Multiple instance learning (MIL) has enabled substantial progress in computational histopathology, where a large amount of patches from gigapixel whole slide images are aggregated into slide-level predictions. Heatmaps are widely used to validate MIL models and to discover tissue biomarkers. Yet, the validity of these heatmaps has barely been investigated. In this work, we introduce a general framework for evaluating the quality of MIL heatmaps without requiring additional labels. We conduct a large-scale benchmark experiment to assess six explanation methods across histopathology task types (classification, regression, survival), MIL model architectures (Attention-, Transformer-, Mamba-based), and patch encoder backbones (UNI2, Virchow2). Our results show that explanation quality mostly depends on MIL model architecture and task type, with perturbation ("Single"), layer-wise relevance propagation (LRP), and integrated gradients (IG) consistently outperforming attention-based and gradient-based saliency heatmaps, which often fail to reflect model decision mechanisms. We further demonstrate the advanced capabilities of the best-performing explanation methods: (i) We provide a proof-of-concept that MIL heatmaps of a bulk gene expression prediction model can be correlated with spatial transcriptomics for biological validation, and (ii) showcase the discovery of distinct model strategies for predicting human papillomavirus (HPV) infection from head and neck cancer slides. Our work highlights the importance of validating MIL heatmaps and establishes that improved explainability can enable more reliable model validation and yield biological insights, making a case for a broader adoption of explainable AI in digital pathology. Our code is provided in a public GitHub repository: https://github.com/bifold-pathomics/xMIL.

Automated interpretability research aims to identify concepts encoded in neural network features to enhance human understanding of model behavior. Within the context of large language models (LLMs) for natural language processing (NLP), current automated neuron-level feature description methods face two key challenges: limited robustness and the assumption that each neuron encodes a single concept (monosemanticity), despite increasing evidence of polysemanticity. This assumption restricts the expressiveness of feature descriptions and limits their ability to capture the full range of behaviors encoded in model internals. To address this, we introduce Polysemantic FeatuRe Identification and Scoring Method (PRISM), a novel framework specifically designed to capture the complexity of features in LLMs. Unlike approaches that assign a single description per neuron, common in many automated interpretability methods in NLP, PRISM produces more nuanced descriptions that account for both monosemantic and polysemantic behavior. We apply PRISM to LLMs and, through extensive benchmarking against existing methods, demonstrate that our approach produces more accurate and faithful feature descriptions, improving both overall description quality (via a description score) and the ability to capture distinct concepts when polysemanticity is present (via a polysemanticity score).

Rationales in the form of manually annotated input spans usually serve as ground truth when evaluating explainability methods in NLP. They are, however, time-consuming and often biased by the annotation process. In this paper, we debate whether human gaze, in the form of webcam-based eye-tracking recordings, poses a valid alternative when evaluating importance scores. We evaluate the additional information provided by gaze data, such as total reading times, gaze entropy, and decoding accuracy with respect to human rationale annotations. We compare WebQAmGaze, a multilingual dataset for information-seeking QA, with attention and explainability-based importance scores for 4 different multilingual Transformer-based language models (mBERT, distil-mBERT, XLMR, and XLMR-L) and 3 languages (English, Spanish, and German). Our pipeline can easily be applied to other tasks and languages. Our findings suggest that gaze data offers valuable linguistic insights that could be leveraged to infer task difficulty and further show a comparable ranking of explainability methods to that of human rationales.

Alexandros Vasileiou, Oliver Eberle. Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers). 2024.

Multiple instance learning (MIL) is an effective and widely used approach for weakly supervised machine learning. In histopathology, MIL models have achieved remarkable success in tasks like tumor detection, biomarker prediction, and outcome prognostication. However, MIL explanation methods are still lagging behind, as they are limited to small bag sizes or disregard instance interactions. We revisit MIL through the lens of explainable AI (XAI) and introduce xMIL, a refined framework with more general assumptions. We demonstrate how to obtain improved MIL explanations using layer-wise relevance propagation (LRP) and conduct extensive evaluation experiments on three toy settings and four real-world histopathology datasets. Our approach consistently outperforms previous explanation attempts with particularly improved faithfulness scores on challenging biomarker prediction tasks. Finally, we showcase how xMIL explanations enable pathologists to extract insights from MIL models, representing a significant advance for knowledge discovery and model debugging in digital histopathology.

