Differentiating autoimmune pancreatitis from pancreatic ductal adenocarcinoma with CT radiomics features.

PURPOSE: The purpose of this study was to determine whether computed tomography (CT)-based machine learning of radiomics features could help distinguish autoimmune pancreatitis (AIP) from pancreatic ductal adenocarcinoma (PDAC). MATERIALS AND METHODS: Eighty-nine patients with AIP (65 men, 24 women; mean age, 59.7±13.9 [SD] years; range: 21-83 years) and 93 patients with PDAC (68 men, 25 women; mean age, 60.1±12.3 [SD] years; range: 36-86 years) were retrospectively included. All patients had dedicated dual-phase pancreatic protocol CT between 2004 and 2018. Thin-slice images (0.75/0.5mm thickness/increment) were compared with thick-slices images (3 or 5mm thickness/increment). Pancreatic regions involved by PDAC or AIP (areas of enlargement, altered enhancement, effacement of pancreatic duct) as well as uninvolved parenchyma were segmented as three-dimensional volumes. Four hundred and thirty-one radiomics features were extracted and a random forest was used to distinguish AIP from PDAC. CT data of 60 AIP and 60 PDAC patients were used for training and those of 29 AIP and 33 PDAC independent patients were used for testing. RESULTS: The pancreas was diffusely involved in 37 (37/89; 41.6%) patients with AIP and not diffusely in 52 (52/89; 58.4%) patients. Using machine learning, 95.2% (59/62; 95% confidence interval [CI]: 89.8-100%), 83.9% (52:67; 95% CI: 74.7-93.0%) and 77.4% (48/62; 95% CI: 67.0-87.8%) of the 62 test patients were correctly classified as either having PDAC or AIP with thin-slice venous phase, thin-slice arterial phase, and thick-slice venous phase CT, respectively. Three of the 29 patients with AIP (3/29; 10.3%) were incorrectly classified as having PDAC but all 33 patients with PDAC (33/33; 100%) were correctly classified with thin-slice venous phase with 89.7% sensitivity (26/29; 95% CI: 78.6-100%) and 100% specificity (33/33; 95% CI: 93-100%) for the diagnosis of AIP, 95.2% accuracy (59/62; 95% CI: 89.8-100%) and area under the curve of 0.975 (95% CI: 0.936-1.0). CONCLUSIONS: Radiomic features help differentiate AIP from PDAC with an overall accuracy of 95.2%.

Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation.

PURPOSE: The purpose of this study was to report procedures developed to annotate abdominal computed tomography (CT) images from subjects without pancreatic disease that will be used as the input for deep convolutional neural networks (DNN) for development of deep learning algorithms for automatic recognition of a normal pancreas. MATERIALS AND METHODS: Dual-phase contrast-enhanced volumetric CT acquired from 2005 to 2009 from potential kidney donors were retrospectively assessed. Four trained human annotators manually and sequentially annotated 22 structures in each datasets, then expert radiologists confirmed the annotation. For efficient annotation and data management, a commercial software package that supports three-dimensional segmentation was used. RESULTS: A total of 1150 dual-phase CT datasets from 575 subjects were annotated. There were 229 men and 346 women (mean age: 45±12years; range: 18-79years). The mean intra-observer intra-subject dual-phase CT volume difference of all annotated structures was 4.27mL (7.65%). The deep network prediction for multi-organ segmentation showed high fidelity with 89.4% and 1.29mm in terms of mean Dice similarity coefficients and mean surface distances, respectively. CONCLUSIONS: A reliable data collection/annotation process for abdominal structures was developed. This process can be used to generate large datasets appropriate for deep learning.

Mapping the landscape of climate engineering.

In the absence of a governance framework for climate engineering technologies such as solar radiation management (SRM), the practices of scientific research and intellectual property acquisition can de facto shape the development of the field. It is therefore important to make visible emerging patterns of research and patenting, which we suggest can effectively be done using bibliometric methods. We explore the challenges in defining the boundary of climate engineering, and set out the research strategy taken in this study. A dataset of 825 scientific publications on climate engineering between 1971 and 2013 was identified, including 193 on SRM; these are analysed in terms of trends, institutions, authors and funders. For our patent dataset, we identified 143 first filings directly or indirectly related to climate engineering technologies-of which 28 were related to SRM technologies-linked to 910 family members. We analyse the main patterns discerned in patent trends, applicants and inventors. We compare our own findings with those of an earlier bibliometric study of climate engineering, and show how our method is consistent with the need for transparency and repeatability, and the need to adjust the method as the field develops. We conclude that bibliometric monitoring techniques can play an important role in the anticipatory governance of climate engineering.

