assume independence between weights, which can be problematic when there are insufficient samples to estimate the model's parameters accurately. In such small data scenarios, leveraging additional structures can improve the model's performance and training stability. To address this, we propose GCondNet, a general approach to enhance neural networks by leveraging implicit structures present in tabular data. We create a graph between samples for each data dimension, and utilise Graph Neural Networks (GNNs) to extract this implicit structure, and for conditioning the parameters of the first layer of an underlying predictor network. By creating many small graphs, GCondNet exploits the data's high-dimensionality, and thus improves the performance of an underlying predictor network. We demonstrate GCondNet's effectiveness on 12 real-world datasets, where it outperforms 14 standard and state-of-the-art methods. The results show that GCondNet is a versatile framework for injecting graph-regularisation into various types of neural networks, including MLPs and tabular Transformers. Code is available at https://github.com/andreimargeloiu/GCondNet., Comment: Published in Transactions on Machine Learning Research (TMLR) 2024. Also accepted and selected for oral presentation at NeurIPS 2023 - Table Representation Learning Workshop

The formalization of existing mathematical proofs is a notoriously difficult process. Despite decades of research on automation and proof assistants, writing formal proofs remains arduous and only accessible to a few experts. While previous studies to automate formalization focused on powerful search algorithms, no attempts were made to take advantage of available informal proofs. In this work, we introduce Draft, Sketch, and Prove (DSP), a method that maps informal proofs to formal proof sketches, and uses the sketches to guide an automated prover by directing its search to easier sub-problems. We investigate two relevant setups where informal proofs are either written by humans or generated by a language model. Our experiments and ablation studies show that large language models are able to produce well-structured formal sketches that follow the same reasoning steps as the informal proofs. Guiding an automated prover with these sketches enhances its performance from 20.9% to 39.3% on a collection of mathematical competition problems.

In this paper we study the practicality and usefulness of incorporating distributed representations of graphs into models within the context of drug pair scoring. We argue that the real world growth and update cycles of drug pair scoring datasets subvert the limitations of transductive learning associated with distributed representations. Furthermore, we argue that the vocabulary of discrete substructure patterns induced over drug sets is not dramatically large due to the limited set of atom types and constraints on bonding patterns enforced by chemistry. Under this pretext, we explore the effectiveness of distributed representations of the molecular graphs of drugs in drug pair scoring tasks such as drug synergy, polypharmacy, and drug-drug interaction prediction. To achieve this, we present a methodology for learning and incorporating distributed representations of graphs within a unified framework for drug pair scoring. Subsequently, we augment a number of recent and state-of-the-art models to utilise our embeddings. We empirically show that the incorporation of these embeddings improves downstream performance of almost every model across different drug pair scoring tasks, even those the original model was not designed for. We publicly release all of our drug embeddings for the DrugCombDB, DrugComb, DrugbankDDI, and TwoSides datasets., Comment: Updated manuscript, 9 main pages, 8 pages reference and appendix

Deploying AI-powered systems requires trustworthy models supporting effective human interactions, going beyond raw prediction accuracy. Concept bottleneck models promote trustworthiness by conditioning classification tasks on an intermediate level of human-like concepts. This enables human interventions which can correct mispredicted concepts to improve the model's performance. However, existing concept bottleneck models are unable to find optimal compromises between high task accuracy, robust concept-based explanations, and effective interventions on concepts -- particularly in real-world conditions where complete and accurate concept supervisions are scarce. To address this, we propose Concept Embedding Models, a novel family of concept bottleneck models which goes beyond the current accuracy-vs-interpretability trade-off by learning interpretable high-dimensional concept representations. Our experiments demonstrate that Concept Embedding Models (1) attain better or competitive task accuracy w.r.t. standard neural models without concepts, (2) provide concept representations capturing meaningful semantics including and beyond their ground truth labels, (3) support test-time concept interventions whose effect in test accuracy surpasses that in standard concept bottleneck models, and (4) scale to real-world conditions where complete concept supervisions are scarce., Comment: To appear at NeurIPS 2022

