Real-world deployment of computer vision systems, including in the discovery processes of biomedical research, requires causal representations that are invariant to contextual nuisances and generalize to new data. Leveraging the internal replicate structure of two novel single-cell fluorescent microscopy datasets, we propose generally applicable tests to assess the extent to which models learn causal representations across increasingly challenging levels of OOD-generalization. We show that despite seemingly strong performance, as assessed by other established metrics, both naive and contemporary baselines designed to ward against confounding, collapse on these tests. We introduce a new method, Interventional Style Transfer (IST), that substantially improves OOD generalization by generating interventional training distributions in which spurious correlations between biological causes and nuisances are mitigated. We publish our code and datasets.
Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.
Analyzing the morphology of cells in microscopy images can provide insights into the mechanism of compounds or the function of genes. Addressing this task requires methods that can not only extract biological information from the images, but also ignore technical variations, ie, changes in experimental procedure or differences between equipments used to collect microscopy images. We propose Treatment ExemplArs with Mixture-of-experts (TEAMs), an embedding learning approach that learns a set of experts that are specialized in capturing technical variations in our training set and then aggregates specialist's predictions at test time. Thus, TEAMs can learn powerful embeddings with less technical variation bias by minimizing the noise from every expert. To train our model, we leverage Treatment Exemplars that enable our approach to capture the distribution of the entire dataset in every minibatch while still fitting into GPU memory. We evaluate our approach on three datasets for tasks like drug discovery, boosting performance on identifying the true mechanism of action of cell treatments by 5.5-11% over the state-of-the-art.
The main goal of this paper is to explore latent topic analysis (LTA), in the context of quantum information retrieval. LTA is a valuable technique for document analysis and representation, which has been extensively used in information retrieval and machine learning. Different LTA techniques have been proposed, some based on geometrical modeling (such as latent semantic analysis, LSA) and others based on a strong statistical foundation. However, these two different approaches are not usually mixed. Quantum information retrieval has the remarkable virtue of combining both geometry and probability in a common principled framework. We built on this quantum framework to propose a new LTA method, which has a clear geometrical motivation but also supports a well-founded probabilistic interpretation. An initial exploratory experimentation was performed on three standard data sets. The results show that the proposed method outperforms LSA on two of the three datasets. These results suggests that the quantum-motivated representation is an alternative for geometrical latent topic modeling worthy of further exploration.
The Flickr30k dataset has become a standard benchmark for sentence-based image description. This paper presents Flickr30k Entities, which augments the 158k captions from Flickr30k with 244k coreference chains, linking mentions of the same entities across different captions for the same image, and associating them with 276k manually annotated bounding boxes. Such annotations are essential for continued progress in automatic image description and grounded language understanding. They enable us to define a new benchmark for localization of textual entity mentions in an image. We present a strong baseline for this task that combines an image-text embedding, detectors for common objects, a color classifier, and a bias towards selecting larger objects. While our baseline rivals in accuracy more complex state-of-the-art models, we show that its gains cannot be easily parlayed into improvements on such tasks as image-sentence retrieval, thus underlining the limitations of current methods and the need for further research.
We present an active detection model for localizing objects in scenes. The model is class-specific and allows an agent to focus attention on candidate regions for identifying the correct location of a target object. This agent learns to deform a bounding box using simple transformation actions, with the goal of determining the most specific location of target objects following top-down reasoning. The proposed localization agent is trained using deep reinforcement learning, and evaluated on the Pascal VOC 2007 dataset. We show that agents guided by the proposed model are able to localize a single instance of an object after analyzing only between 11 and 25 regions in an image, and obtain the best detection results among systems that do not use object proposals for object localization.