MOTIVATION: Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered with targeted tissues are more affordable and routinely generated in many research and clinical studies. Hence, predicting spatial gene expression from the morphological clues embedded in tissue histological images provides a scalable alternative approach to decoding tissue complexity. RESULTS: Here, we present a graph neural network based framework to predict the spatial expression of highly expressed genes from tissue histological images. Extensive experiments on two separate breast cancer data cohorts demonstrate that our method improves the prediction performance compared to the state-of-the-art, and that our model can be used to better delineate spatial domains of biological interest. AVAILABILITY AND IMPLEMENTATION: https://github.com/song0309/asGNN/.

MOTIVATION: While many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partitioning between classical and quantum calculations. RESULTS: We present HypaCADD, a hybrid classical-quantum workflow for finding ligands binding to proteins, while accounting for genetic mutations. We explicitly identify modules of our drug-design workflow currently amenable to replacement by QC: non-intuitively, we identify the mutation-impact predictor as the best candidate. HypaCADD thus combines classical docking and molecular dynamics with quantum machine learning (QML) to infer the impact of mutations. We present a case study with the coronavirus (SARS-CoV-2) protease and associated mutants. We map a classical machine-learning module onto QC, using a neural network constructed from qubit-rotation gates. We have implemented this in simulation and on two commercial quantum computers. We find that the QML models can perform on par with, if not better than, classical baselines. In summary, HypaCADD offers a successful strategy for leveraging QC for CADD. AVAILABILITY AND IMPLEMENTATION: Jupyter Notebooks with Python code are freely available for academic use on GitHub: https://www.github.com/hypahub/hypacadd_notebook. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The concepts of objects and attributes are both important for describing images precisely, since verbal descriptions often contain both adjectives and nouns (e.g. 'I see a shiny red chair'). In this paper, we formulate the problem of joint visual attribute and object class image segmentation as a dense multi-labelling problem, where each pixel in an image can be associated with both an object-class and a set of visual attributes labels. In order to learn the label correlations, we adopt a boosting-based piecewise training approach with respect to the visual appearance and co-occurrence cues. We use a filtering-based mean-field approximation approach for efficient joint inference. Further, we develop a hierarchical model to incorporate region-level object and attribute information. Experiments on the aPASCAL, CORE and attribute augmented NYU indoor scenes datasets show that the proposed approach is able to achieve state-of-the-art results.

Semantic reconstruction of a scene is important for a variety of applications such as 3D modelling, object recognition and autonomous robotic navigation. However, most object labelling methods work in the image domain and fail to capture the information present in 3D space. In this work we propose a principled way to generate object labelling in 3D. Our method builds a triangulated meshed representation of the scene from multiple depth estimates. We then define a CRF over this mesh, which is able to capture the consistency of geometric properties of the objects present in the scene. In this framework, we are able to generate object hypotheses by combining information from multiple sources: geometric properties (from the 3D mesh), and appearance properties (from images). We demonstrate the robustness of our framework in both indoor and outdoor scenes. For indoor scenes we created an augmented version of the NYU indoor scene dataset (RGBD images) with object labelled meshes for training and evaluation. For outdoor scenes, we created ground truth object labellings for the KITTY odometry dataset (stereo image sequence). We observe a significant speed-up in the inference stage by performing labelling on the mesh, and additionally achieve higher accuracies.

Detecting visually salient regions in images is one of the fundamental problems in computer vision. We propose a novel method to decompose an image into large scale perceptually homogeneous elements for efficient salient region detection, using a soft image abstraction representation. By considering both appearance similarity and spatial distribution of image pixels, the proposed representation abstracts out unnecessary image details, allowing the assignment of comparable saliency values across similar regions, and producing perceptually accurate salient region detection. We evaluate our salient region detection approach on the largest publicly available dataset with pixel accurate annotations. The experimental results show that the proposed method outperforms 18 alternate methods, reducing the mean absolute error by 25.2% compared to the previous best result, while being computationally more efficient.

