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Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Variant Stochastic cracking is a significantly more resilient approach to adaptive indexing. It showed [1]that Stochastic cracking uses each query as a hint on how to reorganize data, but not blindly so; it gains resilience and avoids…
We present CREST (Compact Retrieval-Based Speculative Decoding), a redesign of REST that allows it to be effectively "compacted". REST is a drafting technique for speculative decoding based on retrieving exact n-gram matches of the most…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Understanding search queries is critical for shopping search engines to deliver a satisfying customer experience. Popular shopping search engines receive billions of unique queries yearly, each of which can depict any of hundreds of user…
The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery…
Protein sequence generation via stochastic attention produces plausible family members from small alignments without training, but treats all stored sequences equally and cannot direct generation toward a functional subset of interest. We…
Thermostability is an important prerequisite for enzymes employed for industrial applications. Several machine learning based models have thus been formulated for protein classification based on this particular trait. These models have…
This paper focuses on multi-enrollment speaker recognition which naturally occurs in the task of online speaker clustering, and studies the properties of different scoring back-ends in this scenario. First, we show that popular cosine…
An important component of any generation system is the mapping dictionary, a lexicon of elementary semantic expressions and corresponding natural language realizations. Typically, labor-intensive knowledge-based methods are used to…
Unsupervised learning of low-dimensional, semantic representations of words and entities has recently gained attention. In this paper we describe the Semantic Entity Retrieval Toolkit (SERT) that provides implementations of our previously…
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…
Important graph mining problems such as Clustering are computationally demanding. To significantly accelerate these problems, we propose ProbGraph: a graph representation that enables simple and fast approximate parallel graph mining with…
The process of browsing Search Results is one of the major problems with traditional Web search engines for English, European, and any other languages generally, and for Arabic Language particularly. This process is absolutely time…
The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
We introduce ADAPQUEST, a software tool written in Java for the development of adaptive questionnaires based on Bayesian networks. Adaptiveness is intended here as the dynamical choice of the question sequence on the basis of an evolving…
Probabilistic programming languages (PPLs) are expressive means for creating and reasoning about probabilistic models. Unfortunately hybrid probabilistic programs, involving both continuous and discrete structures, are not well supported by…
Modern business applications and scientific databases call for inherently dynamic data storage environments. Such environments are characterized by two challenging features: (a) they have little idle system time to devote on physical…