torchmil: A PyTorch-based library for deep Multiple Instance Learning

Multiple Instance Learning (MIL) is a powerful framework for weakly supervised learning, particularly useful when fine-grained annotations are unavailable. Despite growing interest in deep MIL methods, the field lacks standardized tools for model development, evaluation, and comparison, which hinders reproducibility and accessibility. To address this, we present torchmil, an open-source Python library built on PyTorch. torchmil offers a unified, modular, and extensible framework, featuring basic building blocks for MIL models, a standardized data format, and a curated collection of benchmark datasets and models. The library includes comprehensive documentation and tutorials to support both practitioners and researchers. torchmil aims to accelerate progress in MIL and lower the entry barrier for new users. Available at https://torchmil.readthedocs.io.

Live(r) Die: Predicting Survival in Colorectal Liver Metastasis

Colorectal cancer frequently metastasizes to the liver, significantly reducing long-term survival. While surgical resection is the only potentially curative treatment for colorectal liver metastasis (CRLM), patient outcomes vary widely depending on tumor characteristics along with clinical and genomic factors. Current prognostic models, often based on limited clinical or molecular features, lack sufficient predictive power, especially in multifocal CRLM cases. We present a fully automated framework for surgical outcome prediction from pre- and post-contrast MRI acquired before surgery. Our framework consists of a segmentation pipeline and a radiomics pipeline. The segmentation pipeline learns to segment the liver, tumors, and spleen from partially annotated data by leveraging promptable foundation models to complete missing labels. Also, we propose SAMONAI, a novel zero-shot 3D prompt propagation algorithm that leverages the Segment Anything Model to segment 3D regions of interest from a single point prompt, significantly improving our segmentation pipeline's accuracy and efficiency. The predicted pre- and post-contrast segmentations are then fed into our radiomics pipeline, which extracts features from each tumor and predicts survival using SurvAMINN, a novel autoencoder-based multiple instance neural network for survival analysis. SurvAMINN jointly learns dimensionality reduction and hazard prediction from right-censored survival data, focusing on the most aggressive tumors. Extensive evaluation on an institutional dataset comprising 227 patients demonstrates that our framework surpasses existing clinical and genomic biomarkers, delivering a C-index improvement exceeding 10%. Our results demonstrate the potential of integrating automated segmentation algorithms and radiomics-based survival analysis to deliver accurate, annotation-efficient, and interpretable outcome prediction in CRLM.

Instance-Optimal Matrix Multiplicative Weight Update and Its Quantum Applications

The Matrix Multiplicative Weight Update (MMWU) is a seminal online learning algorithm with numerous applications. Applied to the matrix version of the Learning from Expert Advice (LEA) problem on the $d$-dimensional spectraplex, it is well known that MMWU achieves the minimax-optimal regret bound of $O(\sqrt{T\log d})$, where $T$ is the time horizon. In this paper, we present an improved algorithm achieving the instance-optimal regret bound of $O(\sqrt{T\cdot S(X||d^{-1}I_d)})$, where $X$ is the comparator in the regret, $I_d$ is the identity matrix, and $S(\cdot||\cdot)$ denotes the quantum relative entropy. Furthermore, our algorithm has the same computational complexity as MMWU, indicating that the improvement in the regret bound is ``free''. Technically, we first develop a general potential-based framework for matrix LEA, with MMWU being its special case induced by the standard exponential potential. Then, the crux of our analysis is a new ``one-sided'' Jensen's trace inequality built on a Laplace transform technique, which allows the application of general potential functions beyond exponential to matrix LEA. Our algorithm is finally induced by an optimal potential function from the vector LEA problem, based on the imaginary error function. Complementing the above, we provide a memory lower bound for matrix LEA, and explore the applications of our algorithm in quantum learning theory. We show that it outperforms the state of the art for learning quantum states corrupted by depolarization noise, random quantum states, and Gibbs states. In addition, applying our algorithm to linearized convex losses enables predicting nonlinear quantum properties, such as purity, quantum virtual cooling, and R\'{e}nyi-$2$ correlation.

