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.

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.

We introduce Video Transformer (VidTr) with separable-attention for video classification. Comparing with commonly used 3D networks, VidTr is able to aggregate spatiotemporal 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× while keeping the same performance. To further optimize the model, we propose the standard deviation based topK pooling for attention (pooltopK_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.

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 online github.com/bbrattoli/ZeroShotVideoClassification.

Metric learning seeks to embed images of objects such that class-defined relations are captured by the embedding space. 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. Code is available at https://github.com/Confusezius/metric-learning-mining-interclass-characteristics.

Behavior analysis provides a crucial non-invasive and easily accessible diagnostic tool for biomedical research. A detailed analysis of posture changes during skilled motor tasks can reveal distinct functional deficits and their restoration during recovery. Our specific scenario is based on a neuroscientific study of rodents recovering from a large sensorimotor cortex stroke and skilled forelimb grasping is being recorded. Given large amounts of unlabeled videos that are recorded during such long-term studies, we seek an approach that captures fine-grained details of posture and its change during rehabilitation without costly manual supervision. Therefore, we utilize self-supervision to automatically learn accurate posture and behavior representations for analyzing motor function. Learning our model depends on the following fundamental elements: (i) limb detection based on a fully convolutional network is initialized solely using motion information, (ii) a novel self-supervised training of LSTMs using only temporal permutation yields a detailed representation of behavior, and (iii) back-propagation of this sequence representation also improves the description of individual postures. We establish a novel test dataset with expert annotations for evaluation of fine-grained behavior analysis. Moreover, we demonstrate the generality of our approach by successfully applying it to self-supervised learning of human posture on two standard benchmark datasets.