Identification of In-Droplet Multicellular Communities by Light-Induced Combinatorial DNA Barcoding.

A microdroplet co-culture system is useful for the parallel assessment of numerous possible cell-cell interactions by generating isolated subcommunities from a pool of heterogeneous cells. However, the integration of single-cell sequencing into such analysis has been limited due to the lack of effective molecular identifiers for each in-droplet subcommunity. Herein, we present a strategy for generating in-droplet subcommunity identifiers using DNA-functionalized microparticles encapsulated within microdroplets. These microparticles serve as initial information carriers, where their combinations act as distinct identifiers for in-droplet subcommunity. Upon optical trigger, DNA barcoding molecules encoding the microparticle information are once released in the microdroplets and then tag cell membranes. The tagged DNA molecules then serve as a second information carrier readable by single-cell sequencing to reconstitute the community in silico in the single-cell RNA sequencing data space.

Active Classification With Uncertainty Comparison Queries.

Noisy pairwise comparison feedback has been incorporated to improve the overall query complexity of interactively learning binary classifiers. The positivity comparison oracle is extensively used to provide feedback on which is more likely to be positive in a pair of data points. Because it is impossible to determine accurate labels using this oracle alone without knowing the classification threshold, existing methods still rely on the traditional explicit labeling oracle, which explicitly answers the label given a data point. The current method conducts sorting on all data points and uses explicit labeling oracle to find the classification threshold. However, it has two drawbacks: (1) it needs unnecessary sorting for label inference and (2) it naively adapts quick sort to noisy feedback. In order to avoid these inefficiencies and acquire information of the classification threshold at the same time, we propose a new pairwise comparison oracle concerning uncertainties. This oracle answers which one has higher uncertainty given a pair of data points. We then propose an efficient adaptive labeling algorithm to take advantage of the proposed oracle. In addition, we address the situation where the labeling budget is insufficient compared to the data set size. Furthermore, we confirm the feasibility of the proposed oracle and the performance of the proposed algorithm theoretically and empirically.

Semisupervised Ordinal Regression Based on Empirical Risk Minimization.

Ordinal regression is aimed at predicting an ordinal class label. In this letter, we consider its semisupervised formulation, in which we have unlabeled data along with ordinal-labeled data to train an ordinal regressor. There are several metrics to evaluate the performance of ordinal regression, such as the mean absolute error, mean zero-one error, and mean squared error. However, the existing studies do not take the evaluation metric into account, restrict model choice, and have no theoretical guarantee. To overcome these problems, we propose a novel generic framework for semisupervised ordinal regression based on the empirical risk minimization principle that is applicable to optimizing all of the metrics mentioned above. In addition, our framework has flexible choices of models, surrogate losses, and optimization algorithms without the common geometric assumption on unlabeled data such as the cluster assumption or manifold assumption. We provide an estimation error bound to show that our risk estimator is consistent. Finally, we conduct experiments to show the usefulness of our framework.

Classification From Pairwise Similarities/Dissimilarities and Unlabeled Data via Empirical Risk Minimization.

Pairwise similarities and dissimilarities between data points are often obtained more easily than full labels of data in real-world classification problems. To make use of such pairwise information, an empirical risk minimization approach has been proposed, where an unbiased estimator of the classification risk is computed from only pairwise similarities and unlabeled data. However, this approach has not yet been able to handle pairwise dissimilarities. Semisupervised clustering methods can incorporate both similarities and dissimilarities into their framework; however, they typically require strong geometrical assumptions on the data distribution such as the manifold assumption, which may cause severe performance deterioration. In this letter, we derive an unbiased estimator of the classification risk based on all of similarities and dissimilarities and unlabeled data. We theoretically establish an estimation error bound and experimentally demonstrate the practical usefulness of our empirical risk minimization method.

Artificial Neural Variability for Deep Learning: On Overfitting, Noise Memorization, and Catastrophic Forgetting.

Deep learning is often criticized by two serious issues that rarely exist in natural nervous systems: overfitting and catastrophic forgetting. It can even memorize randomly labeled data, which has little knowledge behind the instance-label pairs. When a deep network continually learns over time by accommodating new tasks, it usually quickly overwrites the knowledge learned from previous tasks. Referred to as the neural variability, it is well known in neuroscience that human brain reactions exhibit substantial variability even in response to the same stimulus. This mechanism balances accuracy and plasticity/flexibility in the motor learning of natural nervous systems. Thus, it motivates us to design a similar mechanism, named artificial neural variability (ANV), that helps artificial neural networks learn some advantages from "natural" neural networks. We rigorously prove that ANV plays as an implicit regularizer of the mutual information between the training data and the learned model. This result theoretically guarantees ANV a strictly improved generalizability, robustness to label noise, and robustness to catastrophic forgetting. We then devise a neural variable risk minimization (NVRM) framework and neural variable optimizers to achieve ANV for conventional network architectures in practice. The empirical studies demonstrate that NVRM can effectively relieve overfitting, label noise memorization, and catastrophic forgetting at negligible costs.

