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Contrast-enhancement pattern analysis is critical in breast magnetic resonance imaging (MRI) to distinguish benign from probably malignant tumors. However, contrast-enhanced image acquisitions are time-consuming and very expensive. As an alternative to physical acquisition, this paper proposes a comprehensive pipeline for the generation of accurate long-term (late) contrast-enhanced breast MRI from the early counterpart. The proposed strategy focuses on preserving the contrast agent pattern in the enhanced regions while maintaining visual properties in the entire synthesized images. To that end, a novel loss function that leverages the biological behavior of contrast agent (CA) in tissue, given by the Time-Intensity (TI) enhancement curve, is proposed to optimize a pixel-attention based generative model. In addition, unlike traditional normalization and standardization methods, we developed a new normalization strategy that maintains the contrast enhancement pattern across the image sequences at multiple timestamps. This ensures the prevalence of the CA pattern after image preprocessing, unlike conventional approaches. Furthermore, in order to objectively evaluate the clinical quality of the synthesized images, two metrics are also introduced to measure the differences between the TI curves of enhanced regions of the acquired and synthesized images. The experimental results showed that the proposed strategy generates images that significantly outperform diagnostic quality in contrast-enhanced regions while maintaining the spatial features of the entire image. This results suggest a potential use of synthetic late enhanced images generated via deep learning in clinical scenarios.

Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To process these single-cells for downstream applications, we present Pycytominer, a user-friendly, open-source python package that implements the bioinformatics steps, known as image-based profiling. We demonstrate Pycytominers usefulness in a machine learning project to predict nuisance compounds that cause undesirable cell injuries., Comment: We updated: Figures (e.g., remove panel from Figure 1) to increase clarity. Consolidated the introduction, results, and discussion into a single section. Added a new analysis to predict compounds that cause undesirable cell injuries. Added three tables including one to highlight image-based profiling software limitations. 14 pages, 2 main figures, 5 supplementary figures, 3 tables

Most neural networks assume that input images have a fixed number of channels (three for RGB images). However, there are many settings where the number of channels may vary, such as microscopy images where the number of channels changes depending on instruments and experimental goals. Yet, there has not been a systemic attempt to create and evaluate neural networks that are invariant to the number and type of channels. As a result, trained models remain specific to individual studies and are hardly reusable for other microscopy settings. In this paper, we present a benchmark for investigating channel-adaptive models in microscopy imaging, which consists of 1) a dataset of varied-channel single-cell images, and 2) a biologically relevant evaluation framework. In addition, we adapted several existing techniques to create channel-adaptive models and compared their performance on this benchmark to fixed-channel, baseline models. We find that channel-adaptive models can generalize better to out-of-domain tasks and can be computationally efficient. We contribute a curated dataset (https://doi.org/10.5281/zenodo.7988357) and an evaluation API (https://github.com/broadinstitute/MorphEm.git) to facilitate objective comparisons in future research and applications., Comment: Accepted at NeurIPS Track on Datasets and Benchmarks, 2023

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., Comment: Accepted at CVPR 2023 CVMI

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., Comment: ICTIR2011 International Conference on the Theory of Information Retrieval

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., Comment: IEEE ICCV 2015

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.