Biagio Brattoli

Michael Dorkenwald, Fanyi Xiao, Biagio Brattoli et al. · amazon-science

We propose SCVRL, a novel contrastive-based framework for self-supervised learning for videos. Differently from previous contrast learning based methods that mostly focus on learning visual semantics (e.g., CVRL), SCVRL is capable of learning both semantic and motion patterns. For that, we reformulate the popular shuffling pretext task within a modern contrastive learning paradigm. We show that our transformer-based network has a natural capacity to learn motion in self-supervised settings and achieves strong performance, outperforming CVRL on four benchmarks.

Jeongun Ryu, Aaron Valero Puche, JaeWoong Shin et al.

Cell detection is a fundamental task in computational pathology that can be used for extracting high-level medical information from whole-slide images. For accurate cell detection, pathologists often zoom out to understand the tissue-level structures and zoom in to classify cells based on their morphology and the surrounding context. However, there is a lack of efforts to reflect such behaviors by pathologists in the cell detection models, mainly due to the lack of datasets containing both cell and tissue annotations with overlapping regions. To overcome this limitation, we propose and publicly release OCELOT, a dataset purposely dedicated to the study of cell-tissue relationships for cell detection in histopathology. OCELOT provides overlapping cell and tissue annotations on images acquired from multiple organs. Within this setting, we also propose multi-task learning approaches that benefit from learning both cell and tissue tasks simultaneously. When compared against a model trained only for the cell detection task, our proposed approaches improve cell detection performance on 3 datasets: proposed OCELOT, public TIGER, and internal CARP datasets. On the OCELOT test set in particular, we show up to 6.79 improvement in F1-score. We believe the contributions of this paper, including the release of the OCELOT dataset at https://lunit-io.github.io/research/publications/ocelot are a crucial starting point toward the important research direction of incorporating cell-tissue relationships in computation pathology.

Biagio Brattoli, Mohammad Mostafavi, Taebum Lee et al.

Despite advancements in methodologies, immunohistochemistry (IHC) remains the most utilized ancillary test for histopathologic and companion diagnostics in targeted therapies. However, objective IHC assessment poses challenges. Artificial intelligence (AI) has emerged as a potential solution, yet its development requires extensive training for each cancer and IHC type, limiting versatility. We developed a Universal IHC (UIHC) analyzer, an AI model for interpreting IHC images regardless of tumor or IHC types, using training datasets from various cancers stained for PD-L1 and/or HER2. This multi-cohort trained model outperforms conventional single-cohort models in interpreting unseen IHCs (Kappa score 0.578 vs. up to 0.509) and consistently shows superior performance across different positive staining cutoff values. Qualitative analysis reveals that UIHC effectively clusters patches based on expression levels. The UIHC model also quantitatively assesses c-MET expression with MET mutations, representing a significant advancement in AI application in the era of personalized medicine and accumulating novel biomarkers.

Biagio Brattoli, Joseph Tighe, Fedor Zhdanov et al.

Trained on large datasets, deep learning (DL) can accurately classify videos into hundreds of diverse classes. However, video data is expensive to annotate. Zero-shot learning (ZSL) proposes one solution to this problem. ZSL trains a model once, and generalizes to new tasks whose classes are not present in the training dataset. We propose the first end-to-end algorithm for ZSL in video classification. Our training procedure builds on insights from recent video classification literature and uses a trainable 3D CNN to learn the visual features. This is in contrast to previous video ZSL methods, which use pretrained feature extractors. We also extend the current benchmarking paradigm: Previous techniques aim to make the test task unknown at training time but fall short of this goal. We encourage domain shift across training and test data and disallow tailoring a ZSL model to a specific test dataset. We outperform the state-of-the-art by a wide margin. Our code, evaluation procedure and model weights are available at github.com/bbrattoli/ZeroShotVideoClassification.

Nawid Sayed, Biagio Brattoli, Björn Ommer

In this paper we present a self-supervised method for representation learning utilizing two different modalities. Based on the observation that cross-modal information has a high semantic meaning we propose a method to effectively exploit this signal. For our approach we utilize video data since it is available on a large scale and provides easily accessible modalities given by RGB and optical flow. We demonstrate state-of-the-art performance on highly contested action recognition datasets in the context of self-supervised learning. We show that our feature representation also transfers to other tasks and conduct extensive ablation studies to validate our core contributions. Code and model can be found at https://github.com/nawidsayed/Cross-and-Learn.

Carlijn Lems, Sander Moonemans, Natálie Klubíčková et al.

