Related papers: RNAmountAlign: efficient software for local, globa…
We propose a simple, scalable, and fast gradient descent algorithm to optimize a nonconvex objective for the rank minimization problem and a closely related family of semidefinite programs. With $O(r^3 \kappa^2 n \log n)$ random…
Software-driven O-RAN architectures enable rapid innovation through frequent, independent updates to virtualized components. However, attributing performance variations to specific software changes is challenging due to the stochastic…
Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…
Aligning large language models (LLMs) with human values is crucial for safe deployment. Inference-time techniques offer granular control over generation; however, they rely on model uncertainty, meaning an internal estimate of how likely…
Finding a provably correct subquadratic synchronization algorithm for many filesystem replicas is one of the main theoretical problems in Operational Transformation (OT) and Conflict-free Replicated Data Types (CRDT) frameworks. Based on…
Allen's interval algebra is one of the most well-known calculi in qualitative temporal reasoning with numerous applications in artificial intelligence. Recently, there has been a surge of improvements in the fine-grained complexity of…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to…
Recurrent neural networks (RNNs) have been widely adopted in temporal sequence analysis, where realtime performance is often in demand. However, RNNs suffer from heavy computational workload as the model often comes with large weight…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
The challenge of location testing for high-dimensional data in statistical inference is notable. Existing literature suggests various methods, many of which impose strong regularity conditions on underlying covariance matrices to ensure…
An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$…
One of the most difficult problems difficult problem in systems biology is to discover protein-protein interactions as well as their associated functions. The analysis and alignment of protein-protein interaction networks (PPIN), which are…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and…
Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…
Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA…
Synchronous programs are used extensively in implementation of safety critical embedded software. Imperative synchronous programming languages model multiple Finite State Machines (FSMs) executing in lockstep at logical clock ticks. The…
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…
For tasks like code synthesis from natural language, code retrieval, and code summarization, data-driven models have shown great promise. However, creating these models require parallel data between natural language (NL) and code with…