Molecular property prediction is a crucial task that guides the design of new compounds, including drugs and materials. While explainable artificial intelligence methods aim to scrutinize model predictions by identifying influential molecular substructures, many existing approaches rely on masking strategies that remove either atoms or atom-level features to assess importance via fidelity metrics. These methods, however, often fail to adhere to the underlying molecular distribution and thus yield unintuitive explanations. In this work, we propose counterfactual masking, a novel framework that replaces masked substructures with chemically reasonable fragments sampled from generative models trained to complete molecular graphs. Rather than evaluating masked predictions against implausible zeroed-out baselines, we assess them relative to counterfactual molecules drawn from the data distribution. Our method offers two key benefits: (1) molecular realism that underpins robust and distribution-consistent explanations, and (2) meaningful counterfactuals that directly indicate how structural modifications may affect predicted properties. We demonstrate that counterfactual masking is well-suited for benchmarking model explainers and yields more actionable insights across multiple datasets and property prediction tasks. Our approach bridges the gap between explainability and molecular design, offering a principled and generative path toward explainable machine learning in chemistry.

Masked Image Modeling (MIM) has emerged as a promising approach for Self-Supervised Learning (SSL) of visual representations. However, the out-of-the-box performance of MIMs is typically inferior to competing approaches. Most users cannot afford fine-tuning due to the need for large amounts of data, high GPU consumption, and specialized user knowledge. Therefore, the practical use of MIM representations is limited. In this paper we ask what is the reason for the poor out-of-the-box performance of MIMs. Is it due to weaker features produced by MIM models, or is it due to suboptimal usage? Through detailed analysis, we show that attention in MIMs is spread almost uniformly over many patches, leading to ineffective aggregation by the [cls] token. Based on this insight, we propose Selective Aggregation to better capture the rich semantic information retained in patch tokens, which significantly improves the out-of-the-box performance of MIM.

Prototypical parts networks combine the power of deep learning with the explainability of case-based reasoning to make accurate, interpretable decisions. They follow the this looks like that reasoning, representing each prototypical part with patches from training images. However, a single image patch comprises multiple visual features, such as color, shape, and texture, making it difficult for users to identify which feature is important to the model. To reduce this ambiguity, we introduce the Lucid Prototypical Parts Network (LucidPPN), a novel prototypical parts network that separates color prototypes from other visual features. Our method employs two reasoning branches: one for non-color visual features, processing grayscale images, and another focusing solely on color information. This separation allows us to clarify whether the model's decisions are based on color, shape, or texture. Additionally, LucidPPN identifies prototypical parts corresponding to semantic parts of classified objects, making comparisons between data classes more intuitive, e.g., when two bird species might differ primarily in belly color. Our experiments demonstrate that the two branches are complementary and together achieve results comparable to baseline methods. More importantly, LucidPPN generates less ambiguous prototypical parts, enhancing user understanding.

The real world is messy and unstructured. Uncovering critical information often requires active, goal-driven exploration. It remains to be seen whether Vision-Language Models (VLMs), which recently emerged as a popular zero-shot tool in many difficult tasks, can operate effectively in such conditions. In this paper, we answer this question by introducing FlySearch, a 3D, outdoor, photorealistic environment for searching and navigating to objects in complex scenes. We define three sets of scenarios with varying difficulty and observe that state-of-the-art VLMs cannot reliably solve even the simplest exploration tasks, with the gap to human performance increasing as the tasks get harder. We identify a set of central causes, ranging from vision hallucination, through context misunderstanding, to task planning failures, and we show that some of them can be addressed by finetuning. We publicly release the benchmark, scenarios, and the underlying codebase.

Active Visual Exploration (AVE) optimizes the utilization of robotic resources in real-world scenarios by sequentially selecting the most informative observations. However, modern methods require a high computational budget due to processing the same observations multiple times through the autoencoder transformers. As a remedy, we introduce a novel approach to AVE called TOken REcycling (TORE). It divides the encoder into extractor and aggregator components. The extractor processes each observation sepa-rately, enabling the reuse of tokens passed to the aggrega-tor. Moreover, to further reduce the computations, we de-crease the decoder to only one block. Through extensive experiments, we demonstrate that TORE outperforms state-of-the-art methods while reducing computational overhead by up to 90%.

