Whole-slide images (WSIs) are critical for cancer diagnosis due to their ultra-high resolution and rich semantic content. However, their massive size and the limited availability of fine-grained annotations pose substantial challenges for conventional supervised learning. We propose DSAGL (Dual-Stream Attention-Guided Learning), a novel weakly supervised classification framework that combines a teacher-student architecture with a dual-stream design. DSAGL explicitly addresses instance-level ambiguity and bag-level semantic consistency by generating multi-scale attention-based pseudo labels and guiding instance-level learning. A shared lightweight encoder (VSSMamba) enables efficient long-range dependency modeling, while a fusion-attentive module (FASA) enhances focus on sparse but diagnostically relevant regions. We further introduce a hybrid loss to enforce mutual consistency between the two streams. Experiments on CIFAR-10, NCT-CRC, and TCGA-Lung datasets demonstrate that DSAGL consistently outperforms state-of-the-art MIL baselines, achieving superior discriminative performance and robustness under weak supervision.
Multiple instance learning (MIL) is a promising approach for weakly supervised classification in pathology using whole slide images (WSIs). However, conventional MIL methods such as Attention-Based Deep Multiple Instance Learning (ABMIL) typically disregard spatial interactions among patches that are crucial to pathological diagnosis. Recent advancements, such as Transformer based MIL (TransMIL), have incorporated spatial context and inter-patch relationships. However, it remains unclear whether explicitly modeling patch relationships yields similar performance gains in ABMIL, which relies solely on Multi-Layer Perceptrons (MLPs). In contrast, TransMIL employs Transformer-based layers, introducing a fundamental architectural shift at the cost of substantially increased computational complexity. In this work, we enhance the ABMIL framework by integrating interaction-aware representations to address this question. Our proposed model, Global ABMIL (GABMIL), explicitly captures inter-instance dependencies while preserving computational efficiency. Experimental results on two publicly available datasets for tumor subtyping in breast and lung cancers demonstrate that GABMIL achieves up to a 7 percentage point improvement in AUPRC and a 5 percentage point increase in the Kappa score over ABMIL, with minimal or no additional computational overhead. These findings underscore the importance of incorporating patch interactions within MIL frameworks. Our code is available at \href{https://github.com/tueimage/GABMIL}{\texttt{GABMIL}}.
Multiple instance learning (MIL) has become a standard paradigm for weakly supervised classification of whole slide images (WSI). However, this paradigm relies on the use of a large number of labelled WSIs for training. The lack of training data and the presence of rare diseases present significant challenges for these methods. Prompt tuning combined with the pre-trained Vision-Language models (VLMs) is an effective solution to the Few-shot Weakly Supervised WSI classification (FSWC) tasks. Nevertheless, applying prompt tuning methods designed for natural images to WSIs presents three significant challenges: 1) These methods fail to fully leverage the prior knowledge from the VLM's text modality; 2) They overlook the essential multi-scale and contextual information in WSIs, leading to suboptimal results; and 3) They lack exploration of instance aggregation methods. To address these problems, we propose a Multi-Scale and Context-focused Prompt Tuning (MSCPT) method for FSWC tasks. Specifically, MSCPT employs the frozen large language model to generate pathological visual language prior knowledge at multi-scale, guiding hierarchical prompt tuning. Additionally, we design a graph prompt tuning module to learn essential contextual information within WSI, and finally, a non-parametric cross-guided instance aggregation module has been introduced to get the WSI-level features. Based on two VLMs, extensive experiments and visualizations on three datasets demonstrated the powerful performance of our MSCPT.
Deep Learning models have been successfully utilized to extract clinically actionable insights from routinely available histology data. Generally, these models require annotations performed by clinicians, which are scarce and costly to generate. The emergence of self-supervised learning (SSL) methods remove this barrier, allowing for large-scale analyses on non-annotated data. However, recent SSL approaches apply increasingly expansive model architectures and larger datasets, causing the rapid escalation of data volumes, hardware prerequisites, and overall expenses, limiting access to these resources to few institutions. Therefore, we investigated the complexity of contrastive SSL in computational pathology in relation to classification performance with the utilization of consumer-grade hardware. Specifically, we analyzed the effects of adaptations in data volume, architecture, and algorithms on downstream classification tasks, emphasizing their impact on computational resources. We trained breast cancer foundation models on a large public patient cohort and validated them on various downstream classification tasks in a weakly supervised manner on two external public patient cohorts. Our experiments demonstrate that we can improve downstream classification performance whilst reducing SSL training duration by 90%. In summary, we propose a set of adaptations which enable the utilization of SSL in computational pathology in non-resource abundant environments.
