MOTIVATION: Mass spectrometry imaging (MSI) characterizes the molecular composition of tissues at spatial resolution, and has a strong potential for distinguishing tissue types, or disease states. This can be achieved by supervised classification, which takes as input MSI spectra, and assigns class labels to subtissue locations. Unfortunately, developing such classifiers is hindered by the limited availability of training sets with subtissue labels as the ground truth. Subtissue labeling is prohibitively expensive, and only rough annotations of the entire tissues are typically available. Classifiers trained on data with approximate labels have sub-optimal performance. RESULTS: To alleviate this challenge, we contribute a semi-supervised approach mi-CNN. mi-CNN implements multiple instance learning with a convolutional neural network (CNN). The multiple instance aspect enables weak supervision from tissue-level annotations when classifying subtissue locations. The convolutional architecture of the CNN captures contextual dependencies between the spectral features. Evaluations on simulated and experimental datasets demonstrated that mi-CNN improved the subtissue classification as compared to traditional classifiers. We propose mi-CNN as an important step toward accurate subtissue classification in MSI, enabling rapid distinction between tissue types and disease states. AVAILABILITY AND IMPLEMENTATION: The data and code are available at https://github.com/Vitek-Lab/mi-CNN_MSI.

BACKGROUND: In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS: We developed ImproViser ( http://www.improviser.uni-freiburg.de) for fully automated peptide mapping of quantitative proteomics data in the protXML data. The tool generates sortable and graphically annotated output, which can be easily shared with further users. As an exemplary application, we show its usage in the proteomic analysis of regulated intramembrane proteolysis. CONCLUSION: ImproViser is the first tool to enable automated peptide mapping of the widely-used protXML format.

We present an FPGA-synthesizable version of the Intel Atom processor core, synthesized to a Virtex-5 based FPGA emulation system. To make the production Atom design in SystemVerilog synthesizable through industry standard EDA tool flow, we transformed and mapped latches in the design, converted clock gating, and replaced nonsynthesizable constructs with FPGA-synthesizable counterparts. Additionally, as the target FPGA emulator is hosted on a PC platform with the Pentium-based CPU socket that supports a significantly different front side bus (FSB) protocol from that of the Atom processor, we replaced the existing bus control logic in the Atom core with an alternate FSB protocol to communicate with the rest of the PC platform. With these efforts, we succeeded in synthesizing the entire Atom processor core to fit within a single Virtex-5 LX330 FPGA. The synthesizable Atom core runs at 50Mhz on the Pentium PC motherboard with fully functional I/O peripherals. It is capable of booting off-the-shelf MS-DOS, Windows XP and Linux operating systems, and executing standard x86 workloads.