Deep Context-Conditioned Anomaly Detection for Tabular Data

Anomaly detection is critical in domains such as cybersecurity and finance, especially when working with large-scale tabular data. Yet, unsupervised anomaly detection -- where no labeled anomalies are available -- remains a significant challenge. Although various deep learning methods have been proposed to model a dataset's joint distribution, real-world tabular data often contain heterogeneous contexts (e.g., different users), making globally rare events normal under certain contexts. Consequently, relying on a single global distribution can overlook these contextual nuances, degrading detection performance. In this paper, we present a context-conditional anomaly detection framework tailored for tabular datasets. Our approach automatically identifies context features and models the conditional data distribution using a simple deep autoencoder. Extensive experiments on multiple tabular benchmark datasets demonstrate that our method outperforms state-of-the-art approaches, underscoring the importance of context in accurately distinguishing anomalous from normal instances.

Evaluating Multiple Instance Learning Strategies for Automated Sebocyte Droplet Counting

Sebocytes are lipid-secreting cells whose differentiation is marked by the accumulation of intracellular lipid droplets, making their quantification a key readout in sebocyte biology. Manual counting is labor-intensive and subjective, motivating automated solutions. Here, we introduce a simple attention-based multiple instance learning (MIL) framework for sebocyte image analysis. Nile Red-stained sebocyte images were annotated into 14 classes according to droplet counts, expanded via data augmentation to about 50,000 cells. Two models were benchmarked: a baseline multi-layer perceptron (MLP) trained on aggregated patch-level counts, and an attention-based MIL model leveraging ResNet-50 features with instance weighting. Experiments using five-fold cross-validation showed that the baseline MLP achieved more stable performance (mean MAE = 5.6) compared with the attention-based MIL, which was less consistent (mean MAE = 10.7) but occasionally superior in specific folds. These findings indicate that simple bag-level aggregation provides a robust baseline for slide-level droplet counting, while attention-based MIL requires task-aligned pooling and regularization to fully realize its potential in sebocyte image analysis.

Learning from Majority Label: A Novel Problem in Multi-class Multiple-Instance Learning

The paper proposes a novel multi-class Multiple-Instance Learning (MIL) problem called Learning from Majority Label (LML). In LML, the majority class of instances in a bag is assigned as the bag-level label. The goal of LML is to train a classification model that estimates the class of each instance using the majority label. This problem is valuable in a variety of applications, including pathology image segmentation, political voting prediction, customer sentiment analysis, and environmental monitoring. To solve LML, we propose a Counting Network trained to produce bag-level majority labels, estimated by counting the number of instances in each class. Furthermore, analysis experiments on the characteristics of LML revealed that bags with a high proportion of the majority class facilitate learning. Based on this result, we developed a Majority Proportion Enhancement Module (MPEM) that increases the proportion of the majority class by removing minority class instances within the bags. Experiments demonstrate the superiority of the proposed method on four datasets compared to conventional MIL methods. Moreover, ablation studies confirmed the effectiveness of each module. The code is available at \href{https://github.com/Shiku-Kaito/Learning-from-Majority-Label-A-Novel-Problem-in-Multi-class-Multiple-Instance-Learning}{here}.

SAC-MIL: Spatial-Aware Correlated Multiple Instance Learning for Histopathology Whole Slide Image Classification

We propose Spatial-Aware Correlated Multiple Instance Learning (SAC-MIL) for performing WSI classification. SAC-MIL consists of a positional encoding module to encode position information and a SAC block to perform full instance correlations. The positional encoding module utilizes the instance coordinates within the slide to encode the spatial relationships instead of the instance index in the input WSI sequence. The positional encoding module can also handle the length extrapolation issue where the training and testing sequences have different lengths. The SAC block is an MLP-based method that performs full instance correlation in linear time complexity with respect to the sequence length. Due to the simple structure of MLP, it is easy to deploy since it does not require custom CUDA kernels, compared to Transformer-based methods for WSI classification. SAC-MIL has achieved state-of-the-art performance on the CAMELYON-16, TCGA-LUNG, and TCGA-BRAC datasets. The code will be released upon acceptance.