The opaque reasoning of Graph Neural Networks induces a lack of human trust. Existing graph network explainers attempt to address this issue by providing post-hoc explanations, however, they fail to make the model itself more interpretable. To fill this gap, we introduce the Concept Encoder Module, the first differentiable concept-discovery approach for graph networks. The proposed approach makes graph networks explainable by design by first discovering graph concepts and then using these to solve the task. Our results demonstrate that this approach allows graph networks to: (i) attain model accuracy comparable with their equivalent vanilla versions, (ii) discover meaningful concepts that achieve high concept completeness and purity scores, (iii) provide high-quality concept-based logic explanations for their prediction, and (iv) support effective interventions at test time: these can increase human trust as well as significantly improve model performance.

The study of representations is of fundamental importance to any form of communication, and our ability to exploit them effectively is paramount. This article presents a novel theory -- Representational Systems Theory -- that is designed to abstractly encode a wide variety of representations from three core perspectives: syntax, entailment, and their properties. By introducing the concept of a construction space, we are able to encode each of these core components under a single, unifying paradigm. Using our Representational Systems Theory, it becomes possible to structurally transform representations in one system into representations in another. An intrinsic facet of our structural transformation technique is representation selection based on properties that representations possess, such as their relative cognitive effectiveness or structural complexity. A major theoretical barrier to providing general structural transformation techniques is a lack of terminating algorithms. Representational Systems Theory permits the derivation of partial transformations when no terminating algorithm can produce a full transformation. Since Representational Systems Theory provides a universal approach to encoding representational systems, a further key barrier is eliminated: the need to devise system-specific structural transformation algorithms, that are necessary when different systems adopt different formalisation approaches. Consequently, Representational Systems Theory is the first general framework that provides a unified approach to encoding representations, supports representation selection via structural transformations, and has the potential for widespread practical application., Comment: 118 pages total: 94 of main paper + 2 of references + 22 of appendices. Submitted to JACM. Authors Gem Stapleton and Daniel Raggi contributed equally to this research

Autoformalization is the process of automatically translating from natural language mathematics to formal specifications and proofs. A successful autoformalization system could advance the fields of formal verification, program synthesis, and artificial intelligence. While the long-term goal of autoformalization seemed elusive for a long time, we show large language models provide new prospects towards this goal. We make the surprising observation that LLMs can correctly translate a significant portion ($25.3\%$) of mathematical competition problems perfectly to formal specifications in Isabelle/HOL. We demonstrate the usefulness of this process by improving a previously introduced neural theorem prover via training on these autoformalized theorems. Our methodology results in a new state-of-the-art result on the MiniF2F theorem proving benchmark, improving the proof rate from $29.6\%$ to $35.2\%$., Comment: 44 pages

In theorem proving, the task of selecting useful premises from a large library to unlock the proof of a given conjecture is crucially important. This presents a challenge for all theorem provers, especially the ones based on language models, due to their relative inability to reason over huge volumes of premises in text form. This paper introduces Thor, a framework integrating language models and automated theorem provers to overcome this difficulty. In Thor, a class of methods called hammers that leverage the power of automated theorem provers are used for premise selection, while all other tasks are designated to language models. Thor increases a language model's success rate on the PISA dataset from $39\%$ to $57\%$, while solving $8.2\%$ of problems neither language models nor automated theorem provers are able to solve on their own. Furthermore, with a significantly smaller computational budget, Thor can achieve a success rate on the MiniF2F dataset that is on par with the best existing methods. Thor can be instantiated for the majority of popular interactive theorem provers via a straightforward protocol we provide.

