SpotNet - Learned iterations for cell detection in image-based immunoassays

Accurate cell detection and counting in the image-based ELISpot and FluoroSpot immunoassays is a challenging task. Recently proposed methodology matches human accuracy by leveraging knowledge of the underlying physical process of these assays and using proximal optimization methods to solve an inverse problem. Nonetheless, thousands of computationally expensive iterations are often needed to reach a near-optimal solution. In this paper, we exploit the structure of the iterations to design a parameterized computation graph, SpotNet, that learns the patterns embedded within several training images and their respective cell information. Further, we compare SpotNet to a convolutional neural network layout customized for cell detection. We show empirical evidence that, while both designs obtain a detection performance on synthetic data far beyond that of a human expert, SpotNet is easier to train and obtains better estimates of particle secretion for each cell.Comment: 5 pages, 4 figures, 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Venice, Italy, April 8-11, 201

Fiber Orientation Estimation Guided by a Deep Network

Diffusion magnetic resonance imaging (dMRI) is currently the only tool for noninvasively imaging the brain's white matter tracts. The fiber orientation (FO) is a key feature computed from dMRI for fiber tract reconstruction. Because the number of FOs in a voxel is usually small, dictionary-based sparse reconstruction has been used to estimate FOs with a relatively small number of diffusion gradients. However, accurate FO estimation in regions with complex FO configurations in the presence of noise can still be challenging. In this work we explore the use of a deep network for FO estimation in a dictionary-based framework and propose an algorithm named Fiber Orientation Reconstruction guided by a Deep Network (FORDN). FORDN consists of two steps. First, we use a smaller dictionary encoding coarse basis FOs to represent the diffusion signals. To estimate the mixture fractions of the dictionary atoms (and thus coarse FOs), a deep network is designed specifically for solving the sparse reconstruction problem. Here, the smaller dictionary is used to reduce the computational cost of training. Second, the coarse FOs inform the final FO estimation, where a larger dictionary encoding dense basis FOs is used and a weighted l1-norm regularized least squares problem is solved to encourage FOs that are consistent with the network output. FORDN was evaluated and compared with state-of-the-art algorithms that estimate FOs using sparse reconstruction on simulated and real dMRI data, and the results demonstrate the benefit of using a deep network for FO estimation.Comment: A shorter version is accepted by MICCAI 201

Learning computationally efficient dictionaries and their implementation as fast transforms

Dictionary learning is a branch of signal processing and machine learning that aims at finding a frame (called dictionary) in which some training data admits a sparse representation. The sparser the representation, the better the dictionary. The resulting dictionary is in general a dense matrix, and its manipulation can be computationally costly both at the learning stage and later in the usage of this dictionary, for tasks such as sparse coding. Dictionary learning is thus limited to relatively small-scale problems. In this paper, inspired by usual fast transforms, we consider a general dictionary structure that allows cheaper manipulation, and propose an algorithm to learn such dictionaries --and their fast implementation-- over training data. The approach is demonstrated experimentally with the factorization of the Hadamard matrix and with synthetic dictionary learning experiments

Discriminative Recurrent Sparse Auto-Encoders

We present the discriminative recurrent sparse auto-encoder model, comprising a recurrent encoder of rectified linear units, unrolled for a fixed number of iterations, and connected to two linear decoders that reconstruct the input and predict its supervised classification. Training via backpropagation-through-time initially minimizes an unsupervised sparse reconstruction error; the loss function is then augmented with a discriminative term on the supervised classification. The depth implicit in the temporally-unrolled form allows the system to exhibit all the power of deep networks, while substantially reducing the number of trainable parameters. From an initially unstructured network the hidden units differentiate into categorical-units, each of which represents an input prototype with a well-defined class; and part-units representing deformations of these prototypes. The learned organization of the recurrent encoder is hierarchical: part-units are driven directly by the input, whereas the activity of categorical-units builds up over time through interactions with the part-units. Even using a small number of hidden units per layer, discriminative recurrent sparse auto-encoders achieve excellent performance on MNIST.Comment: Added clarifications suggested by reviewers. 15 pages, 10 figure