Prototypical parts-based networks are becoming increasingly popular due to their faithful self-explanations. However, their similarity maps are calculated in the penultimate network layer. Therefore, the receptive field of the prototype activation region often depends on parts of the image outside this region, which can lead to misleading interpretations. We name this undesired behavior a spatial explanation misalignment and introduce an interpretability benchmark with a set of dedicated metrics for quantifying this phenomenon. In addition, we propose a method for misalignment compensation and apply it to existing state-of-the-art models. We show the expressiveness of our benchmark and the effectiveness of the proposed compensation methodology through extensive empirical studies.

Today, both science and industry rely heavily on machine learning models, predominantly artificial neural networks, that become increasingly complex and demand more computing resources to be trained. In this paper, we will look holistically at the efficiency of machine learning models and draw the inspirations to address their main challenges from the green sustainable economy principles. Instead of constraining some computations or memory used by the models, we will focus on reusing what is available to them: computations done in the previous processing steps, partial information accessible at run-time, or knowledge gained by the model during previous training sessions in continually learned models. This new research path of zero-waste machine learning can lead to several research questions related to efficiency of contemporary neural networks - how machine learning models can learn better with less data? How they select relevant data samples out of many? Finally, how can they build on top of already trained models to reduce the need for more training samples? Here, we explore all the above questions and attempt to answer them.

In this work, we introduce ProtoNCD, a novel approach to novel class discovery (NCD) that leverages prototypical parts for enhanced interpretability.ProtoNCD extends the ProtoPool methodology to the NCD setting, employing techniques such as knowledge distillation and specialized prototypical parts initialization.Through comprehensive experiments on the CUB-200-2011 dataset, we demonstrate the efficacy of ProtoNCD and its pivotal role in explaining how the reasoning of known classes influences predictions for those newly discovered.

Class-incremental learning is becoming more popular as it helps models widen their applicability while not forgetting what they already know. A trend in this area is to use a mixture-of-expert technique, where different models work together to solve the task. However, the experts are usually trained all at once using whole task data, which makes them all prone to forgetting and increasing computational burden. To address this limitation, we introduce a novel approach named SEED. SEED selects only one, the most optimal expert for a considered task, and uses data from this task to fine-tune only this expert. For this purpose, each expert represents each class with a Gaussian distribution, and the optimal expert is selected based on the similarity of those distributions. Consequently, SEED increases diversity and heterogeneity within the experts while maintaining the high stability of this ensemble method. The extensive experiments demonstrate that SEED achieves state-of-the-art performance in exemplar-free settings across various scenarios, showing the potential of expert diversification through data in continual learning.

Self-supervised learning (SSL) is a powerful technique for learning from unlabeled data. By learning to remain invariant to applied data augmentations, methods such as SimCLR and MoCo can reach quality on par with supervised approaches. However, this invariance may be detrimental for solving downstream tasks that depend on traits affected by augmentations used during pretraining, such as color. In this paper, we propose to foster sensitivity to such characteristics in the representation space by modifying the projector network, a common component of self-supervised architectures. Specifically, we supplement the projector with information about augmentations applied to images. For the projector to take advantage of this auxiliary conditioning when solving the SSL task, the feature extractor learns to preserve the augmentation information in its representations. Our approach, coined Conditional Augmentation-aware Self-supervised Learning (CASSLE), is directly applicable to typical joint-embedding SSL methods regardless of their objective functions. Moreover, it does not require major changes in the network architecture or prior knowledge of downstream tasks. In addition to an analysis of sensitivity towards different data augmentations, we conduct a series of experiments, which show that CASSLE improves over various SSL methods, reaching state-of-the-art performance in multiple downstream tasks.

Partial Multi-label Learning (PML) is a type of weakly supervised learning where each training instance corresponds to a set of candidate labels, among which only some are true. In this paper, we introduce ProPML, a novel probabilistic approach to this problem that extends the binary cross entropy to the PML setup. In contrast to existing methods, it does not require suboptimal disambiguation and, as such, can be applied to any deep architecture. Furthermore, experiments conducted on artificial and real-world datasets indicate that ProPML outperforms existing approaches, especially for high noise in a candidate set.

Lung cancer is a leading cause of cancer-related deaths, and early diagnosis is crucial for its effective treatment. That is why computer-aided tools have been developed to support particular steps of CT scan analysis, including lung segmentation, suspicious region detection, and patient-level diagnosis. However, none of the previous approaches addressed this process comprehensively. To fill this gap, we introduce CompLung, a comprehensive tool for lung cancer diagnosis that performs all of the above-listed steps in an end-to-end manner. We have trained the CompLung architecture using the publicly available LIDC-IDRI dataset extended with lung segmentation masks obtained from our internal radiologists, which we make publicly available to boost the research on this emerging topic. Finally, we conduct extensive experiments and demonstrate the superior performance and interpretability of CompLung compared to existing methods for lung cancer diagnosis.