Accelerated Diffusion-Based Sampling by the Non-Reversible Dynamics with Skew-Symmetric Matrices.

Langevin dynamics (LD) has been extensively studied theoretically and practically as a basic sampling technique. Recently, the incorporation of non-reversible dynamics into LD is attracting attention because it accelerates the mixing speed of LD. Popular choices for non-reversible dynamics include underdamped Langevin dynamics (ULD), which uses second-order dynamics and perturbations with skew-symmetric matrices. Although ULD has been widely used in practice, the application of skew acceleration is limited although it is expected to show superior performance theoretically. Current work lacks a theoretical understanding of issues that are important to practitioners, including the selection criteria for skew-symmetric matrices, quantitative evaluations of acceleration, and the large memory cost of storing skew matrices. In this study, we theoretically and numerically clarify these problems by analyzing acceleration focusing on how the skew-symmetric matrix perturbs the Hessian matrix of potential functions. We also present a practical algorithm that accelerates the standard LD and ULD, which uses novel memory-efficient skew-symmetric matrices under parallel-chain Monte Carlo settings.

Use of Ghost Cytometry to Differentiate Cells with Similar Gross Morphologic Characteristics.

Imaging flow cytometry shows significant potential for increasing our understanding of heterogeneous and complex life systems and is useful for biomedical applications. Ghost cytometry is a recently proposed approach for directly analyzing compressively measured signals of cells, thereby relieving a computational bottleneck for real-time data analysis in high-throughput imaging cytometry. In our previous work, we demonstrated that this image-free approach could distinguish cells from two cell lines prepared with the same fluorescence staining method. However, the demonstration using different cell lines could not exclude the possibility that classification was based on non-morphological factors such as the speed of cells in flow, which could be encoded in the compressed signals. In this study, we show that GC can classify cells from the same cell line but with different fluorescence distributions in space, supporting the strength of our image-free approach for accurate morphological cell analysis. © 2020 International Society for Advancement of Cytometry.

Classification from Triplet Comparison Data.

Learning from triplet comparison data has been extensively studied in the context of metric learning, where we want to learn a distance metric between two instances, and ordinal embedding, where we want to learn an embedding in a Euclidean space of the given instances that preserve the comparison order as much as possible. Unlike fully labeled data, triplet comparison data can be collected in a more accurate and human-friendly way. Although learning from triplet comparison data has been considered in many applications, an important fundamental question of whether we can learn a classifier only from triplet comparison data without all the labels has remained unanswered. In this letter, we give a positive answer to this important question by proposing an unbiased estimator for the classification risk under the empirical risk minimization framework. Since the proposed method is based on the empirical risk minimization framework, it inherently has the advantage that any surrogate loss function and any model, including neural networks, can be easily applied. Furthermore, we theoretically establish an estimation error bound for the proposed empirical risk minimizer. Finally, we provide experimental results to show that our method empirically works well and outperforms various baseline methods.

Deep neural network-based computer-assisted detection of cerebral aneurysms in MR angiography.

BACKGROUND: The usefulness of computer-assisted detection (CAD) for detecting cerebral aneurysms has been reported; therefore, the improved performance of CAD will help to detect cerebral aneurysms. PURPOSE: To develop a CAD system for intracranial aneurysms on unenhanced magnetic resonance angiography (MRA) images based on a deep convolutional neural network (CNN) and a maximum intensity projection (MIP) algorithm, and to demonstrate the usefulness of the system by training and evaluating it using a large dataset. STUDY TYPE: Retrospective study. SUBJECTS: There were 450 cases with intracranial aneurysms. The diagnoses of brain aneurysms were made on the basis of MRA, which was performed as part of a brain screening program. FIELD STRENGTH/SEQUENCE: Noncontrast-enhanced 3D time-of-flight (TOF) MRA on 3T MR scanners. ASSESSMENT: In our CAD, we used a CNN classifier that predicts whether each voxel is inside or outside aneurysms by inputting MIP images generated from a volume of interest (VOI) around the voxel. The CNN was trained in advance using manually inputted labels. We evaluated our method using 450 cases with intracranial aneurysms, 300 of which were used for training, 50 for parameter tuning, and 100 for the final evaluation. STATISTICAL TESTS: Free-response receiver operating characteristic (FROC) analysis. RESULTS: Our CAD system detected 94.2% (98/104) of aneurysms with 2.9 false positives per case (FPs/case). At a sensitivity of 70%, the number of FPs/case was 0.26. DATA CONCLUSION: We showed that the combination of a CNN and an MIP algorithm is useful for the detection of intracranial aneurysms. LEVEL OF EVIDENCE: 4 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018;47:948-953.

