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We introduce Permutation and Structured Perturbation Inference (PSPI), a new problem formulation that abstracts many graph matching tasks that arise in systems biology. PSPI can be viewed as a robust formulation of the permutation inference…
The incorporation of pseudo data in the training of grammatical error correction models has been one of the main factors in improving the performance of such models. However, consensus is lacking on experimental configurations, namely,…
For a quantum error correcting code to be used in practice, it needs to be equipped with an efficient decoding algorithm, which identifies corrections given the observed syndrome of errors.Hypergraph product codes are a promising family of…
The deployment of Large Language Models (LLMs) for code debugging (e.g., C and Python) is widespread, benefiting from their ability to understand and interpret intricate concepts. However, in the semiconductor industry, utilising LLMs to…
We introduce $\mathsf{PREM}$ (Private Relative Error Multiplicative weight update), a new framework for generating synthetic data that achieves a relative error guarantee for statistical queries under $(\varepsilon, \delta)$ differential…
This paper presents RTLFixer, a novel framework enabling automatic syntax errors fixing for Verilog code with Large Language Models (LLMs). Despite LLM's promising capabilities, our analysis indicates that approximately 55% of errors in…
Real-world databases are predominantly relational, comprising multiple interlinked tables that contain complex structural and statistical dependencies. Learning generative models on relational data has shown great promise in generating…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
Inference efficiency in Large Language Models (LLMs) is fundamentally limited by their serial, autoregressive generation, especially as reasoning becomes a key capability and response sequences grow longer. Speculative decoding (SD) offers…
We introduce cellanneal, a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimization of Spearman's rank correlation coefficient between experimental and computational mixture gene expression…
We initiate the probabilistic analysis of linear programming (LP) decoding of low-density parity-check (LDPC) codes. Specifically, we show that for a random LDPC code ensemble, the linear programming decoder of Feldman et al. succeeds in…
We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
We present piXedfit, pixelized spectral energy distribution (SED) fitting, a Python package that provides tools for analyzing spatially resolved properties of galaxies using multiband imaging data alone or in combination with integral field…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
We consider the decoding of convolutional codes using an error trellis constructed based on a submatrix of a given check matrix. In the proposed method, the syndrome-subsequence computed using the remaining submatrix is utilized as…
A branch of automated program repair (APR) techniques look at finding and reusing existing code for bug repair. ssFix is one of such techniques that is syntactic search-based: it searches a code database for code fragments that are…
This paper introduces a framework of parametric descriptive directional types for constraint logic programming (CLP). It proposes a method for locating type errors in CLP programs and presents a prototype debugging tool. The main technique…
Generative models of macromolecules carry abundant and impactful implications for industrial and biomedical efforts in protein engineering. However, existing methods are currently limited to modeling protein structures or sequences,…
This report investigates the relationship between software refactoring and behavior preservation. Existing behavior preservation analyses often lack comprehensive insights into refactoring rejections and do not provide actionable solutions.…