Whole slide image (WSI) classification is a critical task in computational pathology. However, the gigapixel-size of such images remains a major challenge for the current state of deep-learning. Current methods rely on multiple-instance learning (MIL) models with frozen feature extractors. Given the the high number of instances in each image, MIL methods have long assumed independence and permutation-invariance of patches, disregarding the tissue structure and correlation between patches. Recent works started studying this correlation between instances but the computational workload of such a high number of tokens remained a limiting factor. In particular, relative position of patches remains unaddressed. We propose to apply a straightforward encoding module, namely a RoFormer layer , relying on memory-efficient exact self-attention and relative positional encoding. This module can perform full self-attention with relative position encoding on patches of large and arbitrary shaped WSIs, solving the need for correlation between instances and spatial modeling of tissues. We demonstrate that our method outperforms state-of-the-art MIL models on three commonly used public datasets (TCGA-NSCLC, BRACS and Camelyon16)) on weakly supervised classification tasks. Code is available at https://github.com/Sanofi-Public/DDS-RoFormerMIL
Multiple instance learning (MIL) was a weakly supervised learning approach that sought to assign binary class labels to collections of instances known as bags. However, due to their weak supervision nature, the MIL methods were susceptible to overfitting and required assistance in developing comprehensive representations of target instances. While regularization typically effectively combated overfitting, its integration with the MIL model has been frequently overlooked in prior studies. Meanwhile, current regularization methods for MIL have shown limitations in their capacity to uncover a diverse array of representations. In this study, we delve into the realm of regularization within the MIL model, presenting a novel approach in the form of a Progressive Dropout Layer (PDL). We aim to not only address overfitting but also empower the MIL model in uncovering intricate and impactful feature representations. The proposed method was orthogonal to existing MIL methods and could be easily integrated into them to boost performance. Our extensive evaluation across a range of MIL benchmark datasets demonstrated that the incorporation of the PDL into multiple MIL methods not only elevated their classification performance but also augmented their potential for weakly-supervised feature localizations.
This paper presents a CLIP-based unsupervised learning method for annotation-free multi-label image classification, including three stages: initialization, training, and inference. At the initialization stage, we take full advantage of the powerful CLIP model and propose a novel approach to extend CLIP for multi-label predictions based on global-local image-text similarity aggregation. To be more specific, we split each image into snippets and leverage CLIP to generate the similarity vector for the whole image (global) as well as each snippet (local). Then a similarity aggregator is introduced to leverage the global and local similarity vectors. Using the aggregated similarity scores as the initial pseudo labels at the training stage, we propose an optimization framework to train the parameters of the classification network and refine pseudo labels for unobserved labels. During inference, only the classification network is used to predict the labels of the input image. Extensive experiments show that our method outperforms state-of-the-art unsupervised methods on MS-COCO, PASCAL VOC 2007, PASCAL VOC 2012, and NUS datasets and even achieves comparable results to weakly supervised classification methods.
This paper introduces a novel approach to probabilistic deep learning, kernel density matrices, which provide a simpler yet effective mechanism for representing joint probability distributions of both continuous and discrete random variables. In quantum mechanics, a density matrix is the most general way to describe the state of a quantum system. This work extends the concept of density matrices by allowing them to be defined in a reproducing kernel Hilbert space. This abstraction allows the construction of differentiable models for density estimation, inference, and sampling, and enables their integration into end-to-end deep neural models. In doing so, we provide a versatile representation of marginal and joint probability distributions that allows us to develop a differentiable, compositional, and reversible inference procedure that covers a wide range of machine learning tasks, including density estimation, discriminative learning, and generative modeling. The broad applicability of the framework is illustrated by two examples: an image classification model that can be naturally transformed into a conditional generative model, and a model for learning with label proportions that demonstrates the framework's ability to deal with uncertainty in the training samples. The framework is implemented as a library and is available at: https://github.com/fagonzalezo/kdm.
The visual examination of tissue biopsy sections is fundamental for cancer diagnosis, with pathologists analyzing sections at multiple magnifications to discern tumor cells and their subtypes. However, existing attention-based multiple instance learning (MIL) models used for analyzing Whole Slide Images (WSIs) in cancer diagnostics often overlook the contextual information of tumor and neighboring tiles, leading to misclassifications. To address this, we propose the Context-Aware Multiple Instance Learning (CAMIL) architecture. CAMIL incorporates neighbor-constrained attention to consider dependencies among tiles within a WSI and integrates contextual constraints as prior knowledge into the MIL model. We evaluated CAMIL on subtyping non-small cell lung cancer (TCGA-NSCLC) and detecting lymph node (CAMELYON16 and CAMELYON17) metastasis, achieving test AUCs of 97.5\%, 95.9\%, and 88.1\%, respectively, outperforming other state-of-the-art methods. Additionally, CAMIL enhances model interpretability by identifying regions of high diagnostic value.