Efficient Odd-One-Out Anomaly Detection

The recently introduced odd-one-out anomaly detection task involves identifying the odd-looking instances within a multi-object scene. This problem presents several challenges for modern deep learning models, demanding spatial reasoning across multiple views and relational reasoning to understand context and generalize across varying object categories and layouts. We argue that these challenges must be addressed with efficiency in mind. To this end, we propose a DINO-based model that reduces the number of parameters by one third and shortens training time by a factor of three compared to the current state-of-the-art, while maintaining competitive performance. Our experimental evaluation also introduces a Multimodal Large Language Model baseline, providing insights into its current limitations in structured visual reasoning tasks. The project page can be found at https://silviochito.github.io/EfficientOddOneOut/

Gromov-Wasserstein and optimal transport: from assignment problems to probabilistic numeric

The assignment problem, a cornerstone of operations research, seeks an optimal one-to-one mapping between agents and tasks to minimize total cost. This work traces its evolution from classical formulations and algorithms to modern optimal transport (OT) theory, positioning the Quadratic Assignment Problem (QAP) and related structural matching tasks within this framework. We connect the linear assignment problem to Monge's transport problem, Kantorovich's relaxation, and Wasserstein distances, then extend to cases where source and target lie in different metric-measure spaces requiring Gromov-Wasserstein (GW) distances. GW formulations, including the fused GW variant that integrates structural and feature information, naturally address QAP-like problems by optimizing alignment based on both intra-domain distances and cross-domain attributes. Applications include graph matching, keypoint correspondence, and feature-based assignments. We present exact solvers, Genetic Algorithms (GA), and multiple GW variants, including a proposed multi-initialization strategy (GW-MultiInit) that mitigates the risk of getting stuck in local optima alongside entropic Sinkhorn-based approximations and fused GW. Computational experiments on capacitated QAP instances show that GW-MultiInit consistently achieves near-optimal solutions and scales efficiently to large problems where exact methods become impractical, while parameterized EGW and FGW variants provide flexible trade-offs between accuracy and runtime. Our findings provide theoretical foundations, computational insights, and practical guidelines for applying OT and GW methods to QAP and other real-world matching problems, such as those in machine learning and logistics.

VisioFirm: Cross-Platform AI-assisted Annotation Tool for Computer Vision

AI models rely on annotated data to learn pattern and perform prediction. Annotation is usually a labor-intensive step that require associating labels ranging from a simple classification label to more complex tasks such as object detection, oriented bounding box estimation, and instance segmentation. Traditional tools often require extensive manual input, limiting scalability for large datasets. To address this, we introduce VisioFirm, an open-source web application designed to streamline image labeling through AI-assisted automation. VisioFirm integrates state-of-the-art foundation models into an interface with a filtering pipeline to reduce human-in-the-loop efforts. This hybrid approach employs CLIP combined with pre-trained detectors like Ultralytics models for common classes and zero-shot models such as Grounding DINO for custom labels, generating initial annotations with low-confidence thresholding to maximize recall. Through this framework, when tested on COCO-type of classes, initial prediction have been proven to be mostly correct though the users can refine these via interactive tools supporting bounding boxes, oriented bounding boxes, and polygons. Additionally, VisioFirm has on-the-fly segmentation powered by Segment Anything accelerated through WebGPU for browser-side efficiency. The tool supports multiple export formats (YOLO, COCO, Pascal VOC, CSV) and operates offline after model caching, enhancing accessibility. VisioFirm demonstrates up to 90\% reduction in manual effort through benchmarks on diverse datasets, while maintaining high annotation accuracy via clustering of connected CLIP-based disambiguate components and IoU-graph for redundant detection suppression. VisioFirm can be accessed from \href{https://github.com/OschAI/VisioFirm}{https://github.com/OschAI/VisioFirm}.