Multiple Instance Learning (MIL) is a weakly-supervised problem in which one label is assigned to the whole bag of instances. An important class of MIL models is instance-based, where we first classify instances and then aggregate those predictions to obtain a bag label. The most common MIL model is when we consider a bag as positive if at least one of its instances has a positive label. However, this reasoning does not hold in many real-life scenarios, where the positive bag label is often a consequence of a certain percentage of positive instances. To address this issue, we introduce a dedicated instance-based method called ProMIL, based on deep neural networks and Bernstein polynomial estimation. An important advantage of ProMIL is that it can automatically detect the optimal percentage level for decision-making. We show that ProMIL outperforms standard instance-based MIL in real-world medical applications. We make the code available.

Continual learning enables incremental learning of new tasks without forgetting those previously learned, resulting in positive knowledge transfer that can enhance performance on both new and old tasks. However, continual learning poses new challenges for interpretability, as the rationale behind model predictions may change over time, leading to interpretability concept drift. We address this problem by proposing Interpretable Class-InCremental LEarning (ICICLE), an exemplar-free approach that adopts a prototypical part-based approach. It consists of three crucial novelties: interpretability regularization that distills previously learned concepts while preserving user-friendly positive reasoning; proximity-based prototype initialization strategy dedicated to the fine-grained setting; and task-recency bias compensation devoted to prototypical parts. Our experimental results demonstrate that ICICLE reduces the interpretability concept drift and outperforms the existing exemplar-free methods of common class-incremental learning when applied to concept-based models.

Active visual exploration addresses the issue of limited sensor capabilities in real-world scenarios, where successive observations are actively chosen based on the environment. To tackle this problem, we introduce a new technique called Attention-Map Entropy (AME). It leverages the internal uncertainty of the transformer-based model to determine the most informative observations. In contrast to existing solutions, it does not require additional loss components, which simplifies the training. Through experiments, which also mimic retina-like sensors, we show that such simplified training significantly improves the performance of reconstruction, segmentation and classification on publicly available datasets.

We introduce ProtoSeg, a novel model for interpretable semantic image segmentation, which constructs its predictions using similar patches from the training set. To achieve accuracy comparable to baseline methods, we adapt the mechanism of prototypical parts and introduce a diversity loss function that increases the variety of prototypes within each class. We show that ProtoSeg discovers semantic concepts, in contrast to standard segmentation models. Experiments conducted on Pascal VOC and Cityscapes datasets confirm the precision and transparency of the presented method.

Recent years have seen a surge in research on combining deep neural networks with other methods, including decision trees and graphs. There are at least three advantages of incorporating decision trees and graphs: they are easy to interpret since they are based on sequential decisions, they can make decisions faster, and they provide a hierarchy of classes. However, one of the well-known drawbacks of decision trees, as compared to decision graphs, is that decision trees cannot reuse the decision nodes. Nevertheless, decision graphs were not commonly used in deep learning due to the lack of efficient gradient-based training techniques. In this paper, we fill this gap and provide a general paradigm based on Markov processes, which allows for efficient training of the special type of decision graphs, which we call Self-Organizing Neural Graphs (SONG). We provide a theoretical study on SONG, complemented by experiments conducted on Letter, Connect4, MNIST, CIFAR, and TinyImageNet datasets, showing that our method performs on par or better than existing decision models.

Preliminary microbiological diagnosis usually relies on microscopic examination and, due to the routine culture and bacteriological examination, lasts up to 11 days. Hence, many deep learning methods based on microscopic images were recently introduced to replace the time-consuming bacteriological examination. They shorten the diagnosis by 1-2 days but still require iterative culture to obtain monoculture samples. In this work, we present a feasibility study for further shortening the diagnosis time by analyzing polyculture images. It is possible with multi-MIL, a novel multi-label classification method based on multiple instance learning. To evaluate our approach, we introduce a dataset containing microscopic images for all combinations of four considered bacteria species. We obtain ROC AUC above 0.9, proving the feasibility of the method and opening the path for future experiments with a larger number of species.