Recently, Krahenbuhl and Koltun proposed an efficient inference method for densely connected pairwise random fields using the mean-field approximation for a Conditional Random Field (CRF). However, they restrict their pairwise weights to take the form of a weighted combination of Gaussian kernels where each Gaussian component is allowed to take only zero mean, and can only be rescaled by a single value for each label pair. Further, their method is sensitive to initialization. In this paper, we propose methods to alleviate these issues. First, we propose a hierarchical mean-field approach where labelling from the coarser level is propagated to the finer level for better initialisation. Further, we use SIFT-flow based label transfer to provide a good initial condition at the coarsest level. Second, we allow our approach to take general Gaussian pairwise weights, where we learn the mean, the co-variance matrix, and the mixing co-efficient for every mixture component. We propose a variation of Expectation Maximization (EM) for piecewise learning of the parameters of the mixture model determined by the maximum likelihood function. Finally, we demonstrate the efficiency and accuracy offered by our method for object class segmentation problems on two challenging datasets: PascalVOC-10 segmentation and CamVid datasets. We show that we are able to achieve state of the art performance on the CamVid dataset, and an almost 3% improvement on the PascalVOC10 dataset compared to baseline graph-cut and mean-field methods, while also reducing the inference time by almost a factor of 3 compared to graph-cuts based methods.

A large number of problems in computer vision can be modeled as energy minimization problems in a markov random field (MRF) framework. Many methods have been developed over the years for efficient inference, especially in pairwise MRFs. In general there is a trade-off between the complexity/efficiency of the algorithm and its convergence properties, with certain problems requiring more complex inference to handle general pairwise potentials. Graphcuts based α-expansion performs well on certain classes of energies, and sequential tree reweighted message passing (TRWS) and loopy belief propagation (LBP) can be used for non-submodular cases. These methods though suffer from poor convergence and often oscillate between solutions. In this paper, we propose a tiered move making algorithm which is an iterative method. Each move to the next configuration is based on the current labeling and an optimal tiered move, where each tiered move requires one application of the dynamic programming based tiered labeling method introduced in Felzenszwalb et. al. [2]. The algorithm converges to a local minimum for any general pairwise potential, and we give a theoretical analysis of the properties of the algorithm, characterizing the situations in which we can expect good performance. We evaluate the algorithm on many benchmark labeling problems such as stereo, image segmentation, image stitching and image denoising, as well as random energy minimization. Our method consistently gets better energy values than α-expansion, LBP, quadratic pseudo-boolean optimization (QPBO), and is competitive with TRWS.

In this work, we propose a method for instance based human segmentation in images and videos, extending the recent detector-based conditional random field model of Ladicky et.al. Instance based human segmentation involves pixel level labeling of an image, partitioning it into distinct human instances and background. To achieve our goal, we add three new components to their framework. First, we include human partsbased detection potentials to take advantage of the structure present in human instances. Further, in order to generate a consistent segmentation from different human parts, we incorporate shape prior information, which biases the segmentation to characteristic overall human shapes. Also, we enhance the representative power of the energy function by adopting exemplar instance based matching terms, which helps our method to adapt easily to different human sizes and poses. Finally, we extensively evaluate our proposed method on the Buffy dataset with our new segmented ground truth images, and show a substantial improvement over existing CRF methods. These new annotations will be made available for future use as well.

Object recognition has made great strides recently. However, the best methods, such as those based on kernel-SVMs are highly computationally intensive. The problem of how to accelerate the evaluation process without decreasing accuracy is thus of current interest. In this paper, we deal with this problem by using the idea of ranking. We propose a cascaded architecture which using the ranking SVM generates an ordered set of proposals for windows containing object instances. The top ranking windows may then be fed to a more complex detector. Our experiments demonstrate that our approach is robust, achieving higher overlap-recall values using fewer output proposals than the state-of-the-art. Our use of simple gradient features and linear convolution indicates that our method is also faster than the state-of-the-art.

