Cell tracking is an omnipresent image analysis task in live-cell microscopy. It is similar to multiple object tracking (MOT), however, each frame contains hundreds of similar-looking objects that can divide, making it a challenging problem. Current state-of-the-art approaches follow the tracking-by-detection paradigm, i.e. first all cells are detected per frame and successively linked in a second step to form biologically consistent cell tracks. Linking is commonly solved via discrete optimization methods, which require manual tuning of hyperparameters for each dataset and are therefore cumbersome to use in practice. Here we propose Trackastra, a general purpose cell tracking approach that uses a simple transformer architecture to directly learn pairwise associations of cells within a temporal window from annotated data. Importantly, unlike existing transformer-based MOT pipelines, our learning architecture also accounts for dividing objects such as cells and allows for accurate tracking even with simple greedy linking, thus making strides towards removing the requirement for a complex linking step. The proposed architecture operates on the full spatio-temporal context of detections within a time window by avoiding the computational burden of processing dense images. We show that our tracking approach performs on par with or better than highly tuned state-of-the-art cell tracking algorithms for various biological datasets, such as bacteria, cell cultures and fluorescent particles. We provide code at //github.com/weigertlab/trackastra.
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Optic deconvolution in light microscopy (LM) refers to recovering the object details from images, revealing the ground truth of samples. Traditional explicit methods in LM rely on the point spread function (PSF) during image acquisition. Yet, these approaches often fall short due to inaccurate PSF models and noise artifacts, hampering the overall restoration quality. In this paper, we approached the optic deconvolution as an inverse problem. Motivated by the nonstandard-form compression scheme introduced by Beylkin, Coifman, and Rokhlin (BCR), we proposed an innovative physics-informed neural network Multi-Stage Residual-BCR Net (m-rBCR) to approximate the optic deconvolution. We validated the m-rBCR model on four microscopy datasets - two simulated microscopy datasets from ImageNet and BioSR, real dSTORM microscopy images, and real widefield microscopy images. In contrast to the explicit deconvolution methods (e.g. Richardson-Lucy) and other state-of-the-art NN models (U-Net, DDPM, CARE, DnCNN, ESRGAN, RCAN, Noise2Noise, MPRNet, and MIMO-U-Net), the m-rBCR model demonstrates superior performance to other candidates by PSNR and SSIM in two real microscopy datasets and the simulated BioSR dataset. In the simulated ImageNet dataset, m-rBCR ranks the second-best place (right after MIMO-U-Net). With the backbone from the optical physics, m-rBCR exploits the trainable parameters with better performances (from ~30 times fewer than the benchmark MIMO-U-Net to ~210 times than ESRGAN). This enables m-rBCR to achieve a shorter runtime (from ~3 times faster than MIMO-U-Net to ~300 times faster than DDPM). To summarize, by leveraging physics constraints our model reduced potentially redundant parameters significantly in expertise-oriented NN candidates and achieved high efficiency with superior performance.
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with biomedical data. When metadata are not well-structured or precise, the associated data are harder to find and are often burdensome to reuse, analyze or integrate with other datasets due to the upfront curation effort required to make the data usable -- typically through retrospective standardization and cleaning of the (meta)data. With the goal of facilitating the task of standardizing metadata -- either in bulk or in a one-by-one fashion; for example, to support auto-completion of biomedical entities in forms -- we have developed an open-source tool called text2term that maps free-text descriptions of biomedical entities to controlled terms in ontologies. The tool is highly configurable and can be used in multiple ways that cater to different users and expertise levels -- it is available on PyPI and can be used programmatically as any Python package; it can also be used via a command-line interface; or via our hosted, graphical user interface-based Web application (//text2term.hms.harvard.edu); or by deploying a local instance of our interactive application using Docker.
Nowadays, most of the hyperspectral image (HSI) fusion experiments are based on simulated datasets to compare different fusion methods. However, most of the spectral response functions and spatial downsampling functions used to create the simulated datasets are not entirely accurate, resulting in deviations in spatial and spectral features between the generated images for fusion and the real images for fusion. This reduces the credibility of the fusion algorithm, causing unfairness in the comparison between different algorithms and hindering the development of the field of hyperspectral image fusion. Therefore, we release a real HSI/MSI/PAN image dataset to promote the development of the field of hyperspectral image fusion. These three images are spatially registered, meaning fusion can be performed between HSI and MSI, HSI and PAN image, MSI and PAN image, as well as among HSI, MSI, and PAN image. This real dataset could be available at //aistudio.baidu.com/datasetdetail/281612. The related code to process the data could be available at //github.com/rs-lsl/CSSNet.
