Co-regularized Alignment for Unsupervised Domain Adaptation

Deep neural networks, trained with large amount of labeled data, can fail to generalize well when tested with examples from a \emph{target domain} whose distribution differs from the training data distribution, referred as the \emph{source domain}. It can be expensive or even infeasible to obtain required amount of labeled data in all possible domains. Unsupervised domain adaptation sets out to address this problem, aiming to learn a good predictive model for the target domain using labeled examples from the source domain but only unlabeled examples from the target domain. Domain alignment approaches this problem by matching the source and target feature distributions, and has been used as a key component in many state-of-the-art domain adaptation methods. However, matching the marginal feature distributions does not guarantee that the corresponding class conditional distributions will be aligned across the two domains. We propose co-regularized domain alignment for unsupervised domain adaptation, which constructs multiple diverse feature spaces and aligns source and target distributions in each of them individually, while encouraging that alignments agree with each other with regard to the class predictions on the unlabeled target examples. The proposed method is generic and can be used to improve any domain adaptation method which uses domain alignment. We instantiate it in the context of a recent state-of-the-art method and observe that it provides significant performance improvements on several domain adaptation benchmarks.Comment: NIPS 2018 accepted versio

3D Registration of Aerial and Ground Robots for Disaster Response: An Evaluation of Features, Descriptors, and Transformation Estimation

Global registration of heterogeneous ground and aerial mapping data is a challenging task. This is especially difficult in disaster response scenarios when we have no prior information on the environment and cannot assume the regular order of man-made environments or meaningful semantic cues. In this work we extensively evaluate different approaches to globally register UGV generated 3D point-cloud data from LiDAR sensors with UAV generated point-cloud maps from vision sensors. The approaches are realizations of different selections for: a) local features: key-points or segments; b) descriptors: FPFH, SHOT, or ESF; and c) transformation estimations: RANSAC or FGR. Additionally, we compare the results against standard approaches like applying ICP after a good prior transformation has been given. The evaluation criteria include the distance which a UGV needs to travel to successfully localize, the registration error, and the computational cost. In this context, we report our findings on effectively performing the task on two new Search and Rescue datasets. Our results have the potential to help the community take informed decisions when registering point-cloud maps from ground robots to those from aerial robots.Comment: Awarded Best Paper at the 15th IEEE International Symposium on Safety, Security, and Rescue Robotics 2017 (SSRR 2017

Structure-function mapping of a heptameric module in the nuclear pore complex.

The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ~600-kD heptameric Nup84 complex, to a precision of ~1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain-mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC's interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution

Precise multimodal optical control of neural ensemble activity.

Understanding brain function requires technologies that can control the activity of large populations of neurons with high fidelity in space and time. We developed a multiphoton holographic approach to activate or suppress the activity of ensembles of cortical neurons with cellular resolution and sub-millisecond precision. Since existing opsins were inadequate, we engineered new soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR1, optimized for multiphoton activation and suppression. Employing a three-dimensional all-optical read-write interface, we demonstrate the ability to simultaneously photostimulate up to 50 neurons distributed in three dimensions in a 550 × 550 × 100-µm3 volume of brain tissue. This approach allows the synthesis and editing of complex neural activity patterns needed to gain insight into the principles of neural codes

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

Simultaneous measurement of cosmology and intrinsic alignments using joint cosmic shear and galaxy number density correlations

Cosmic shear is a powerful method to constrain cosmology, provided that any systematic effects are under control. The intrinsic alignment of galaxies is expected to severely bias parameter estimates if not taken into account. We explore the potential of a joint analysis of tomographic galaxy ellipticity, galaxy number density, and ellipticity-number density cross-correlations to simultaneously constrain cosmology and self-calibrate unknown intrinsic alignment and galaxy bias contributions. We treat intrinsic alignments and galaxy biasing as free functions of scale and redshift and marginalise over the resulting parameter sets. Constraints on cosmology are calculated by combining the likelihoods from all two-point correlations between galaxy ellipticity and galaxy number density. The information required for these calculations is already available in a standard cosmic shear dataset. We include contributions to these functions from cosmic shear, intrinsic alignments, galaxy clustering and magnification effects. In a Fisher matrix analysis we compare our constraints with those from cosmic shear alone in the absence of intrinsic alignments. For a potential future large area survey, such as Euclid, the extra information from the additional correlation functions can make up for the additional free parameters in the intrinsic alignment and galaxy bias terms, depending on the flexibility in the models. For example, the Dark Energy Task Force figure of merit is recovered even when more than 100 free parameters are marginalised over. We find that the redshift quality requirements are similar to those calculated in the absence of intrinsic alignments.Comment: 22 pages, 10 figures; extended discussion, otherwise minor changes to match accepted version; published in Astronomy and Astrophysic

Coupled non-parametric shape and moment-based inter-shape pose priors for multiple basal ganglia structure segmentation

This paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images. We present a set of 2D and 3D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy

Galaxy alignments: Observations and impact on cosmology

Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the physics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of galaxy alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments have taken on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes galaxy alignments, commonly referred to as intrinsic alignments, an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigation techniques which attempt to remove contamination by intrinsic alignments.Comment: 52 pages excl. references, 16 figures; minor changes to match version published in Space Science Reviews; part of a topical volume on galaxy alignments, with companion papers arXiv:1504.05456 and arXiv:1504.0554