Fuhui Long

Bio: Fuhui Long is an academic researcher from Allen Institute for Brain Science. The author has contributed to research in topics: Automatic image annotation & Visualization. The author has an hindex of 28, co-authored 50 publications receiving 11769 citations. Previous affiliations of Fuhui Long include Lawrence Berkeley National Laboratory & Stanford University.

Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy

Abstract: Feature selection is an important problem for pattern classification systems. We study how to select good features according to the maximal statistical dependency criterion based on mutual information. Because of the difficulty in directly implementing the maximal dependency condition, we first derive an equivalent form, called minimal-redundancy-maximal-relevance criterion (mRMR), for first-order incremental feature selection. Then, we present a two-stage feature selection algorithm by combining mRMR and other more sophisticated feature selectors (e.g., wrappers). This allows us to select a compact set of superior features at very low cost. We perform extensive experimental comparison of our algorithm and other methods using three different classifiers (naive Bayes, support vector machine, and linear discriminate analysis) and four different data sets (handwritten digits, arrhythmia, NCI cancer cell lines, and lymphoma tissues). The results confirm that mRMR leads to promising improvement on feature selection and classification accuracy.

V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

Abstract: The V3D system provides three-dimensional (3D) visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops V3D streamlines the online analysis, measurement and proofreading of complicated image patterns by combining ergonomic functions for selecting a location in an image directly in 3D space and for displaying biological measurements, such as from fluorescent probes, using the overlaid surface objects V3D runs on all major computer platforms and can be enhanced by software plug-ins to address specific biological problems To demonstrate this extensibility, we built a V3D-based application, V3D-Neuron, to reconstruct complex 3D neuronal structures from high-resolution brain images V3D-Neuron can precisely digitize the morphology of a single neuron in a fruitfly brain in minutes, with about a 17-fold improvement in reliability and tenfold savings in time compared with other neuron reconstruction tools Using V3D-Neuron, we demonstrate the feasibility of building a 3D digital atlas of neurite tracts in the fruitfly brain

Fundamentals of Content-Based Image Retrieval

Abstract: We introduce in this chapter some fundamental theories for content-based image retrieval. Section 1.1 looks at the development of content-based image retrieval techniques. Then, as the emphasis of this chapter, we introduce in detail in Section 1.2 some widely used methods for visual content descriptions. After that, we briefly address similarity/distance measures between visual features, the indexing schemes, query formation, relevance feedback, and system performance evaluation in Sections 1.3, 1.4 and 1.5. Details of these techniques are discussed in subsequent chapters. Finally, we draw a conclusion in Section 1.6.

An anatomic transcriptional atlas of human glioblastoma

Abstract: Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor’s molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.

Fiji: an open-source platform for biological-image analysis

Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Extreme Learning Machine for Regression and Multiclass Classification

Abstract: Due to the simplicity of their implementations, least square support vector machine (LS-SVM) and proximal support vector machine (PSVM) have been widely used in binary classification applications. The conventional LS-SVM and PSVM cannot be used in regression and multiclass classification applications directly, although variants of LS-SVM and PSVM have been proposed to handle such cases. This paper shows that both LS-SVM and PSVM can be simplified further and a unified learning framework of LS-SVM, PSVM, and other regularization algorithms referred to extreme learning machine (ELM) can be built. ELM works for the “generalized” single-hidden-layer feedforward networks (SLFNs), but the hidden layer (or called feature mapping) in ELM need not be tuned. Such SLFNs include but are not limited to SVM, polynomial network, and the conventional feedforward neural networks. This paper shows the following: 1) ELM provides a unified learning platform with a widespread type of feature mappings and can be applied in regression and multiclass classification applications directly; 2) from the optimization method point of view, ELM has milder optimization constraints compared to LS-SVM and PSVM; 3) in theory, compared to ELM, LS-SVM and PSVM achieve suboptimal solutions and require higher computational complexity; and 4) in theory, ELM can approximate any target continuous function and classify any disjoint regions. As verified by the simulation results, ELM tends to have better scalability and achieve similar (for regression and binary class cases) or much better (for multiclass cases) generalization performance at much faster learning speed (up to thousands times) than traditional SVM and LS-SVM.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

ImageJ2: ImageJ for the next generation of scientific image data

Abstract: ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science. We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ’s development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.