Classification of spatially unaligned fMRI scans.

The analysis of fMRI data is challenging because they consist generally of a relatively modest signal contained in a high-dimensional space: a single scan can contain millions of voxel recordings over space and time. We present a method for classification and discrimination among fMRI that is based on modeling the scans as distance matrices, where each matrix measures the divergence of spatial network signals that fluctuate over time. We used single-subject independent components analysis (ICA), decomposing an fMRI scan into a set of statistically independent spatial networks, to extract spatial networks and time courses from each subject that have unique relationship with the other components within that subject. Mathematical properties of these relationships reveal information about the infrastructure of the brain by measuring the interaction between and strength of the components. Our technique is unique, in that it does not require spatial alignment of the scans across subjects. Instead, the classifications are made solely on the temporal activity taken by the subject's unique ICs. Multiple scans are not required and multivariate classification is implementable, and the algorithm is effectively blind to the subject-uniform underlying task paradigm. Classification accuracy of up to 90% was realized on a resting-scanned schizophrenia/normal dataset and a tasked multivariate Alzheimer's/old/young dataset. We propose that the ICs represent a plausible set of imaging basis functions consistent with network-driven theories of neural activity in which the observed signal is an aggregate of independent spatial networks having possibly dependent temporal activity.

Efficient multilevel brain tumor segmentation with integrated bayesian model classification.

We present a new method for automatic segmentation of heterogeneous image data that takes a step toward bridging the gap between bottom-up affinity-based segmentation methods and top-down generative model based approaches. The main contribution of the paper is a Bayesian formulation for incorporating soft model assignments into the calculation of affinities, which are conventionally model free. We integrate the resulting model-aware affinities into the multilevel segmentation by weighted aggregation algorithm, and apply the technique to the task of detecting and segmenting brain tumor and edema in multichannel magnetic resonance (MR) volumes. The computationally efficient method runs orders of magnitude faster than current state-of-the-art techniques giving comparable or improved results. Our quantitative results indicate the benefit of incorporating model-aware affinities into the segmentation process for the difficult case of glioblastoma multiforme brain tumor.

Manhattan world: orientation and outlier detection by Bayesian inference.

This letter argues that many visual scenes are based on a "Manhattan" three-dimensional grid that imposes regularities on the image statistics. We construct a Bayesian model that implements this assumption and estimates the viewer orientation relative to the Manhattan grid. For many images, these estimates are good approximations to the viewer orientation (as estimated manually by the authors). These estimates also make it easy to detect outlier structures that are unaligned to the grid. To determine the applicability of the Manhattan world model, we implement a null hypothesis model that assumes that the image statistics are independent of any three-dimensional scene structure. We then use the log-likelihood ratio test to determine whether an image satisfies the Manhattan world assumption. Our results show that if an image is estimated to be Manhattan, then the Bayesian model's estimates of viewer direction are almost always accurate (according to our manual estimates), and vice versa.

The concave-convex procedure.

The concave-convex procedure (CCCP) is a way to construct discrete-time iterative dynamical systems that are guaranteed to decrease global optimization and energy functions monotonically. This procedure can be applied to almost any optimization problem, and many existing algorithms can be interpreted in terms of it. In particular, we prove that all expectation-maximization algorithms and classes of Legendre minimization and variational bounding algorithms can be reexpressed in terms of CCCP. We show that many existing neural network and mean-field theory algorithms are also examples of CCCP. The generalized iterative scaling algorithm and Sinkhorn's algorithm can also be expressed as CCCP by changing variables. CCCP can be used both as a new way to understand, and prove the convergence of, existing optimization algorithms and as a procedure for generating new algorithms.

Bayesian A* tree search with expected O(N) node expansions: applications to road tracking.

