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We introduce Retrieval-Based Speculative Decoding (REST), a novel algorithm designed to speed up language model generation. The key insight driving the development of REST is the observation that the process of text generation often…
Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…
PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for…
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
Biclustering is a two way clustering approach involving simultaneous clustering along two dimensions of the data matrix. Finding biclusters of web objects (i.e. web users and web pages) is an emerging topic in the context of web usage…
Scatterplots are one of the simplest and most commonly-used visualizations for understanding quantitative, multidimensional data. However, since scatterplots only depict two attributes at a time, analysts often need to manually generate and…
In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in…
The number of videos being produced and consequently stored in databases for video streaming platforms has been increasing exponentially over time. This vast database should be easily index-able to find the requisite clip or video to match…
Finding patterns in data and being able to retrieve information from those patterns is an important task in Information retrieval. Complex search requirements which are not fulfilled by simple string matching and require exploring certain…
Formulating selective information needs results in queries that implicitly specify set operations, such as intersection, union, and difference. For instance, one might search for "shorebirds that are not sandpipers" or "science-fiction…
Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of…
Issue-reproducing tests fail on buggy code and pass once a patch is applied, thus increasing developers' confidence that the issue has been resolved and will not be re-introduced. However, past research has shown that developers often…
It is demonstrated earlier that the exact Smith-Waterman algorithm yields more accurate results than the members of the heuristic BLAST family of algorithms. Unfortunately, the Smith-Waterman algorithm is much slower than the BLAST and its…
Modern application development allows applications to be composed using lightweight HTTP services. Testing such an application requires the availability of services that the application makes requests to. However, access to dependent…
Answer set programming (ASP) is a popular declarative programming paradigm with a wide range of applications in artificial intelligence. Oftentimes, when modeling an AI problem with ASP, and in particular when we are interested beyond…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
Categorical sequence clustering plays a crucial role in various fields, but the lack of interpretability in cluster assignments poses significant challenges. Sequences inherently lack explicit features, and existing sequence clustering…
A novel approach to protein multiple sequence alignment is discussed: substantially this method counterparts with substitution matrix based methods (like Blosum or PAM based methods), and implies a more deterministic approach to…