[Detection of the antigenic peptides in pHLA complexes by ultrafiltration-high performance liquid chromatography].

Recombinant HLA-Ⅰ molecules/antigenic peptide complexes (pHLA complexes) are applied in the research of human T cell-specific immune responses. The preparation of pHLA complex is based on genetic engineering and protein in vitro dilution and folding-refolding technology. In an in vitro refolding system, recombinant HLA-Ⅰ molecules correctly fold and bind with antigenic peptides to form complexes. In this study, ultrafiltration-high performance liquid chromatography (ultrafiltration-HPLC) was used for quantitative determination of the antigenic peptides in recombinant pHLA complexes, especially for those in a small amount of prepared products. By adding the recombinant HLA-Ⅰ molecules and antigenic peptides into the refolding buffer, the heavy chain (HC) and light chain (ß2m) of recombinant HLA-Ⅰ molecules were refolded and bond with the VYF antigenic peptide containing anchor residues to form a pHLA complex. The unbound free antigenic peptide VYF was removed by ultrafiltration to retain the complex. Finally, the pHLA complex was treated by acid to destroy its interaction, thus releasing the antigenic peptide. The results showed that the prepared recombinant pHLA complex was recognized by HLA-Ⅰ molecule specific antibody W6/32, which indicated that the recombinant HLA-Ⅰ class molecule had correct folding and was identified as pHLA complex. The antigen peptide VYF contained in the pHLA complex was also detected by ultrafiltration-HPLC, so it is feasible to apply ultrafiltration-HPLC for determination of pHLA complex. Compared with Western blotting, the concentration of antigenic peptides detected by ultrafiltration-HPLC was 0-9 µg/mL. The binding conditions can be optimized according to the amount of antigenic peptides bound in the complex in order to improve the folding efficiency of HLA-Ⅰ molecules and promote the binding of HLA-Ⅰ molecules to antigenic peptides. The production rate of pHLA complexes in the refolding system can also be calculated according to the content of antigenic peptides bound by pHLA complexes. Therefore, ultrafiltration-HPLC in this study can be used for the quality control of the preparation process of pHLA complexes, and may facilitate the research of T cell-specific immunity, artificial antigen-presenting cells, and development of specific tetramer probe applications.

Efficient patch-based approach for compressive depth imaging.

We present efficient camera hardware and algorithms to capture images with extended depth of field. The camera moves its focal plane via a liquid lens and modulates the scene at different focal planes by shifting a fixed binary mask, with synchronization achieved by using the same triangular wave to control the focal plane and the pizeoelectronic translator that shifts the mask. Efficient algorithms are developed to reconstruct the all-in-focus image and the depth map from a single coded exposure, and various sparsity priors are investigated to enhance the reconstruction, including group sparsity, tree structure, and dictionary learning. The algorithms naturally admit a parallel computational structure due to the independent patch-level operations. Experimental results on both simulation and real datasets demonstrate the efficacy of the new hardware and the inversion algorithms.

Compressive sensing by learning a Gaussian mixture model from measurements.

Compressive sensing of signals drawn from a Gaussian mixture model (GMM) admits closed-form minimum mean squared error reconstruction from incomplete linear measurements. An accurate GMM signal model is usually not available a priori, because it is difficult to obtain training signals that match the statistics of the signals being sensed. We propose to solve that problem by learning the signal model in situ, based directly on the compressive measurements of the signals, without resorting to other signals to train a model. A key feature of our method is that the signals being sensed are treated as random variables and are integrated out in the likelihood. We derive a maximum marginal likelihood estimator (MMLE) that maximizes the likelihood of the GMM of the underlying signals given only their linear compressive measurements. We extend the MMLE to a GMM with dominantly low-rank covariance matrices, to gain computational speedup. We report extensive experimental results on image inpainting, compressive sensing of high-speed video, and compressive hyperspectral imaging (the latter two based on real compressive cameras). The results demonstrate that the proposed methods outperform state-of-the-art methods by significant margins.

Video compressive sensing using Gaussian mixture models.

A Gaussian mixture model (GMM)-based algorithm is proposed for video reconstruction from temporally compressed video measurements. The GMM is used to model spatio-temporal video patches, and the reconstruction can be efficiently computed based on analytic expressions. The GMM-based inversion method benefits from online adaptive learning and parallel computation. We demonstrate the efficacy of the proposed inversion method with videos reconstructed from simulated compressive video measurements, and from a real compressive video camera. We also use the GMM as a tool to investigate adaptive video compressive sensing, i.e., adaptive rate of temporal compression.

An active learning approach for rapid characterization of endothelial cells in human tumors.