In recent years, there has been significant work on increasing both interpretability and debuggability of a Deep Neural Network (DNN) by extracting a rule-based model that approximates its decision boundary. Nevertheless, current DNN rule extraction methods that consider a DNN's latent space when extracting rules, known as decompositional algorithms, are either restricted to single-layer DNNs or intractable as the size of the DNN or data grows. In this paper, we address these limitations by introducing ECLAIRE, a novel polynomial-time rule extraction algorithm capable of scaling to both large DNN architectures and large training datasets. We evaluate ECLAIRE on a wide variety of tasks, ranging from breast cancer prognosis to particle detection, and show that it consistently extracts more accurate and comprehensible rule sets than the current state-of-the-art methods while using orders of magnitude less computational resources. We make all of our methods available, including a rule set visualisation interface, through the open-source REMIX library (https://github.com/mateoespinosa/remix)., Comment: Accepted at NeurIPS 2021 Workshop on eXplainable AI approaches for debugging and diagnosis (XAI4Debugging)

Concept bottleneck models map from raw inputs to concepts, and then from concepts to targets. Such models aim to incorporate pre-specified, high-level concepts into the learning procedure, and have been motivated to meet three desiderata: interpretability, predictability, and intervenability. However, we find that concept bottleneck models struggle to meet these goals. Using post hoc interpretability methods, we demonstrate that concepts do not correspond to anything semantically meaningful in input space, thus calling into question the usefulness of concept bottleneck models in their current form., Comment: Accepted at ICLR 2021 Workshop on Responsible AI

Despite their remarkable performance on a wide range of visual tasks, machine learning technologies often succumb to data distribution shifts. Consequently, a range of recent work explores techniques for detecting these shifts. Unfortunately, current techniques offer no explanations about what triggers the detection of shifts, thus limiting their utility to provide actionable insights. In this work, we present Concept Bottleneck Shift Detection (CBSD): a novel explainable shift detection method. CBSD provides explanations by identifying and ranking the degree to which high-level human-understandable concepts are affected by shifts. Using two case studies (dSprites and 3dshapes), we demonstrate how CBSD can accurately detect underlying concepts that are affected by shifts and achieve higher detection accuracy compared to state-of-the-art shift detection methods., Comment: ICLR 2021 Workshop (RobustML), 16 pages, 14 figures; typos corrected

Concept-based explanations have emerged as a popular way of extracting human-interpretable representations from deep discriminative models. At the same time, the disentanglement learning literature has focused on extracting similar representations in an unsupervised or weakly-supervised way, using deep generative models. Despite the overlapping goals and potential synergies, to our knowledge, there has not yet been a systematic comparison of the limitations and trade-offs between concept-based explanations and disentanglement approaches. In this paper, we give an overview of these fields, comparing and contrasting their properties and behaviours on a diverse set of tasks, and highlighting their potential strengths and limitations. In particular, we demonstrate that state-of-the-art approaches from both classes can be data inefficient, sensitive to the specific nature of the classification/regression task, or sensitive to the employed concept representation., Comment: Presented at the RAI, WeaSul, and RobustML workshops at The Ninth International Conference on Learning Representations (ICLR) 2021

Recurrent Neural Networks (RNNs) have achieved remarkable performance on a range of tasks. A key step to further empowering RNN-based approaches is improving their explainability and interpretability. In this work we present MEME: a model extraction approach capable of approximating RNNs with interpretable models represented by human-understandable concepts and their interactions. We demonstrate how MEME can be applied to two multivariate, continuous data case studies: Room Occupation Prediction, and In-Hospital Mortality Prediction. Using these case-studies, we show how our extracted models can be used to interpret RNNs both locally and globally, by approximating RNN decision-making via interpretable concept interactions., Comment: Presented at the HAMLETS workshop at the 34th Conference on Neural Information Processing Systems (NeurIPS 2020)