Foundation models with visual question answering capabilities for digital pathology are emerging. Such unprecedented technology requires independent benchmarking to assess its potential in assisting pathologists in routine diagnostics. We created DALPHIN, the first multicentric open benchmark for pathology AI copilots, comprising 1236 images from 300 cases, spanning 130 rare to common diagnoses, 6 countries, and 14 subspecialties. The DALPHIN design and dataset are introduced alongside a human performance benchmark of 31 pathologists from 10 countries with varying expertise. We report results for two general-purpose (GPT-5, Gemini 2.5 Pro) and one pathology-specific copilot (PathChat+) for sequential and independent answer generation. We observed no statistically significant difference from expert-level performance in four of six tasks for PathChat, 2/6 tasks for Gemini, and 1/6 tasks for GPT. DALPHIN is publicly released with sequestered, indirectly accessible ground truth to foster robust and enduring benchmarking. Data, methods, and the evaluation platform are accessible through dalphin.grand-challenge.org.

JaeWoong Shin, Jeongun Ryu, Aaron Valero Puche et al.

Pathologists routinely alternate between different magnifications when examining Whole-Slide Images, allowing them to evaluate both broad tissue morphology and intricate cellular details to form comprehensive diagnoses. However, existing deep learning-based cell detection models struggle to replicate these behaviors and learn the interdependent semantics between structures at different magnifications. A key barrier in the field is the lack of datasets with multi-scale overlapping cell and tissue annotations. The OCELOT 2023 challenge was initiated to gather insights from the community to validate the hypothesis that understanding cell and tissue (cell-tissue) interactions is crucial for achieving human-level performance, and to accelerate the research in this field. The challenge dataset includes overlapping cell detection and tissue segmentation annotations from six organs, comprising 673 pairs sourced from 306 The Cancer Genome Atlas (TCGA) Whole-Slide Images with hematoxylin and eosin staining, divided into training, validation, and test subsets. Participants presented models that significantly enhanced the understanding of cell-tissue relationships. Top entries achieved up to a 7.99 increase in F1-score on the test set compared to the baseline cell-only model that did not incorporate cell-tissue relationships. This is a substantial improvement in performance over traditional cell-only detection methods, demonstrating the need for incorporating multi-scale semantics into the models. This paper provides a comparative analysis of the methods used by participants, highlighting innovative strategies implemented in the OCELOT 2023 challenge.

Biagio Brattoli, Jack Shi, Jongchan Park et al.

Identifying actionable driver mutations in non-small cell lung cancer (NSCLC) can impact treatment decisions and significantly improve patient outcomes. Despite guideline recommendations, broader adoption of genetic testing remains challenging due to limited availability and lengthy turnaround times. Machine Learning (ML) methods for Computational Pathology (CPath) offer a potential solution; however, research often focuses on only one or two common mutations, limiting the clinical value of these tools and the pool of patients who can benefit from them. This study evaluates various Multiple Instance Learning (MIL) techniques to detect six key actionable NSCLC driver mutations: ALK, BRAF, EGFR, ERBB2, KRAS, and MET ex14. Additionally, we introduce an Asymmetric Transformer Decoder model that employs queries and key-values of varying dimensions to maintain a low query dimensionality. This approach efficiently extracts information from patch embeddings and minimizes overfitting risks, proving highly adaptable to the MIL setting. Moreover, we present a method to directly utilize tissue type in the model, addressing a typical MIL limitation where either all regions or only some specific regions are analyzed, neglecting biological relevance. Our method outperforms top MIL models by an average of 3%, and over 4% when predicting rare mutations such as ERBB2 and BRAF, moving ML-based tests closer to being practical alternatives to standard genetic testing.

Gianluca Carloni, Biagio Brattoli, Seongho Keum et al.

Computational pathology (CPath) has shown great potential in mining actionable insights from Whole Slide Images (WSIs). Deep Learning (DL) has been at the center of modern CPath, and while it delivers unprecedented performance, it is also known that DL may be affected by irrelevant details, such as those introduced during scanning by different commercially available scanners. This may lead to scanner bias, where the model outputs for the same tissue acquired by different scanners may vary. In turn, it hinders the trust of clinicians in CPath-based tools and their deployment in real-world clinical practices. Recent pathology Foundation Models (FMs) promise to provide better domain generalization capabilities. In this paper, we benchmark FMs using a multi-scanner dataset and show that FMs still suffer from scanner bias. Following this observation, we propose ScanGen, a contrastive loss function applied during task-specific fine-tuning that mitigates scanner bias, thereby enhancing the models' robustness to scanner variations. Our approach is applied to the Multiple Instance Learning task of Epidermal Growth Factor Receptor (EGFR) mutation prediction from H\&E-stained WSIs in lung cancer. We observe that ScanGen notably enhances the ability to generalize across scanners, while retaining or improving the performance of EGFR mutation prediction.