Currently, no available pathological or molecular measures of tumor angiogenesis predict response to antiangiogenic therapies used in clinical practice. Recognizing that tumor endothelial cells (EC) and EC activation and survival signaling are the direct targets of these therapies, we sought to develop an automated platform for quantifying activity of critical signaling pathways and other biological events in EC of patient tumors by histopathology. Computer image analysis of EC in highly heterogeneous human tumors by a statistical classifier trained using examples selected by human experts performed poorly due to subjectivity and selection bias. We hypothesized that the analysis can be optimized by a more active process to aid experts in identifying informative training examples. To test this hypothesis, we incorporated a novel active learning (AL) algorithm into FARSIGHT image analysis software that aids the expert by seeking out informative examples for the operator to label. The resulting FARSIGHT-AL system identified EC with specificity and sensitivity consistently greater than 0.9 and outperformed traditional supervised classification algorithms. The system modeled individual operator preferences and generated reproducible results. Using the results of EC classification, we also quantified proliferation (Ki67) and activity in important signal transduction pathways (MAP kinase, STAT3) in immunostained human clear cell renal cell carcinoma and other tumors. FARSIGHT-AL enables characterization of EC in conventionally preserved human tumors in a more automated process suitable for testing and validating in clinical trials. The results of our study support a unique opportunity for quantifying angiogenesis in a manner that can now be tested for its ability to identify novel predictive and response biomarkers.

Coded aperture compressive temporal imaging.

We use mechanical translation of a coded aperture for code division multiple access compression of video. We discuss the compressed video's temporal resolution and present experimental results for reconstructions of > 10 frames of temporal data per coded snapshot.

Classification with Incomplete Data Using Dirichlet Process Priors.

A non-parametric hierarchical Bayesian framework is developed for designing a classifier, based on a mixture of simple (linear) classifiers. Each simple classifier is termed a local "expert", and the number of experts and their construction are manifested via a Dirichlet process formulation. The simple form of the "experts" allows analytical handling of incomplete data. The model is extended to allow simultaneous design of classifiers on multiple data sets, termed multi-task learning, with this also performed non-parametrically via the Dirichlet process. Fast inference is performed using variational Bayesian (VB) analysis, and example results are presented for several data sets. We also perform inference via Gibbs sampling, to which we compare the VB results.

Semisupervised multitask learning.

Context plays an important role when performing classification, and in this paper we examine context from two perspectives. First, the classification of items within a single task is placed within the context of distinct concurrent or previous classification tasks (multiple distinct data collections). This is referred to as multi-task learning (MTL), and is implemented here in a statistical manner, using a simplified form of the Dirichlet process. In addition, when performing many classification tasks one has simultaneous access to all unlabeled data that must be classified, and therefore there is an opportunity to place the classification of any one feature vector within the context of all unlabeled feature vectors; this is referred to as semi-supervised learning. In this paper we integrate MTL and semi-supervised learning into a single framework, thereby exploiting two forms of contextual information. Example results are presented on a "toy" example, to demonstrate the concept, and the algorithm is also applied to three real data sets.

Kernel-matching pursuits with arbitrary loss functions.

The purpose of this research is to develop a classifier capable of state-of-the-art performance in both computational efficiency and generalization ability while allowing the algorithm designer to choose arbitrary loss functions as appropriate for a give problem domain. This is critical in applications involving heavily imbalanced, noisy, or non-Gaussian distributed data. To achieve this goal, a kernel-matching pursuit (KMP) framework is formulated where the objective is margin maximization rather than the standard error minimization. This approach enables excellent performance and computational savings in the presence of large, imbalanced training data sets and facilitates the development of two general algorithms. These algorithms support the use of arbitrary loss functions allowing the algorithm designer to control the degree to which outliers are penalized and the manner in which non-Gaussian distributed data is handled. Example loss functions are provided and algorithm performance is illustrated in two groups of experimental results. The first group demonstrates that the proposed algorithms perform equivalent to several state-of-the-art machine learning algorithms on well-published, balanced data. The second group of results illustrates superior performance by the proposed algorithms on imbalanced, non-Gaussian data achieved by employing loss functions appropriate for the data characteristics and problem domain.

On classification with incomplete data.

We address the incomplete-data problem in which feature vectors to be classified are missing data (features). A (supervised) logistic regression algorithm for the classification of incomplete data is developed. Single or multiple imputation for the missing data is avoided by performing analytic integration with an estimated conditional density function (conditioned on the observed data). Conditional density functions are estimated using a Gaussian mixture model (GMM), with parameter estimation performed using both Expectation-Maximization (EM) and Variational Bayesian EM (VB-EM). The proposed supervised algorithm is then extended to the semisupervised case by incorporating graph-based regularization. The semisupervised algorithm utilizes all available data-both incomplete and complete, as well as labeled and unlabeled. Experimental results of the proposed classification algorithms are shown.

Application of the theory of optimal experiments to adaptive electromagnetic-induction sensing of buried targets.

A mobile electromagnetic-induction (EMI) sensor is considered for detection and characterization of buried conducting and/or ferrous targets. The sensor may be placed on a robot and, here, we consider design of an optimal adaptive-search strategy. A frequency-dependent magnetic-dipole model is used to characterize the target at EMI frequencies. The goal of the search is accurate characterization of the dipole-model parameters, denoted bythe vector theta; the target position and orientation are a subset of theta. The sensor position and operating frequency are denoted by the parameter vector p and a measurement is represented by the pair (p, O), where O denotes the observed data. The parametersp are fixed for a given measurement, but, in the context of a sequence of measurements p may be changed adaptively. In a locally optimal sequence of measurements, we desire the optimal sensor parameters, P(N+1) for estimation of theta, based on the previous measurements (p(n), On)n=1,N. The search strategy is based on the theory of optimal experiments, as discussed in detail and demonstrated via several numerical examples.