An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols

We describe an effort to annotate a corpus of natural language instructions consisting of 622 wet lab protocols to facilitate automatic or semi-automatic conversion of protocols into a machine-readable format and benefit biological research. Experimental results demonstrate the utility of our corpus for developing machine learning approaches to shallow semantic parsing of instructional texts. We make our annotated Wet Lab Protocol Corpus available to the research community

Immunoglobulin G4-related disease - diagnostic dilemma and importance of clinical judgement: a case report

Immunoglobulin G4 (IgG4)-related disease is a multi-organ, immune-mediated, fibro-inflammatory disorder characterized by tumefactive masses in the affected organs. Incidence and prevalence of IgG4-related disease (RD) are not clearly known and have slight male preponderance. It often involves multiple organs at the time of presentation or over the course of disease mimicking malignancy, Sjogren's syndrome, antineutrophil cytoplasmic antibodies associated vasculitis, infections. A thorough workup is needed to rule out these mimickers. A 33-year-old gentleman presented to us with history of progressive swelling in the right peri-orbital region for four years. On evaluation, abdominal imaging was notable for the sausage-shaped pancreas and hypoenchancing nodules in bilateral kidneys. Histological examination of right lacrimal gland revealed lymphoplasmacytic infiltrate and storiform fibrosis. Serum IgG4 levels were normal, and immunostaining was negative. A diagnosis of IgG4-RD was suggested because of multi-organ involvement, classical radiological and histopathological features. Awareness about IgG4-RD, an under-recognized entity is essential, as it is treatable, and early recognition may help in a favourable outcome. Appropriate use of clinicopathological, serological and imaging features in the right clinical context may help in accurate diagnosis. Elevated serum IgG4 levels and biopsy are not mandatory for the diagnosis

A Little Fog for a Large Turn

Small, carefully crafted perturbations called adversarial perturbations can easily fool neural networks. However, these perturbations are largely additive and not naturally found. We turn our attention to the field of Autonomous navigation wherein adverse weather conditions such as fog have a drastic effect on the predictions of these systems. These weather conditions are capable of acting like natural adversaries that can help in testing models. To this end, we introduce a general notion of adversarial perturbations, which can be created using generative models and provide a methodology inspired by Cycle-Consistent Generative Adversarial Networks to generate adversarial weather conditions for a given image. Our formulation and results show that these images provide a suitable testbed for steering models used in Autonomous navigation models. Our work also presents a more natural and general definition of Adversarial perturbations based on Perceptual Similarity.Comment: Accepted to WACV 202

iGPSe: A Visual Analytic System for Integrative Genomic Based Cancer Patient Stratification

Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied prognosis and response to treatment and likelihood for recurrence and metastasis. Recently, integrative genomics (or panomics) approaches are often adopted with the goal of combining multiple types of omics data to identify integrative biomarkers for stratification of patients into groups with different clinical outcomes. Results: In this paper we present a visual analytic system called Interactive Genomics Patient Stratification explorer (iGPSe) which significantly reduces the computing burden for biomedical researchers in the process of exploring complicated integrative genomics data. Our system integrates unsupervised clustering with graph and parallel sets visualization and allows direct comparison of clinical outcomes via survival analysis. Using a breast cancer dataset obtained from the The Cancer Genome Atlas (TCGA) project, we are able to quickly explore different combinations of gene expression (mRNA) and microRNA features and identify potential combined markers for survival prediction. Conclusions: Visualization plays an important role in the process of stratifying given population patients. Visual tools allowed for the selection of possibly features across various datasets for the given patient population. We essentially made a case for visualization for a very important problem in translational informatics.Comment: BioVis 2014 conferenc

A Bilinear Illumination Model for Robust Face Recognition

We present a technique to generate an illumination subspace for arbitrary 3D faces based on the statistics of measured illuminations under variable lighting conditions from many subjects. A bilinear model based on the higher-order singular value decomposition is used to create a compact illumination subspace given arbitrary shape parameters from a parametric 3D face model. Using a fitting procedure based on minimizing the distance of the input image to the dynamically changing illumination subspace, we reconstruct a shape-specific illumination subspace from a single photograph. We use the reconstructed illumination subspace in various face recognition experiments with variable lighting conditions and obtain accuracies which are very competitive with previous methods that require specific training sessions or multiple images of the subject.Engineering and Applied Science

A comment on Guo et al. [arXiv:2206.11228]

In a recent article, Guo et al. [arXiv:2206.11228] report that adversarially trained neural representations in deep networks may already be as robust as corresponding primate IT neural representations. While we find the paper's primary experiment illuminating, we have doubts about the interpretation and phrasing of the results presented in the paper

Estimation of 3D Faces and Illumination from Single Photographs Using a Bilineaur Illumination Model

3D Face modeling is still one of the biggest challenges in computer graphics. In this paper we present a novel framework that acquires the 3D shape, texture, pose and illumination of a face from a single photograph. Additionally, we show how we can recreate a face under varying illumination conditions. Or, essentially relight it. Using a custom-built face scanning system, we have collected 3D face scans and light reflection images of a large and diverse group of human subjects . We derive a morphable face model for 3D face shapes and accompanying textures by transforming the data into a linear vector sub-space. The acquired images of faces under variable illumination are then used to derive a bilinear illumination model that spans 3D face shape and illumination variations. Using both models we, in turn, propose a novel fitting framework that estimates the parameters of the morphable model given a single photograph. Our framework can deal with complex face reflectance and lighting environments in an efficient and robust manner. In the results section of our paper, we compare our methods to existing ones and demonstrate its efficacy in reconstructing 3D face models when provided with a single photograph. We also provide several examples of facial relighting (on 2D images) by performing adequate decomposition of the estimated illumination using our framework.Engineering and Applied Science

Finding Optimal Views for 3D Face Shape Modeling

A fundamental problem in multi-view 3D face modeling is the determination of the set of optimal views (poses) required for accurate 3D shape estimation of a generic face. There is no analytical solution to this problem, instead (partial) solutions require (near) exhaustive combinatorial search, hence the inherent computational difficulty of this task. We build on our previous modeling framework [Silhouette-based 3D face shape recovery, Model-based 3D face capture using shape-from-silhouettes] which uses an efficient contour-based silhouette method and extend it by aggressive pruning of the view-sphere with view clustering and various imaging constraints. A multi-view optimization search is performed using both model-based (eigenheads) and data-driven (visual hull) methods, yielding comparable best views. These constitute the first reported set of optimal views for 3D face shape capture and provide useful empirical guidelines for the design of 3D face recognition systems.Engineering and Applied Science