Facial keypoint localization is an important step for face recognition. The “Average of Synthetic Exact Filter (ASEF)” approach [2] finds a correlation filter for each training image and averages them together. The resulting classifier is efficient as the filtering can be implemented in the Fourier domain and performance is good for frontal images. However, it cannot cope with a range of poses. In this paper, we generalize this approach to find keypoints using a technique that (i) combines together information from training images in a more principled way than averaging, (ii) can be extended to form non-linear combinations of filters and (iii) can adapt based on context (e.g. pose). These innovations are presented within a greedy boosting-style probabilistic framework. We demonstrate state of the art performance of these algorithms using a challenging data set.

We introduce a novel bilinear boosting algorithm, which extends the multi-class boosting framework of JointBoost to optimize a bilinear objective function. This allows style parameters to be introduced to aid classification, where style is any factor which the classes vary with systematically, modeled by a vector quantity. The algorithm allows learning to take place across different styles. We apply this Style Parameterized Boosting framework (StyP-Boost) to two object class segmentation tasks: road surface segmentation and general scene parsing. In the former the style parameters represent global surface appearance, and in the latter the probability of belonging to a scene-class. We show how our framework improves on 1) learning without style, and 2) learning independent classifiers within each style. Further, we achieve state-of-the-art results on the Corel database for scene parsing.

Unsupervised over-segmentation of an image into super-pixels is a common preprocessing step for image parsing algorithms. Superpixels are used as both regions of support for feature vectors and as a starting point for the final segmentation. Recent algorithms that construct superpixels that conform to a regular grid (or superpixel lattice) have used greedy solutions. In this paper we show that we can construct a globally optimal solution in either the horizontal or vertical direction using a single graph cut. The solution takes into account both edges in the image, and the coherence of the resulting superpixel regions. We show that our method outperforms existing algorithms for computing superpixel lattices. Additionally, we show that performance can be comparable or better than other contemporary segmentation algorithms which are not constrained to produce a lattice.

In this study we propose a deformable pattern recognition method with CUDA implementation. In order to achieve the proper correspondence between foreground pixels of input and prototype images, a pair of distance maps are generated from input and prototype images, whose pixel values are given based on the distance to the nearest foreground pixel. Then a regularization technique computes the horizontal and vertical displacements based on these distance maps. The dissimilarity is measured based on the eight-directional derivative of input and prototype images in order to leverage characteristic information on the curvature of line segments that might be lost after the deformation. The prototype-parallel displacement computation on CUDA and the gradual prototype elimination technique are employed for reducing the computational time without sacrificing the accuracy. A simulation shows that the proposed method with the k-nearest neighbor classifier gives the error rate of 0.57% for the MNIST handwritten digit database.

Boundary detection is a fundamental problem in computer vision. However, bound-ary detection is difficult as it involves integrating multiple cues (intensity, color, texture) as well as trying to incorporate object class or scene level descriptions to mitigate the am-biguity of the local signal. In this paper we investigate incorporating a priori information into boundary detection. We learn a probabilistic model that describes a prior for object boundaries over small patches of the image. We then incorporate this boundary model into a mixture of multiscale conditional random fields, where the mixture components represent different contexts formed by clustering overall spatial distributions of bound-aries across images and image regions (vistas). We demonstrate this approach using challenging real-world road scenes. Importantly, we show that recent spectral methods that have been used in state-of-the-art boundary detection algorithms do not generalize well to these complex scenes. We show that our algorithm successfully learns these boundary distributions and can exploit this knowledge to improve state-of-the-art bound-ary detectors. 1

Image parsing remains difficult due to the need to combine local and contextual information when labeling a scene. We approach this problem by using the epitome as a prior over label configurations. Several properties make it suited to this task. First, it allows a condensed patch-based representation. Second, efficient E-M based learning and inference algorithms can be used. Third, non-stationarity is easily incorporated. We consider three existing priors, and show how each can be extended using the epitome. The simplest prior assumes patches of labels are drawn independently from either a mixture model or an epitome. Next we investigate a `conditional epitome' model, which substitutes an epitome for a conditional mixture model. Finally, we develop an `epitome tree' model, which combines the epitome with a tree structured belief network prior. Each model is combined with a per-pixel classifier to perform segmentation. In each case, the epitomized form of the prior provides superior segmentation performance, with the epitome tree performing best overall. We also apply the same models to denoising binary images, with similar results.