Many perception, reasoning, and learning problems can be expressed as Bayesian inference. We point out that formulating a problem as Bayesian inference implies specifying a probability distribution on the ensemble of problem instances. This ensemble can be used for analyzing the expected complexity of algorithms and also the algorithm-independent limits of inference. We illustrate this problem by analyzing the complexity of tree search. In particular, we study the problem of road detection, as formulated by Geman and Jedynak (1996). We prove that the expected convergence is linear in the size of the road (the depth of the tree) even though the worst-case performance is exponential. We also put a bound on the constant of the convergence and place a bound on the error rates.

CCCP algorithms to minimize the Bethe and Kikuchi free energies: convergent alternatives to belief propagation.

This article introduces a class of discrete iterative algorithms that are provably convergent alternatives to belief propagation (BP) and generalized belief propagation (GBP). Our work builds on recent results by Yedidia, Freeman, and Weiss (2000), who showed that the fixed points of BP and GBP algorithms correspond to extrema of the Bethe and Kikuchi free energies, respectively. We obtain two algorithms by applying CCCP to the Bethe and Kikuchi free energies, respectively (CCCP is a procedure, introduced here, for obtaining discrete iterative algorithms by decomposing a cost function into a concave and a convex part). We implement our CCCP algorithms on two- and three-dimensional spin glasses and compare their results to BP and GBP. Our simulations show that the CCCP algorithms are stable and converge very quickly (the speed of CCCP is similar to that of BP and GBP). Unlike CCCP, BP will often not converge for these problems (GBP usually, but not always, converges). The results found by CCCP applied to the Bethe or Kikuchi free energies are equivalent, or slightly better than, those found by BP or GBP, respectively (when BP and GBP converge). Note that for these, and other problems, BP and GBP give very accurate results (see Yedidia et al., 2000), and failure to converge is their major error mode. Finally, we point out that our algorithms have a large range of inference and learning applications.

Probabilistic motion estimation based on temporal coherence.

We develop a theory for the temporal integration of visual motion motivated by psychophysical experiments. The theory proposes that input data are temporally grouped and used to predict and estimate the motion flows in the image sequence. This temporal grouping can be considered a generalization of the data association techniques that engineers use to study motion sequences. Our temporal grouping theory is expressed in terms of the Bayesian generalization of standard Kalman filtering. To implement the theory, we derive a parallel network that shares some properties of cortical networks. Computer simulations of this network demonstrate that our theory qualitatively accounts for psychophysical experiments on motion occlusion and motion outliers. In deriving our theory, we assumed spatial factorizability of the probability distributions and made the approximation of updating the marginal distributions of velocity at each point. This allowed us to perform local computations and simplified our implementation. We argue that these approximations are suitable for the stimuli we are considering (for which spatial coherence effects are negligible).

Robust principal component analysis by self-organizing rules based on statistical physics approach.

This paper applies statistical physics to the problem of robust principal component analysis (PCA). The commonly used PCA learning rules are first related to energy functions. These functions are generalized by adding a binary decision field with a given prior distribution so that outliers in the data are dealt with explicitly in order to make PCA robust. Each of the generalized energy functions is then used to define a Gibbs distribution from which a marginal distribution is obtained by summing over the binary decision field. The marginal distribution defines an effective energy function, from which self-organizing rules have been developed for robust PCA. Under the presence of outliers, both the standard PCA methods and the existing self-organizing PCA rules studied in the literature of neural networks perform quite poorly. By contrast, the robust rules proposed here resist outliers well and perform excellently for fulfilling various PCA-like tasks such as obtaining the first principal component vector, the first k principal component vectors, and directly finding the subspace spanned by the first k vector principal component vectors without solving for each vector individually. Comparative experiments have been made, and the results show that the authors' robust rules improve the performances of the existing PCA algorithms significantly when outliers are present.

Dependence of speed and direction perception on cinematogram dot density.