We investigate the influence of adversarial training on the interpretability of convolutional neural networks (CNNs), specifically applied to diagnosing skin cancer. We show that gradient-based saliency maps of adversarially trained CNNs are significantly sharper and more visually coherent than those of standardly trained CNNs. Furthermore, we show that adversarially trained networks highlight regions with significant color variation within the lesion, a common characteristic of melanoma. We find that fine-tuning a robust network with a small learning rate further improves saliency maps' sharpness. Lastly, we provide preliminary work suggesting that robustifying the first layers to extract robust low-level features leads to visually coherent explanations., Comment: To appear at NeurIPS 2020 workshop "Medical Imaging meets NeurIPS (MED-NEURIPS)"

Stratifying cancer patients based on their gene expression levels allows improving diagnosis, survival analysis and treatment planning. However, such data is extremely highly dimensional as it contains expression values for over 20000 genes per patient, and the number of samples in the datasets is low. To deal with such settings, we propose to incorporate prior biological knowledge about genes from ontologies into the machine learning system for the task of patient classification given their gene expression data. We use ontology embeddings that capture the semantic similarities between the genes to direct a Graph Convolutional Network, and therefore sparsify the network connections. We show this approach provides an advantage for predicting clinical targets from high-dimensional low-sample data., Comment: 4 pages + 2 page references, 15th Machine Learning in Computational Biology (MLCB) meeting, 2020

The ability to hypothesise, develop abstract concepts based on concrete observations and apply these hypotheses to justify future actions has been paramount in human development. An existing line of research in outfitting intelligent machines with abstract reasoning capabilities revolves around the Raven's Progressive Matrices (RPM). There have been many breakthroughs in supervised approaches to solving RPM in recent years. However, this process requires external assistance, and thus it cannot be claimed that machines have achieved reasoning ability comparable to humans. Namely, humans can solve RPM problems without supervision or prior experience once the RPM rule that relations can only exist row/column-wise is properly introduced. In this paper, we introduce a pairwise relations discriminator (PRD), a technique to develop unsupervised models with sufficient reasoning abilities to tackle an RPM problem. PRD reframes the RPM problem into a relation comparison task, which we can solve without requiring the labelling of the RPM problem. We can identify the optimal candidate by adapting the application of PRD to the RPM problem. Our approach, the PRD, establishes a new state-of-the-art unsupervised learning benchmark with an accuracy of 55.9% on the I-RAVEN, presenting a significant improvement and a step forward in equipping machines with abstract reasoning.

Deep Neural Networks (DNNs) have achieved remarkable performance on a range of tasks. A key step to further empowering DNN-based approaches is improving their explainability. In this work we present CME: a concept-based model extraction framework, used for analysing DNN models via concept-based extracted models. Using two case studies (dSprites, and Caltech UCSD Birds), we demonstrate how CME can be used to (i) analyse the concept information learned by a DNN model (ii) analyse how a DNN uses this concept information when predicting output labels (iii) identify key concept information that can further improve DNN predictive performance (for one of the case studies, we showed how model accuracy can be improved by over 14%, using only 30% of the available concepts)., Comment: Presented at the AIMLAI workshop at the 29th ACM International Conference on Information and Knowledge Management (CIKM 2020)

We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven by the use of topological clustering algorithms on protein-protein networks which incorporate inductive biases stemming from network biology research in protein complex discovery. This structurally constrains the hypothesis space over the possible computational graph factorisation whose parameters can then be learned through supervised or unsupervised task settings. The sparse construction of the computational graph enables the differential protein complex activity analysis whilst also interpreting the individual contributions of genes/proteins involved in each individual protein complex. In our experiments analysing a variety of cancer phenotypes, we show that the proposed methods outperform SVM, Fully-Connected MLP, and Randomly-Connected MLPs in all tasks. Our work introduces a scalable method for incorporating large interaction networks as prior knowledge to drive the construction of powerful computational models amenable to introspective study., Comment: 7 Pages, 2 Figures