Carbon stocks of particle board and fiberboard in Japan.

The carbon stock function of harvested wood products (HWPs) is attracting attention among climate change countermeasures. Among HWPs, particle board (PB) and fiberboard (FB) mainly use recycled materials. This study estimated carbon stocks of PB and FB and their annual changes over the past 70 years in Japan using three methods of the Intergovernmental Panel on Climate Change guidelines: Tiers 1-3. Tier 1 uses first order decay (FOD), a 25-year half-life, and the Food and Agriculture Organization of the United Nations database. Tier 2 uses FOD, a 25-year half-life, and Japan-specific statistics. Tier 3 uses a log-normal distribution for the decay function and a 38-63-year half-life of building PB/FB. Japan's PB and FB carbon stocks have increased for the past 70 years. The latest carbon stock in early 2022 and the annual change in carbon stock in 2021 was 21.83 million t-C and 0.42 million t-C/year, respectively for Tier 3. Tier 3 has the highest estimation accuracy by using decay functions and half-lives that match the actual conditions of building PB and FB, whereas Tiers 1 and 2 were underestimates. Approximately 40% of the carbon stock is derived from waste wood, which extends its utilization.

Activity-dependent organization of prefrontal hub-networks for associative learning and signal transformation.

Associative learning is crucial for adapting to environmental changes. Interactions among neuronal populations involving the dorso-medial prefrontal cortex (dmPFC) are proposed to regulate associative learning, but how these neuronal populations store and process information about the association remains unclear. Here we developed a pipeline for longitudinal two-photon imaging and computational dissection of neural population activities in male mouse dmPFC during fear-conditioning procedures, enabling us to detect learning-dependent changes in the dmPFC network topology. Using regularized regression methods and graphical modeling, we found that fear conditioning drove dmPFC reorganization to generate a neuronal ensemble encoding conditioned responses (CR) characterized by enhanced internal coactivity, functional connectivity, and association with conditioned stimuli (CS). Importantly, neurons strongly responding to unconditioned stimuli during conditioning subsequently became hubs of this novel associative network for the CS-to-CR transformation. Altogether, we demonstrate learning-dependent dynamic modulation of population coding structured on the activity-dependent formation of the hub network within the dmPFC.

Versatile anomaly detection method for medical images with semi-supervised flow-based generative models.

PURPOSE: Radiologists interpret many medical images and clinical practice demands timely interpretation, resulting in a heavy workload. To reduce the workload, here we formulate and validate a method that can handle different types of medical image and can detect virtually all types of lesion in a medical image. For the first time, we show that two flow-based deep generative (FDG) models can predict the logarithm posterior probability in a semi-supervised approach. METHODS: We adopt two FDG models in conjunction with Bayes' theorem to predict the logarithm posterior probability that a medical image is normal. We trained one of the FDG models with normal images and the other FDG model with normal and non-normal images. RESULTS: We validated the method using two types of medical image: chest X-ray images (CXRs) and brain computed tomography images (BCTs). The area under the receiver operating characteristic curve for pneumonia-like opacities in CXRs was 0.839 on average, and for infarction in BCTs was 0.904. CONCLUSION: We formulated a method of predicting the logarithm posterior probability using two FDG models. We validated that the method can detect abnormal findings in CXRs and BCTs with both an acceptable performance for testing and a comparatively light workload for training.

In silico-labeled ghost cytometry.

Characterization and isolation of a large population of cells are indispensable procedures in biological sciences. Flow cytometry is one of the standards that offers a method to characterize and isolate cells at high throughput. When performing flow cytometry, cells are molecularly stained with fluorescent labels to adopt biomolecular specificity which is essential for characterizing cells. However, molecular staining is costly and its chemical toxicity can cause side effects to the cells which becomes a critical issue when the cells are used downstream as medical products or for further analysis. Here, we introduce a high-throughput stain-free flow cytometry called in silico-labeled ghost cytometry which characterizes and sorts cells using machine-predicted labels. Instead of detecting molecular stains, we use machine learning to derive the molecular labels from compressive data obtained with diffractive and scattering imaging methods. By directly using the compressive 'imaging' data, our system can accurately assign the designated label to each cell in real time and perform sorting based on this judgment. With this method, we were able to distinguish different cell states, cell types derived from human induced pluripotent stem (iPS) cells, and subtypes of peripheral white blood cells using only stain-free modalities. Our method will find applications in cell manufacturing for regenerative medicine as well as in cell-based medical diagnostic assays in which fluorescence labeling of the cells is undesirable.