In the present experiments, we find that with abrupt decreases in dot density of random-dot cinematograms, perceived speed decreases, while with abrupt increases in dot density, perceived speed increases. Further, in steady-state conditions, perceived speed is also affected in the same way, but to a lesser degree, by the dot density of cinematograms. Direction discrimination of random-dot cinematograms is enhanced when dot density increases abruptly from one stimulus to the next, but is degraded when dot density decreases abruptly. Finally, speed discrimination remains constant even when density changes abruptly. The perceived-speed and direction-discrimination data are consistent with the Motion Coherence theory which motivated this study, and with models that include a smoothing stage similar to this theory. Of the other models that we consider, most predict that increasing dot density reduces perceived speed. The speed-discrimination data could not distinguish between the different theories.

Deformable templates for face recognition.

We describe an approach for extracting facial features from images and for determining the spatial organization between these features using the concept of a deformable template. This is a parameterized geometric model of the object to be recognized together with a measure of how well it fits the image data. Variations in the parameters correspond to allowable deformations of the object and can be specified by a probabilistic model. After the extraction stage the parameters of the deformable template can be used for object description and recognition.

A model for the estimate of local image velocity by cells in the visual cortex.

Some computational theories of motion perception assume that the first stage en route to this perception is the local estimate of image velocity. However, this assumption is not supported by data from the primary visual cortex. Its motion sensitive cells are not selective to velocity, but rather are directionally selective and tuned to spatio-temporal frequencies. Accordingly, physiologically based theories start with filters selective to oriented spatio-temporal frequencies. This paper shows that computational and physiological theories do not necessarily conflict, because such filters may, as a population, compute velocity locally. To prove this point, we show how to combine the outputs of a class of frequency tuned filters to detect local image velocity. Furthermore, we show that the combination of filters may simulate 'Pattern' cells in the middle temporal area (MT), whereas each filter simulates primary visual cortex cells. These simulations include three properties of the primary cortex. First, the spatio-temporal frequency tuning curves of the individual filters display approximate space-time separability. Secondly, their direction-of-motion tuning curves depend on the distribution of orientations of the components of the Fourier decomposition and speed of the stimulus. Thirdly, the filters show facilitation and suppression for responses to apparent motions in the preferred and null directions, respectively. It is suggested that the MT's role is not to solve the aperture problem, but to estimate velocities from primary cortex information. The spatial integration that accounts for motion coherence may be postponed to a later cortical stage.

Stereo and eye movement.

We describe a method to solve stereo correspondence using controlled eye (or camera) movements. Eye movements supply additional image frames and monocular depth estimate, which can be used to constrain stereo matching. Because the eye movements are small, traditional stereo techniques of stereo with multiple frame will not work. We develop an alternative approach using a systematic analysis to define a probability distribution for the errors. Our matching strategy then matches the most probable points first, thereby reducing the ambiguity for the remaining matches. We demonstrate this algorithms with several examples.

Energy functions for early vision and analog networks.

This paper describes attempts to model the modules of early vision in terms of minimizing energy functions, in particular energy functions allowing discontinuities in the solution. It examines the success of using Hopfield-style analog networks for solving such problems. Finally it discusses the limitations of the energy function approach.

Quadrature and the development of orientation selective cortical cells by Hebb rules.

We describe a new theoretical scenario for the development of orientation selective cells in a self-organizing feedforward network with modifiable synapses. A suitable choice of Hebb rule leads to a system that develops symmetric and antisymmetric response fields (quadrature pairs) at the same time as directional selectivity occurs using inhibition between neighboring cells. Quadrature phase relationships between the response properties of adjacent cortical cells is suggestive of several highly efficient information processing strategies.

A computational theory for the perception of coherent visual motion.

When we see motion, our perception of how one image feature moves depends on the behaviour of other features nearby. In particular, the Gestaltists proposed the law of shared common fate, in which features tend to be perceived as moving together, that is, coherently. Recent psychophysical findings, such as the cooperativity of the motion system and motion capture, support this law. Computationally, coherence is a sensible assumption, because if two features are close then they probably belong to the same object and thus tend to move together. Moreover, the measurement of local motion may be inaccurate and so the integration of motion information over large areas may help to improve the performance. Present theories of visual motion, however, do not account fully for these coherent motion percepts. We propose here a theory that does account for these phenomena and also provides a solution to the aperture problem, where the local information in the image flow is insufficient to specify the motion uniquely.