Machine learning (ML) methods, which fit to data the parameters of a given parameterized model class, have garnered significant interest as potential methods for learning surrogate models for complex engineering systems for which traditional simulation is expensive. However, in many scientific and engineering settings, generating high-fidelity data on which to train ML models is expensive, and the available budget for generating training data is limited, so that high-fidelity training data are scarce. ML models trained on scarce data have high variance, resulting in poor expected generalization performance. We propose a new multifidelity training approach for scientific machine learning via linear regression that exploits the scientific context where data of varying fidelities and costs are available: for example, high-fidelity data may be generated by an expensive fully resolved physics simulation whereas lower-fidelity data may arise from a cheaper model based on simplifying assumptions. We use the multifidelity data within an approximate control variate framework to define new multifidelity Monte Carlo estimators for linear regression models. We provide bias and variance analysis of our new estimators that guarantee the approach's accuracy and improved robustness to scarce high-fidelity data. Numerical results demonstrate that our multifidelity training approach achieves similar accuracy to the standard high-fidelity only approach with orders-of-magnitude reduced high-fidelity data requirements.
Column selection is an essential tool for structure-preserving low-rank approximation, with wide-ranging applications across many fields, such as data science, machine learning, and theoretical chemistry. In this work, we develop unified methodologies for fast, efficient, and theoretically guaranteed column selection. First we derive and implement a sparsity-exploiting deterministic algorithm applicable to tasks including kernel approximation and CUR decomposition. Next, we develop a matrix-free formalism relying on a randomization scheme satisfying guaranteed concentration bounds, applying this construction both to CUR decomposition and to the approximation of matrix functions of graph Laplacians. Importantly, the randomization is only relevant for the computation of the scores that we use for column selection, not the selection itself given these scores. For both deterministic and matrix-free algorithms, we bound the performance favorably relative to the expected performance of determinantal point process (DPP) sampling and, in select scenarios, that of exactly optimal subset selection. The general case requires new analysis of the DPP expectation. Finally, we demonstrate strong real-world performance of our algorithms on a diverse set of example approximation tasks.
The Lippmann--Schwinger--Lanczos (LSL) algorithm has recently been shown to provide an efficient tool for imaging and direct inversion of synthetic aperture radar data in multi-scattering environments \cite{DrMoZa3}, where the data set is limited to the monostatic, a.k.a. single input/single output (SISO) measurements. The approach is based on constructing data-driven estimates of internal fields via a reduced-order model (ROM) framework and then plugging them into the Lippmann-Schwinger integral equation. However, the approximations of the internal solutions may have more error due to missing the off diagonal elements of the multiple input/multiple output (MIMO) matrix valued transfer function. This, in turn, may result in multiple echoes in the image. Here we present a ROM-based data completion algorithm to mitigate this problem. First, we apply the LSL algorithm to the SISO data as in \cite{DrMoZa3} to obtain approximate reconstructions as well as the estimate of internal field. Next, we use these estimates to calculate a forward Lippmann-Schwinger integral to populate the missing off-diagonal data (the lifting step). Finally, to update the reconstructions, we solve the Lippmann-Schwinger equation using the original SISO data, where the internal fields are constructed from the lifted MIMO data. The steps of obtaining the approximate reconstructions and internal fields and populating the missing MIMO data entries can be repeated for complex models to improve the images even further. Efficiency of the proposed approach is demonstrated on 2D and 2.5D numerical examples, where we see reconstructions are improved substantially.
Neural networks used in computations with more advanced algebras than real numbers perform better in some applications. However, there is no general framework for constructing hypercomplex neural networks. We propose a library integrated with Keras that can do computations within TensorFlow and PyTorch. It provides Dense and Convolutional 1D, 2D, and 3D layers architectures.
Fully tensorial theory of hypercomplex neural networks is given. The key point is to observe that the algebra multiplication can be represented as a rank three tensor. This approach is attractive for neural network libraries that support effective tensorial operations.
We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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