Weakly-supervised classification of histopathology slides is a computationally intensive task, with a typical whole slide image (WSI) containing billions of pixels to process. We propose Discriminative Region Active Sampling for Multiple Instance Learning (DRAS-MIL), a computationally efficient slide classification method using attention scores to focus sampling on highly discriminative regions. We apply this to the diagnosis of ovarian cancer histological subtypes, which is an essential part of the patient care pathway as different subtypes have different genetic and molecular profiles, treatment options, and patient outcomes. We use a dataset of 714 WSIs acquired from 147 epithelial ovarian cancer patients at Leeds Teaching Hospitals NHS Trust to distinguish the most common subtype, high-grade serous carcinoma, from the other four subtypes (low-grade serous, endometrioid, clear cell, and mucinous carcinomas) combined. We demonstrate that DRAS-MIL can achieve similar classification performance to exhaustive slide analysis, with a 3-fold cross-validated AUC of 0.8679 compared to 0.8781 with standard attention-based MIL classification. Our approach uses at most 18% as much memory as the standard approach, while taking 33% of the time when evaluating on a GPU and only 14% on a CPU alone. Reducing prediction time and memory requirements may benefit clinical deployment and the democratisation of AI, reducing the extent to which computational hardware limits end-user adoption.
We consider the problem of Learning from Label Proportions (LLP), a weakly supervised classification setup where instances are grouped into "bags", and only the frequency of class labels at each bag is available. Albeit, the objective of the learner is to achieve low task loss at an individual instance level. Here we propose Easyllp: a flexible and simple-to-implement debiasing approach based on aggregate labels, which operates on arbitrary loss functions. Our technique allows us to accurately estimate the expected loss of an arbitrary model at an individual level. We showcase the flexibility of our approach by applying it to popular learning frameworks, like Empirical Risk Minimization (ERM) and Stochastic Gradient Descent (SGD) with provable guarantees on instance level performance. More concretely, we exhibit a variance reduction technique that makes the quality of LLP learning deteriorate only by a factor of k (k being bag size) in both ERM and SGD setups, as compared to full supervision. Finally, we validate our theoretical results on multiple datasets demonstrating our algorithm performs as well or better than previous LLP approaches in spite of its simplicity.
Weakly-supervised text classification aims to train a classifier using only class descriptions and unlabeled data. Recent research shows that keyword-driven methods can achieve state-of-the-art performance on various tasks. However, these methods not only rely on carefully-crafted class descriptions to obtain class-specific keywords but also require substantial amount of unlabeled data and takes a long time to train. This paper proposes FastClass, an efficient weakly-supervised classification approach. It uses dense text representation to retrieve class-relevant documents from external unlabeled corpus and selects an optimal subset to train a classifier. Compared to keyword-driven methods, our approach is less reliant on initial class descriptions as it no longer needs to expand each class description into a set of class-specific keywords. Experiments on a wide range of classification tasks show that the proposed approach frequently outperforms keyword-driven models in terms of classification accuracy and often enjoys orders-of-magnitude faster training speed.
The need to learn from positive and unlabeled data, or PU learning, arises in many applications and has attracted increasing interest. While random forests are known to perform well on many tasks with positive and negative data, recent PU algorithms are generally based on deep neural networks, and the potential of tree-based PU learning is under-explored. In this paper, we propose new random forest algorithms for PU-learning. Key to our approach is a new interpretation of decision tree algorithms for positive and negative data as \emph{recursive greedy risk minimization algorithms}. We extend this perspective to the PU setting to develop new decision tree learning algorithms that directly minimizes PU-data based estimators for the expected risk. This allows us to develop an efficient PU random forest algorithm, PU extra trees. Our approach features three desirable properties: it is robust to the choice of the loss function in the sense that various loss functions lead to the same decision trees; it requires little hyperparameter tuning as compared to neural network based PU learning; it supports a feature importance that directly measures a feature's contribution to risk minimization. Our algorithms demonstrate strong performance on several datasets. Our code is available at \url{https://github.com/puetpaper/PUExtraTrees}.
In weakly-supervised text classification, only label names act as sources of supervision. Predominant approaches to weakly-supervised text classification utilize a two-phase framework, where test samples are first assigned pseudo-labels and are then used to train a neural text classifier. In most previous work, the pseudo-labeling step is dependent on obtaining seed words that best capture the relevance of each class label. We present LIME, a framework for weakly-supervised text classification that entirely replaces the brittle seed-word generation process with entailment-based pseudo-classification. We find that combining weakly-supervised classification and textual entailment mitigates shortcomings of both, resulting in a more streamlined and effective classification pipeline. With just an off-the-shelf textual entailment model, LIME outperforms recent baselines in weakly-supervised text classification and achieves state-of-the-art in 4 benchmarks. We open source our code at https://github.com/seongminp/LIME.