Advances in object detection have made it possible to collect large databases of certain objects. In this paper we exploit these datasets for within-object classification. For example, we classify gender in face images, pose in pedestrian images and phenotype in cell images. Previous work has mainly targeted the above tasks individually using object specific representations. Here, we propose a general Bayesian framework for within-object classification. Images are represented as a regular grid of non-overlapping patches. In training, these patches are approximated by a predefined library. In inference, the choice of approximating patch determines the classification decision. We propose a Bayesian framework in which we marginalize over the patch frequency parameters to provide a posterior probability for the class. We test our algorithm on several challenging “real world” databases.

Unsupervised over-segmentation of an image into super-pixels is a common preprocessing step for image parsing algorithms. Superpixels are used as both regions of support for feature vectors and as a starting point for the final segmentation. In this paper we investigate incorporating a priori information into superpixel segmentations. We learn a probabilistic model that describes the spatial density of the object boundaries in the image. We then describe an over-segmentation algorithm that partitions this density roughly equally between superpixels whilst still attempting to capture local object boundaries. We demonstrate this approach using road scenes where objects in the center of the image tend to be more distant and smaller than those at the edge. We show that our algorithm successfully learns this foveated spatial distribution and can exploit this knowledge to improve the segmentation. Lastly, we introduce a new metric for evaluating vision labeling problems. We measure performance on a challenging real-world dataset and illustrate the limitations of conventional evaluation metrics.

We consider the problem of parsing facial features from an image labeling perspective. We learn a per-pixel unary classifier, and a prior over expected label configurations, allowing us to estimate a dense labeling of facial images by part (e.g. hair, mouth, moustache, hat). This approach deals naturally with large variations in shape and appearance characteristic of unconstrained facial images, and also the problem of detecting classes that may be present or absent. We use an Adaboost-based unary classifier, and develop a family of priors based on `epitomes' which are shown to be particularly effective in capturing the non-stationary aspects of face label distributions.

Unsupervised over-segmentation of an image into superpixels is a common preprocessing step for image parsing algorithms. Ideally, every pixel within each superpixel region will belong to the same real-world object. Existing algorithms generate superpixels that forfeit many useful properties of the regular topology of the original pixels: for example, the nth superpixel has no consistent position or relationship with its neighbors. We propose a novel algorithm that produces superpixels that are forced to conform to a grid (a regular superpixel lattice). Despite this added topological constraint, our algorithm is comparable in terms of speed and accuracy to alternative segmentation approaches. To demonstrate this, we use evaluation metrics based on (i) image reconstruction (ii) comparison to human-segmented images and (iii) stability of segmentation over subsequent frames of video sequences.

Face recognition algorithms perform very unreliably when the pose of the probe face is different from the gallery face: typical feature vectors vary more with pose than with identity. We propose a generative model that creates a one-to-many mapping from an idealized "identity" space to the observed data space. In identity space, the representation for each individual does not vary with pose. We model the measured feature vector as being generated by a pose-contingent linear transformation of the identity variable in the presence of Gaussian noise. We term this model "tied" factor analysis. The choice of linear transformation (factors) depends on the pose, but the loadings are constant (tied) for a given individual. We use the EM algorithm to estimate the linear transformations and the noise parameters from training data. We propose a probabilistic distance metric which allows a full posterior over possible matches to be established. We introduce a novel feature extraction process and investigate recognition performance using the FERET, XM2VTS and PIE databases. Recognition performance compares favourably to contemporary approaches.