Gene Expression based Survival Prediction for Cancer Patients: A Topic Modeling Approach

Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As standard survival prediction models have a hard time coping with the high-dimensionality of such gene expression (GE) data, many projects use some dimensionality reduction techniques to overcome this hurdle. We introduce a novel methodology, inspired by topic modeling from the natural language domain, to derive expressive features from the high-dimensional GE data. There, a document is represented as a mixture over a relatively small number of topics, where each topic corresponds to a distribution over the words; here, to accommodate the heterogeneity of a patient's cancer, we represent each patient (~document) as a mixture over cancer-topics, where each cancer-topic is a mixture over GE values (~words). This required some extensions to the standard LDA model eg: to accommodate the "real-valued" expression values - leading to our novel "discretized" Latent Dirichlet Allocation (dLDA) procedure. We initially focus on the METABRIC dataset, which describes breast cancer patients using the r=49,576 GE values, from microarrays. Our results show that our approach provides survival estimates that are more accurate than standard models, in terms of the standard Concordance measure. We then validate this approach by running it on the Pan-kidney (KIPAN) dataset, over r=15,529 GE values - here using the mRNAseq modality - and find that it again achieves excellent results. In both cases, we also show that the resulting model is calibrated, using the recent "D-calibrated" measure. These successes, in two different cancer types and expression modalities, demonstrates the generality, and the effectiveness, of this approach

ARPA Whitepaper

We propose a secure computation solution for blockchain networks. The correctness of computation is verifiable even under malicious majority condition using information-theoretic Message Authentication Code (MAC), and the privacy is preserved using Secret-Sharing. With state-of-the-art multiparty computation protocol and a layer2 solution, our privacy-preserving computation guarantees data security on blockchain, cryptographically, while reducing the heavy-lifting computation job to a few nodes. This breakthrough has several implications on the future of decentralized networks. First, secure computation can be used to support Private Smart Contracts, where consensus is reached without exposing the information in the public contract. Second, it enables data to be shared and used in trustless network, without disclosing the raw data during data-at-use, where data ownership and data usage is safely separated. Last but not least, computation and verification processes are separated, which can be perceived as computational sharding, this effectively makes the transaction processing speed linear to the number of participating nodes. Our objective is to deploy our secure computation network as an layer2 solution to any blockchain system. Smart Contracts\cite{smartcontract} will be used as bridge to link the blockchain and computation networks. Additionally, they will be used as verifier to ensure that outsourced computation is completed correctly. In order to achieve this, we first develop a general MPC network with advanced features, such as: 1) Secure Computation, 2) Off-chain Computation, 3) Verifiable Computation, and 4)Support dApps' needs like privacy-preserving data exchange

Toward Consistent Creation of Marine Information Overlays: Configuration of ESRI’s PLTS Nautical Solution

This project presents a set of tools to facilitate interoperability between an ArcGIS geodatabase model and the S-57 international standard for nautical data. Additionally configurations and workflows were developed for consistent creation of nautical data in accordance with said standard. Central to this interoperability are Marine Information Overlays (MIO), which are additional navigation information to the Electronic Nautical Chart database. MIO data is intended to provide safe and efficient ship routing. Semantic mapping between the marine objects in the S-57 standard and the MIO model preserves the essential components of each. Data interoperability is realized through the use of semantic mapping via a configured PLTS Nautical Solution import/export engine and standards are supported through the use of this software

Mass-Market Receiver for Static Positioning: Tests and Statistical Analyses

Nowadays, there are several low cost GPS receivers able to provide both pseudorange and carrier phase measurements in the L1band, that allow to have good realtime performances in outdoor condition. The present paper describes a set of dedicated tests in order to evaluate the positioning accuracy in static conditions. The quality of the pseudorange and the carrier phase measurements let hope for interesting results. The use of such kind of receiver could be extended to a large number of professional applications, like engineering fields: survey, georeferencing, monitoring, cadastral mapping and cadastral road. In this work, the receivers performance is verified considering a single frequency solution trying to fix the phase ambiguity, when possible. Different solutions are defined: code, float and fix solutions. In order to solve the phase ambiguities different methods are considered. Each test performed is statistically analyzed, highlighting the effects of different factors on precision and accurac

Modeling Algorithms in SystemC and ACL2

We describe the formal language MASC, based on a subset of SystemC and intended for modeling algorithms to be implemented in hardware. By means of a special-purpose parser, an algorithm coded in SystemC is converted to a MASC model for the purpose of documentation, which in turn is translated to ACL2 for formal verification. The parser also generates a SystemC variant that is suitable as input to a high-level synthesis tool. As an illustration of this methodology, we describe a proof of correctness of a simple 32-bit radix-4 multiplier.Comment: In Proceedings ACL2 2014, arXiv:1406.123

Research on Voyage Navigation S/W Development Architecture Using Open Source Base GIS Modules

Recently, as the number of voyage accident is increasing, massive damage of human life and property is following depends on scale of accident. ECDIS is navigation equipment essential for safe sailing and clean marine environment. However, ECDIS S/W is relatively expensive, and ocean-related international organizations such as IMO and IHO are designing the programs mainly for medium and large ships. OPEN CPN, SeaClear are existing as product based on Open Source Project, however they are lack of functions to use in actual voyage. ECDIS development by making combination with modules based on open source could be an alternative to follow the standards and develop efficiently

TRIDEnT: Building Decentralized Incentives for Collaborative Security

Sophisticated mass attacks, especially when exploiting zero-day vulnerabilities, have the potential to cause destructive damage to organizations and critical infrastructure. To timely detect and contain such attacks, collaboration among the defenders is critical. By correlating real-time detection information (alerts) from multiple sources (collaborative intrusion detection), defenders can detect attacks and take the appropriate defensive measures in time. However, although the technical tools to facilitate collaboration exist, real-world adoption of such collaborative security mechanisms is still underwhelming. This is largely due to a lack of trust and participation incentives for companies and organizations. This paper proposes TRIDEnT, a novel collaborative platform that aims to enable and incentivize parties to exchange network alert data, thus increasing their overall detection capabilities. TRIDEnT allows parties that may be in a competitive relationship, to selectively advertise, sell and acquire security alerts in the form of (near) real-time peer-to-peer streams. To validate the basic principles behind TRIDEnT, we present an intuitive game-theoretic model of alert sharing, that is of independent interest, and show that collaboration is bound to take place infinitely often. Furthermore, to demonstrate the feasibility of our approach, we instantiate our design in a decentralized manner using Ethereum smart contracts and provide a fully functional prototype.Comment: 28 page