Semi-supervised learning and weakly supervised learning are important paradigms that aim to reduce the growing demand for labeled data in current machine learning applications. In this paper, we introduce a novel analysis of the classical label propagation algorithm (LPA) (Zhu & Ghahramani, 2002) that moreover takes advantage of useful prior information, specifically probabilistic hypothesized labels on the unlabeled data. We provide an error bound that exploits both the local geometric properties of the underlying graph and the quality of the prior information. We also propose a framework to incorporate multiple sources of noisy information. In particular, we consider the setting of weak supervision, where our sources of information are weak labelers. We demonstrate the ability of our approach on multiple benchmark weakly supervised classification tasks, showing improvements upon existing semi-supervised and weakly supervised methods.
Complementary-label learning (CLL) is widely used in weakly supervised classification, but it faces a significant challenge in real-world datasets when confronted with class-imbalanced training samples. In such scenarios, the number of samples in one class is considerably lower than in other classes, which consequently leads to a decline in the accuracy of predictions. Unfortunately, existing CLL approaches have not investigate this problem. To alleviate this challenge, we propose a novel problem setting that enables learning from class-imbalanced complementary labels for multi-class classification. To tackle this problem, we propose a novel CLL approach called Weighted Complementary-Label Learning (WCLL). The proposed method models a weighted empirical risk minimization loss by utilizing the class-imbalanced complementary labels, which is also applicable to multi-class imbalanced training samples. Furthermore, we derive an estimation error bound to provide theoretical assurance. To evaluate our approach, we conduct extensive experiments on several widely-used benchmark datasets and a real-world dataset, and compare our method with existing state-of-the-art methods. The proposed approach shows significant improvement in these datasets, even in the case of multiple class-imbalanced scenarios. Notably, the proposed method not only utilizes complementary labels to train a classifier but also solves the problem of class imbalance.
A significant proportion of clinical physiologic monitoring alarms are false. This often leads to alarm fatigue in clinical personnel, inevitably compromising patient safety. To combat this issue, researchers have attempted to build Machine Learning (ML) models capable of accurately adjudicating Vital Sign (VS) alerts raised at the bedside of hemodynamically monitored patients as real or artifact. Previous studies have utilized supervised ML techniques that require substantial amounts of hand-labeled data. However, manually harvesting such data can be costly, time-consuming, and mundane, and is a key factor limiting the widespread adoption of ML in healthcare (HC). Instead, we explore the use of multiple, individually imperfect heuristics to automatically assign probabilistic labels to unlabeled training data using weak supervision. Our weakly supervised models perform competitively with traditional supervised techniques and require less involvement from domain experts, demonstrating their use as efficient and practical alternatives to supervised learning in HC applications of ML.
Learning from label proportions (LLP) is a weakly supervised classification problem where data points are grouped into bags, and the label proportions within each bag are observed instead of the instance-level labels. The task is to learn a classifier to predict the individual labels of future individual instances. Prior work on LLP for multi-class data has yet to develop a theoretically grounded algorithm. In this work, we provide a theoretically grounded approach to LLP based on a reduction to learning with label noise, using the forward correction (FC) loss of \citet{Patrini2017MakingDN}. We establish an excess risk bound and generalization error analysis for our approach, while also extending the theory of the FC loss which may be of independent interest. Our approach demonstrates improved empirical performance in deep learning scenarios across multiple datasets and architectures, compared to the leading existing methods.
It is easier to hear birds than see them, however, they still play an essential role in nature and they are excellent indicators of deteriorating environmental quality and pollution. Recent advances in Machine Learning and Convolutional Neural Networks allow us to detect and classify bird sounds, by doing this, we can assist researchers in monitoring the status and trends of bird populations and biodiversity in ecosystems. We propose a sound detection and classification pipeline for analyzing complex soundscape recordings and identify birdcalls in the background. Our pipeline learns from weak labels, classifies fine-grained bird vocalizations in the wild, and is robust against background sounds (e.g., airplanes, rain, etc). Our solution achieved 10th place of 816 teams at the BirdCLEF 2021 Challenge hosted on Kaggle.
This paper describes a system prepared at Brno University of Technology for ICDAR 2021 Competition on Historical Document Classification, experiments leading to its design, and the main findings. The solved tasks include script and font classification, document origin localization, and dating. We combined patch-level and line-level approaches, where the line-level system utilizes an existing, publicly available page layout analysis engine. In both systems, neural networks provide local predictions which are combined into page-level decisions, and the results of both systems are fused using linear or log-linear interpolation. We propose loss functions suitable for weakly supervised classification problem where multiple possible labels are provided, and we propose loss functions suitable for interval regression in the dating task. The line-level system significantly improves results in script and font classification and in the dating task. The full system achieved 98.48 %, 88.84 %, and 79.69 % accuracy in the font, script, and location classification tasks respectively. In the dating task, our system achieved a mean absolute error of 21.91 years. Our system achieved the best results in all tasks and became the overall winner of the competition.