Recent sequence modeling approaches using selective state space sequence models, referred to as Mamba models, have seen a surge of interest. These models allow efficient processing of long sequences in linear time and are rapidly being adopted in a wide range of applications such as language modeling, demonstrating promising performance. To foster their reliable use in real-world scenarios, it is crucial to augment their transparency. Our work bridges this critical gap by bringing explainability, particularly Layer-wise Relevance Propagation (LRP), to the Mamba architecture. Guided by the axiom of relevance conservation, we identify specific components in the Mamba architecture, which cause unfaithful explanations. To remedy this issue, we propose MambaLRP, a novel algorithm within the LRP framework, which ensures a more stable and reliable relevance propagation through these components. Our proposed method is theoretically sound and excels in achieving state-of-the-art explanation performance across a diverse range of models and datasets. Moreover, MambaLRP facilitates a deeper inspection of Mamba architectures, uncovering various biases and evaluating their significance. It also enables the analysis of previous speculations regarding the long-range capabilities of Mamba models.

Contrastive explanations, where one decision is explained in contrast to another, are supposed to be closer to how humans explain a decision than non-contrastive explanations, where the decision is not necessarily referenced to an alternative.This claim has never been empirically validated.We analyze four English text-classification datasets (SST2, DynaSent, BIOS and DBpedia-Animals).We fine-tune and extract explanations from three different models (RoBERTa, GTP-2, and T5), each in three different sizes and apply three post-hoc explainability methods (LRP, GradientxInput, GradNorm).We furthermore collect and release human rationale annotations for a subset of 100 samples from the BIOS dataset for contrastive and non-contrastive settings.A crosscomparison between model-based rationales and human annotations, both in contrastive and non-contrastive settings, yields a high agreement between the two settings for models as well as for humans.Moreover, model-based explanations computed in both settings align equally well with human rationales.Thus, we empirically find that humans do not necessarily explain in a contrastive manner.

Learned self-attention functions in state-of-theart NLP models often correlate with human attention.We investigate whether self-attention in large-scale pre-trained language models is as predictive of human eye fixation patterns during task-reading as classical cognitive models of human attention.We compare attention functions across two task-specific reading datasets for sentiment analysis and relation extraction.We find the predictiveness of large-scale pretrained self-attention for human attention depends on 'what is in the tail', e.g., the syntactic nature of rare contexts.Further, we observe that task-specific fine-tuning does not increase the correlation with human task-specific reading.Through an input reduction experiment we give complementary insights on the sparsity and fidelity trade-off, showing that lowerentropy attention vectors are more faithful.

Transformers have become an important workhorse of machine learning, with numerous applications. This necessitates the development of reliable methods for increasing their transparency. Multiple interpretability methods, often based on gradient information, have been proposed. We show that the gradient in a Transformer reflects the function only locally, and thus fails to reliably identify the contribution of input features to the prediction. We identify Attention Heads and LayerNorm as main reasons for such unreliable explanations and propose a more stable way for propagation through these layers. Our proposal, which can be seen as a proper extension of the well-established LRP method to Transformers, is shown both theoretically and empirically to overcome the deficiency of a simple gradient-based approach, and achieves state-of-the-art explanation performance on a broad range of Transformer models and datasets.

Many learning algorithms such as kernel machines, nearest neighbors, clustering, or anomaly detection, are based on distances or similarities. Before similarities are used for training an actual machine learning model, we would like to verify that they are bound to meaningful patterns in the data. In this paper, we propose to make similarities interpretable by augmenting them with an explanation. We develop BiLRP, a scalable and theoretically founded method to systematically decompose the output of an already trained deep similarity model on pairs of input features. Our method can be expressed as a composition of LRP explanations, which were shown in previous works to scale to highly nonlinear models. Through an extensive set of experiments, we demonstrate that BiLRP robustly explains complex similarity models, e.g., built on VGG-16 deep neural network features. Additionally, we apply our method to an open problem in digital humanities: detailed assessment of similarity between historical documents, such as astronomical tables. Here again, BiLRP provides insight and brings verifiability into a highly engineered and problem-specific similarity model.

Graph Neural Networks (GNNs) are a popular approach for predicting graph structured data. As GNNs tightly entangle the input graph into the neural network structure, common explainable AI approaches are not applicable. To a large extent, GNNs have remained black-boxes for the user so far. In this paper, we show that GNNs can in fact be naturally explained using higher-order expansions, i.e., by identifying groups of edges that jointly contribute to the prediction. Practically, we find that such explanations can be extracted using a nested attribution scheme, where existing techniques such as layer-wise relevance propagation (LRP) can be applied at each step. The output is a collection of walks into the input graph that are relevant for the prediction. Our novel explanation method, which we denote by GNN-LRP, is applicable to a broad range of graph neural networks and lets us extract practically relevant insights on sentiment analysis of text data, structure-property relationships in quantum chemistry, and image classification.