Deep Graph Neural Networks (GNNs) show promising performance on a range of graph tasks, yet at present are costly to run and lack many of the optimisations applied to DNNs. We show, for the first time, how to systematically quantise GNNs with minimal or no loss in performance using Network Architecture Search (NAS). We define the possible quantisation search space of GNNs. The proposed novel NAS mechanism, named Low Precision Graph NAS (LPGNAS), constrains both architecture and quantisation choices to be differentiable. LPGNAS learns the optimal architecture coupled with the best quantisation strategy for different components in the GNN automatically using back-propagation in a single search round. On eight different datasets, solving the task of classifying unseen nodes in a graph, LPGNAS generates quantised models with significant reductions in both model and buffer sizes but with similar accuracy to manually designed networks and other NAS results. In particular, on the Pubmed dataset, LPGNAS shows a better size-accuracy Pareto frontier compared to seven other manual and searched baselines, offering a 2.3 times reduction in model size but a 0.4% increase in accuracy when compared to the best NAS competitor. Finally, from our collected quantisation statistics on a wide range of datasets, we suggest a W4A8 (4-bit weights, 8-bit activations) quantisation strategy might be the bottleneck for naive GNN quantisations.

Abstract reasoning, particularly in the visual domain, is a complex human ability, but it remains a challenging problem for artificial neural learning systems. In this work we propose MXGNet, a multilayer graph neural network for multi-panel diagrammatic reasoning tasks. MXGNet combines three powerful concepts, namely, object-level representation, graph neural networks and multiplex graphs, for solving visual reasoning tasks. MXGNet first extracts object-level representations for each element in all panels of the diagrams, and then forms a multi-layer multiplex graph capturing multiple relations between objects across different diagram panels. MXGNet summarises the multiple graphs extracted from the diagrams of the task, and uses this summarisation to pick the most probable answer from the given candidates. We have tested MXGNet on two types of diagrammatic reasoning tasks, namely Diagram Syllogisms and Raven Progressive Matrices (RPM). For an Euler Diagram Syllogism task MXGNet achieves state-of-the-art accuracy of 99.8%. For PGM and RAVEN, two comprehensive datasets for RPM reasoning, MXGNet outperforms the state-of-the-art models by a considerable margin.

While modern deep neural architectures generalise well when test data is sampled from the same distribution as training data, they fail badly for cases when the test data distribution differs from the training distribution even along a few dimensions. This lack of out-of-distribution generalisation is increasingly manifested when the tasks become more abstract and complex, such as in relational reasoning. In this paper we propose a neuroscience-inspired inductive-biased module that can be readily amalgamated with current neural network architectures to improve out-of-distribution (o.o.d) generalisation performance on relational reasoning tasks. This module learns to project high-dimensional object representations to low-dimensional manifolds for more efficient and generalisable relational comparisons. We show that neural nets with this inductive bias achieve considerably better o.o.d generalisation performance for a range of relational reasoning tasks. We finally analyse the proposed inductive bias module to understand the importance of lower dimension projection, and propose an augmentation to the algorithmic alignment theory to better measure algorithmic alignment with generalisation.

We present the first differentiable Network Architecture Search (NAS) for Graph Neural Networks (GNNs). GNNs show promising performance on a wide range of tasks, but require a large amount of architecture engineering. First, graphs are inherently a non-Euclidean and sophisticated data structure, leading to poor adaptivity of GNN architectures across different datasets. Second, a typical graph block contains numerous different components, such as aggregation and attention, generating a large combinatorial search space. To counter these problems, we propose a Probabilistic Dual Network Architecture Search (PDNAS) framework for GNNs. PDNAS not only optimises the operations within a single graph block (micro-architecture), but also considers how these blocks should be connected to each other (macro-architecture). The dual architecture (micro- and marco-architectures) optimisation allows PDNAS to find deeper GNNs on diverse datasets with better performance compared to other graph NAS methods. Moreover, we use a fully gradient-based search approach to update architectural parameters, making it the first differentiable graph NAS method. PDNAS outperforms existing hand-designed GNNs and NAS results, for example, on the PPI dataset, PDNAS beats its best competitors by 1.67 and 0.17 in F1 scores.