Abstract The rapid development of histopathology scanners allowed the digital transformation of pathology. Current devices fastly and accurately digitize histology slides on many magnifications, resulting in whole slide images (WSI). However, direct application of supervised deep learning methods to WSI highest magnification is impossible due to hardware limitations. That is why WSI classification is usually analyzed using standard Multiple Instance Learning (MIL) approaches, that do not explain their predictions, which is crucial for medical applications. In this work, we fill this gap by introducing ProtoMIL, a novel self-explainable MIL method inspired by the case-based reasoning process that operates on visual prototypes. Thanks to incorporating prototypical features into objects description, ProtoMIL unprecedentedly joins the model accuracy and fine-grained interpretability, as confirmed by the experiments conducted on five recognized whole-slide image datasets.

Recently introduced self-supervised methods for image representation learning provide on par or superior results to their fully supervised competitors, yet the corresponding efforts to explain the self-supervised approaches lag behind. Motivated by this observation, we introduce a novel visual probing framework for explaining the self-supervised models by leveraging probing tasks employed previously in natural language processing. The probing tasks require knowledge about semantic relationships between image parts. Hence, we propose a systematic approach to obtain analogs of natural language in vision, such as visual words, context, and taxonomy. We show the effectiveness and applicability of those analogs in the context of explaining self-supervised representations. Our key findings emphasize that relations between language and vision can serve as an effective yet intuitive tool for discovering how machine learning models work, independently of data modality. Our work opens a plethora of research pathways towards more explainable and transparent AI.

In this work, we automatically distinguish between different clones of the same bacteria species (Klebsiella pneumoniae) based only on microscopic images. It is a challenging task, previously seemed unreachable due to the high clones' similarity. For this purpose, we apply a multi-step algorithm with attention-based deep multiple instance learning, which returns parts of the image crucial to the prediction. Except for obtaining high accuracy, we introduce extensive explainability based on persistence homology, increasing the understandability and trust in the model. Our work opens a plethora of research pathways towards cheaper and faster epidemiological management.

In this work, we introduce an extension to ProtoPNet called ProtoPShare which shares prototypical parts between classes. To obtain prototype sharing we prune prototypical parts using a novel data-dependent similarity. Our approach substantially reduces the number of prototypes needed to preserve baseline accuracy and finds prototypical similarities between classes. We show the effectiveness of ProtoPShare on the CUB-200-2011 and the Stanford Cars datasets and confirm the semantic consistency of its prototypical parts in user-study.

Not all supervised learning problems are described by a pair of a fixed-size input tensor and a label. In some cases, especially in medical image analysis, a label corresponds to a bag of instances (e.g. image patches), and to classify such bag, aggregation of information from all of the instances is needed. There have been several attempts to create a model working with a bag of instances, however, they are assuming that there are no dependencies within the bag and the label is connected to at least one instance. In this work, we introduce Self-Attention Attention-based MIL Pooling (SA-AbMILP) aggregation operation to account for the dependencies between instances. We conduct several experiments on MNIST, histological, microbiological, and retinal databases to show that SA-AbMILP performs better than other models. Additionally, we investigate kernel variations of Self-Attention and their influence on the results.

Persistent homology (PH) is a rigorous mathematical theory that provides a robust descriptor of data in the form of persistence diagrams (PDs). PDs exhibit, however, complex structure and are difficult to integrate in today's machine learning workflows. This paper introduces persistence bag-of-words: a novel and stable vectorized representation of PDs that enables the seamless integration with machine learning. Comprehensive experiments show that the new representation achieves state-of-the-art performance and beyond in much less time than alternative approaches.

We propose a general, theoretically justified mechanism for processing missing data by neural networks. Our idea is to replace typical neuron's response in the first hidden layer by its expected value. This approach can be applied for various types of networks at minimal cost in their modification. Moreover, in contrast to recent approaches, it does not require complete data for training. Experimental results performed on different types of architectures show that our method gives better results than typical imputation strategies and other methods dedicated for incomplete data.

In this paper, we present an application which aid an evaluation of the arterial diameter changes, based on ultrasound videos.The designed, implemented and verified algorithm uses the techniques of image processing, image analysis and pattern recognition, such as filtering, profile plot analysis and active contour method.Except determining the artery diameter over time it is also able to retrieve ECG from ultrasound video.The results obtained for both signals are synchronized, therefore it is possible to obtain the artery diameters in R wave points, which is a novel approach.Experiments were performed to assess the software validation by comparing the outcomes obtained with the evaluated algorithm with those manually-acquiredthe correlation is high.This is the first stage of the research in which we will build the cardiovascular predictive model to search for the new cardiovascular factors.