In this work, we propose a LMDS-based binding-site search for improving the search speed of the Patch-Surfer method. Patch-Surfer is efficient in recognition of protein-ligand binding partners, further speedup is necessary to address multiple-user access. Futher speedup is realised by exploiting Landmark Multi-Dimensional Scaling (LMDS). It computes embedding coordinates for data points based o...

The Community Structure-Activity Resource (CSAR) benchmark exercise provides a unique opportunity for researchers to objectively evaluate the performance of protein-ligand docking methods. Patch-Surfer and PL-PatchSurfer, molecular surface-based methods for predicting binding ligands of proteins developed in our group, were tested on both CSAR 2013 and 2014 benchmark exercises in combination wi...

This paper presents a new ranking algorithm MFCRank for topic-specific Web search systems. The basic idea is to correlate two types of similarity information into a unified link analysis model so that the rich content and link features in Web collections can be exploited efficiently to improve the ranking performance. First, a new surfer model JBC is proposed, under which the topic similarity i...

Hyperlink analysis is a successful approach to define algorithms which compute the relevance of a document on the basis of the citation graph. In this paper we propose a technique to learn the parameters of the page ranking model using a set of pages labeled as relevant or not relevant by a supervisor. In particular we describe a learning algorithm applied to a scheme similar to PageRank. The r...

The Web today includes many pages intended to deceive search engines, in which content or links are created to attain an unwarranted result ranking. Since the links among web pages are used to calculate authority, ranking systems should take into consideration which pages contain content to be trusted and which do not. In this paper, we assume the existence of a mechanism, such as, but not limi...

In this paper, we reflect on the design, development, and deployment of G-nome Surfer; a multi-touch tabletop user interface for collaborative exploration of genomic data. G-nome Surfer lowers the threshold for using advanced bioinformatics tools, reduces the mental workload associated with manipulating genomic information, and fosters effective collaboration. We describe our two-year-long effo...

PageRank is the algorithm used by the Google search engine for ranking web pages. PageRank Algorithm calculates for each page a relative importance score which can be interpreted as the frequency of how often a page is visited by a surfer. The purpose of this work is to provide a mathematical analysis of the PageRank Algorithm. We analyze the random surfer model and the linear algebra behind it...