Yanyi Zhang, Xinyu Li, Chunhui Liu et al.

We introduce Video Transformer (VidTr) with separable-attention for video classification. Comparing with commonly used 3D networks, VidTr is able to aggregate spatio-temporal information via stacked attentions and provide better performance with higher efficiency. We first introduce the vanilla video transformer and show that transformer module is able to perform spatio-temporal modeling from raw pixels, but with heavy memory usage. We then present VidTr which reduces the memory cost by 3.3$\times$ while keeping the same performance. To further optimize the model, we propose the standard deviation based topK pooling for attention ($pool_{topK\_std}$), which reduces the computation by dropping non-informative features along temporal dimension. VidTr achieves state-of-the-art performance on five commonly used datasets with lower computational requirement, showing both the efficiency and effectiveness of our design. Finally, error analysis and visualization show that VidTr is especially good at predicting actions that require long-term temporal reasoning.

Biagio Brattoli, Uta Buechler, Michael Dorkenwald et al.

Motor behaviour analysis is essential to biomedical research and clinical diagnostics as it provides a non-invasive strategy for identifying motor impairment and its change caused by interventions. State-of-the-art instrumented movement analysis is time- and cost-intensive, since it requires placing physical or virtual markers. Besides the effort required for marking keypoints or annotations necessary for training or finetuning a detector, users need to know the interesting behaviour beforehand to provide meaningful keypoints. We introduce unsupervised behaviour analysis and magnification (uBAM), an automatic deep learning algorithm for analysing behaviour by discovering and magnifying deviations. A central aspect is unsupervised learning of posture and behaviour representations to enable an objective comparison of movement. Besides discovering and quantifying deviations in behaviour, we also propose a generative model for visually magnifying subtle behaviour differences directly in a video without requiring a detour via keypoints or annotations. Essential for this magnification of deviations even across different individuals is a disentangling of appearance and behaviour. Evaluations on rodents and human patients with neurological diseases demonstrate the wide applicability of our approach. Moreover, combining optogenetic stimulation with our unsupervised behaviour analysis shows its suitability as a non-invasive diagnostic tool correlating function to brain plasticity.

Timo Milbich, Karsten Roth, Biagio Brattoli et al.

Learning the similarity between images constitutes the foundation for numerous vision tasks. The common paradigm is discriminative metric learning, which seeks an embedding that separates different training classes. However, the main challenge is to learn a metric that not only generalizes from training to novel, but related, test samples. It should also transfer to different object classes. So what complementary information is missed by the discriminative paradigm? Besides finding characteristics that separate between classes, we also need them to likely occur in novel categories, which is indicated if they are shared across training classes. This work investigates how to learn such characteristics without the need for extra annotations or training data. By formulating our approach as a novel triplet sampling strategy, it can be easily applied on top of recent ranking loss frameworks. Experiments show that, independent of the underlying network architecture and the specific ranking loss, our approach significantly improves performance in deep metric learning, leading to new the state-of-the-art results on various standard benchmark datasets. Preliminary early access page can be found here: https://ieeexplore.ieee.org/document/9141449

Karsten Roth, Biagio Brattoli, Björn Ommer

Metric learning seeks to embed images of objects suchthat class-defined relations are captured by the embeddingspace. However, variability in images is not just due to different depicted object classes, but also depends on other latent characteristics such as viewpoint or illumination. In addition to these structured properties, random noise further obstructs the visual relations of interest. The common approach to metric learning is to enforce a representation that is invariant under all factors but the ones of interest. In contrast, we propose to explicitly learn the latent characteristics that are shared by and go across object classes. We can then directly explain away structured visual variability, rather than assuming it to be unknown random noise. We propose a novel surrogate task to learn visual characteristics shared across classes with a separate encoder. This encoder is trained jointly with the encoder for class information by reducing their mutual information. On five standard image retrieval benchmarks the approach significantly improves upon the state-of-the-art.

Uta Büchler, Biagio Brattoli, Björn Ommer

Self-supervised learning of convolutional neural networks can harness large amounts of cheap unlabeled data to train powerful feature representations. As surrogate task, we jointly address ordering of visual data in the spatial and temporal domain. The permutations of training samples, which are at the core of self-supervision by ordering, have so far been sampled randomly from a fixed preselected set. Based on deep reinforcement learning we propose a sampling policy that adapts to the state of the network, which is being trained. Therefore, new permutations are sampled according to their expected utility for updating the convolutional feature representation. Experimental evaluation on unsupervised and transfer learning tasks demonstrates competitive performance on standard benchmarks for image and video classification and nearest neighbor retrieval.