Chemical structure matching using correlation matrix memories

This paper describes the application of the Relaxation By Elimination (RBE) method to matching the 3D structure of molecules in chemical databases within the frame work of binary correlation matrix memories. The paper illustrates that, when combined with distributed representations, the method maps well onto these networks, allowing high performance implementation in parallel systems. It outlines the motivation, the neural architecture, the RBE method and presents some results of matching small molecules against a database of 100,000 models

Ranking relations using analogies in biological and information networks

Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects $\mathbf{S}=\{A^{(1)}:B^{(1)},A^{(2)}:B^{(2)},\ldots,A^{(N)}:B ^{(N)}\}$, measures how well other pairs A:B fit in with the set $\mathbf{S}$. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in $\mathbf{S}$? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS321 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

References to past designs

Designing by adaptation is almost invariably a dominantambiguity feature of designing, and references to past designs are ubiquitous in design discourse. Object references serve as indices into designers' stocks of design concepts, in which memories for concrete embodiments and exemplars are tightly bound to solution principles. Thinking and talking by reference to past designs serves as a way to reduce the overwhelming complexity of complex design tasks by enabling designers to use parsimonious mental representations to which details can be added as needed. However object references can be ambiguous, and import more of the past design than is intended or may be desirable

How Reliably Misrepresenting Olfactory Experiences Justify True Beliefs

This chapter argues that olfactory experiences represent either everyday objects or ad hoc olfactory objects as having primitive olfactory properties, which happen to be uninstantiated. On this picture, olfactory experiences reliably misrepresent: they falsely represent everyday objects or ad hoc objects as having properties they do not have, and they misrepresent in the same way on multiple occasions. One might worry that this view is incompatible with the plausible claim that olfactory experiences at least sometimes justify true beliefs about the world. This chapter argues that there is no such incompatibility. Since olfactory experiences reliably misrepresent, they can lead to true and justified beliefs about putatively smelly objects

Y(4140): Possible options

We discuss possible options for interpreting the newly observed state Y(4140) by the CDF collaboration in $B^+\to J/\psi\phi K^+$ decay above the $J/\psi\phi$ threshold, and argue that it is more likely to be a $D_s^*$-$D_s^*$ molecular state or an exotic ($J^{PC}=1^{-+}$) hybrid charmonium. We have discussed decay modes which would allow unambiguous identification of the hybrid charmonium option.Comment: 3 pages Revte

Drug prescription support in dental clinics through drug corpus mining

The rapid increase in the volume and variety of data poses a challenge to safe drug prescription for the dentist. The increasing number of patients that take multiple drugs further exerts pressure on the dentist to make the right decision at point-of-care. Hence, a robust decision support system will enable dentists to make decisions on drug prescription quickly and accurately. Based on the assumption that similar drug pairs have a higher similarity ratio, this paper suggests an innovative approach to obtain the similarity ratio between the drug that the dentist is going to prescribe and the drug that the patient is currently taking. We conducted experiments to obtain the similarity ratios of both positive and negative drug pairs, by using feature vectors generated from term similarities and word embeddings of biomedical text corpus. This model can be easily adapted and implemented for use in a dental clinic to assist the dentist in deciding if a drug is suitable for prescription, taking into consideration the medical profile of the patients. Experimental evaluation of our model’s association of the similarity ratio between two drugs yielded a superior F score of 89%. Hence, such an approach, when integrated within the clinical work flow, will reduce prescription errors and thereby increase the health outcomes of patients