The study of probability model for compound similarity searching

Information Retrieval or IR system main task is to retrieve relevant documents according to the users query. One of IR most popular retrieval model is the Vector Space Model. This model assumes relevance based on similarity, which is defined as the distance between query and document in the concept space. All currently existing chemical compound database systems have adapt the vector space model to calculate the similarity of a database entry to a query compound. However, it assumes that fragments represented by the bits are independent of one another, which is not necessarily true. Hence, the possibility of applying another IR model is explored, which is the Probabilistic Model, for chemical compound searching. This model estimates the probabilities of a chemical structure to have the same bioactivity as a target compound. It is envisioned that by ranking chemical structures in decreasing order of their probability of relevance to the query structure, the effectiveness of a molecular similarity searching system can be increased. Both fragment dependencies and independencies assumption are taken into consideration in achieving improvement towards compound similarity searching system. After conducting a series of simulated similarity searching, it is concluded that PM approaches really did perform better than the existing similarity searching. It gave better result in all evaluation criteria to confirm this statement. In terms of which probability model performs better, the BD model shown improvement over the BIR model

Inference, Learning, and Population Size: Projectivity for SRL Models

A subtle difference between propositional and relational data is that in many relational models, marginal probabilities depend on the population or domain size. This paper connects the dependence on population size to the classic notion of projectivity from statistical theory: Projectivity implies that relational predictions are robust with respect to changes in domain size. We discuss projectivity for a number of common SRL systems, and identify syntactic fragments that are guaranteed to yield projective models. The syntactic conditions are restrictive, which suggests that projectivity is difficult to achieve in SRL, and care must be taken when working with different domain sizes

Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

Sparse Learning over Infinite Subgraph Features

We present a supervised-learning algorithm from graph data (a set of graphs) for arbitrary twice-differentiable loss functions and sparse linear models over all possible subgraph features. To date, it has been shown that under all possible subgraph features, several types of sparse learning, such as Adaboost, LPBoost, LARS/LASSO, and sparse PLS regression, can be performed. Particularly emphasis is placed on simultaneous learning of relevant features from an infinite set of candidates. We first generalize techniques used in all these preceding studies to derive an unifying bounding technique for arbitrary separable functions. We then carefully use this bounding to make block coordinate gradient descent feasible over infinite subgraph features, resulting in a fast converging algorithm that can solve a wider class of sparse learning problems over graph data. We also empirically study the differences from the existing approaches in convergence property, selected subgraph features, and search-space sizes. We further discuss several unnoticed issues in sparse learning over all possible subgraph features.Comment: 42 pages, 24 figures, 4 table