Data science has become prevalent in a large variety of domains. Inherent in its practice is an exploratory, probing, and fact finding journey, which consists of the assembly, adaptation, and execution of complex data science pipelines. The trustworthiness of the results of such pipelines rests entirely on their ability to be reproduced with fidelity, which is difficult if pipelines are not documented or recorded minutely and consistently. This difficulty has led to a reproducibility crisis and presents a major obstacle to the safe adoption of the pipeline results in production environments. The crisis can be resolved if the provenance for each data science pipeline is captured transparently as pipelines are executed. However, due to the complexity of modern data science pipelines, transparently capturing sufficient provenance to allow for reproducibility is challenging. As a result, most existing systems require users to augment their code or use specific tools to capture provenance, which hinders productivity and results in a lack of adoption. In this paper, we present Ursprung, 1 a transparent provenance collection system designed for data science environments. 2 The Ursprung philosophy is to capture provenance and build lineage by integrating with the execution environment to automatically track static and runtime configuration parameters of data science pipelines. Rather than requiring data scientists to make changes to their code, Ursprung records basic provenance information from system-level sources and combines it with provenance from application-level sources (e.g., log files, stdout), which can be accessed and recorded through a domain-specific language. In our evaluation, we show that Ursprung is able to capture sufficient provenance for a variety of use cases and only adds an overhead of up to 4%.

In this paper we present a new method of uncovering patients with aortic valve diseases in large electronic health record systems through learning with multimodal data. The method automatically extracts clinically-relevant valvular disease features from five multimodal sources of information including structured diagnosis, echocardiogram reports, and echocardiogram imaging studies. It combines these partial evidence features in a random forests learning framework to predict patients likely to have the disease. Results of a retrospective clinical study from a 1000 patient dataset are presented that indicate that over 25 % new patients with moderate to severe aortic stenosis can be automatically discovered by our method that were previously missed from the records. These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies.

In this paper, we propose a new and accurate technique for uncertainty analysis and uncertainty visualization based on fiber orientation distribution function (ODF) glyphs, associated with high angular resolution diffusion imaging (HARDI). Our visualization applies volume rendering techniques to an ensemble of 3D ODF glyphs, which we call SIP functions of diffusion shapes, to capture their variability due to underlying uncertainty. This rendering elucidates the complex heteroscedastic structural variation in these shapes. Furthermore, we quantify the extent of this variation by measuring the fraction of the volume of these shapes, which is consistent across all noise levels, the certain volume ratio. Our uncertainty analysis and visualization framework is then applied to synthetic data, as well as to HARDI human-brain data, to study the impact of various image acquisition parameters and background noise levels on the diffusion shapes.

We present a novel formulation of non-Abelian invariant feature detection. By choosing suitable measuring functions, we show that the measuring space and the corresponding feature space are equivariant with respect to the SL(2, Ropf) Lie transformation group. This group is non-Abelian and may be decomposed via the Iwasawa decomposition into meaningful transformations on images. We calculate the induced representations of this group on the measuring space. Then, via these representations we construct a set of three PDEs determining an invariant function of the features. We show that this set of equations is solved by the discriminant of a binary form of order n. Hence, the discriminant plays the role of an invariant feature detector with respect to this transformation group.

We present regularization by invariant denoising/smoothing of Diffusion Tensor MRI (DTI). Our solution to the problem emerges from a pure geometric point of view. The image domain and the image's values are combined together and described as a (mathematical) fiber bundle. The space of all possible DT images is the space of sections of this fiber bundle. DT image is a map that attaches a three-dimensional symmetric and positive-definite (SPD) matrix to each volume element. We treat the more general space Pnof n-dimensional SPD matrices and introduce a natural GL(n)-invariant metric via the underlying algebraic structure. A metric over sections of the fiber bundle is induced then in terms of the natural metric on Pn. This turns P3tensors, and in general Pntensors, into a Riemannian symmetric spaces. By means of the Beltrami framework we define a GL(n)-invariant functional over the space of sections. Then, by calculus of variations we derive the invariant equations of motion. We show that by choosing the Iwasawa coordinates the analytical calculations as well as the numerical implementation become simple. These coordinates evolve with respect to the geometry of the section via the induced metric. The numerical implementation of these flows via standard finite difference schemes is straightforward. The result is a full GL(n) invariant algorithm which is at least as fast and efficient as the Log-Euclidean method. Finally, we demonstrate this framework on real DTI data.