Implementing machine learning methods for imaging flow cytometry.

In this review, we focus on the applications of machine learning methods for analyzing image data acquired in imaging flow cytometry technologies. We propose that the analysis approaches can be categorized into two groups based on the type of data, raw imaging signals or features explicitly extracted from images, being analyzed by a trained model. We hope that this categorization is helpful for understanding uniqueness, differences and opportunities when the machine learning-based analysis is implemented in recently developed 'imaging' cell sorters.

Novel platform for development, training, and validation of computer-assisted detection/diagnosis software.

PURPOSE: To build a novel, open-source, purely web-based platform system to address problems in the development and clinical use of computer-assisted detection/diagnosis (CAD) software. The new platform system will replace the existing system for the development and validation of CAD software, Clinical Infrastructure for Radiologic Computation of United Solutions (CIRCUS). METHODS: In our new system, the two top-level applications visible to users are the web-based image database (CIRCUS DB; database) and the Docker plug-in-based CAD execution platform (CIRCUS CS; clinical server). These applications are built on top of a shared application programming interface server, a three-dimensional image viewer component, and an image repository. RESULTS: We successfully installed our new system into a Linux server at two clinical sites. A total of 1954 cases were registered in CIRCUS DB. We have been utilizing CIRCUS CS with four Docker-based CAD plug-ins. CONCLUSIONS: We have successfully built a new version of the CIRCUS system. Our platform was successfully implemented at two clinical sites, and we plan to publish it as an open-source software project.

Convex formulation of multiple instance learning from positive and unlabeled bags.

Multiple instance learning (MIL) is a variation of traditional supervised learning problems where data (referred to as bags) are composed of sub-elements (referred to as instances) and only bag labels are available. MIL has a variety of applications such as content-based image retrieval, text categorization, and medical diagnosis. Most of the previous work for MIL assume that training bags are fully labeled. However, it is often difficult to obtain an enough number of labeled bags in practical situations, while many unlabeled bags are available. A learning framework called PU classification (positive and unlabeled classification) can address this problem. In this paper, we propose a convex PU classification method to solve an MIL problem. We experimentally show that the proposed method achieves better performance with significantly lower computation costs than an existing method for PU-MIL.

Ghost cytometry.

Ghost imaging is a technique used to produce an object's image without using a spatially resolving detector. Here we develop a technique we term "ghost cytometry," an image-free ultrafast fluorescence "imaging" cytometry based on a single-pixel detector. Spatial information obtained from the motion of cells relative to a static randomly patterned optical structure is compressively converted into signals that arrive sequentially at a single-pixel detector. Combinatorial use of the temporal waveform with the intensity distribution of the random pattern allows us to computationally reconstruct cell morphology. More importantly, we show that applying machine-learning methods directly on the compressed waveforms without image reconstruction enables efficient image-free morphology-based cytometry. Despite a compact and inexpensive instrumentation, image-free ghost cytometry achieves accurate and high-throughput cell classification and selective sorting on the basis of cell morphology without a specific biomarker, both of which have been challenging to accomplish using conventional flow cytometers.

Inter-observer variance and the need for standardization in the morphological classification of myelodysplastic syndrome.

In this era of genome medicine, the sub-classification of myeloid neoplasms, including myelodysplastic syndrome (MDS), is now supported by genetic testing in selected cases. However, as the initial suspicion and primary diagnosis of the disease still largely relies on morphological features and numbers of hematopoietic cells, the establishment of a uniform diagnostic basis, especially for cell morphology, is essential. In this study, we collected nearly 100,000 hematopoietic cell images from 499 peripheral blood smear specimens from patients with MDS and used these to evaluate the standardization of morphological classification by medical technologists. The observers in this study ranged between two to eleven for each image, and the images were classified according to MDS criteria through a web-based system. We found considerable inter-observer variance in the assessment of dysplastic features. Observers did not recognize cytoplasmic hypo-granularity unless almost all granules in neutrophils were absent. Pseudo Pelger-Huët anomalies were also often overlooked, except for cells with a very typical "pince-nez" appearance. Taken together, this study suggests a requirement for further standardization in terms of morphological cell classification, and a need for the development of automatic cell classification-supporting devices for the accurate diagnosis of MDS.