Related papers: siDPT: siRNA Efficacy Prediction via Debiased Pref…

A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers.…

In recommender systems (RSs), predicting the next item that a user interacts with is critical for user retention. While the last decade has seen an explosion of RSs aimed at identifying relevant items that match user preferences, there is…

Synthetic control is a causal inference tool used to estimate the treatment effects of an intervention by creating synthetic counterfactual data. This approach combines measurements from other similar observations (i.e., donor pool ) to…

MiRNAs, due to their role in gene regulation, have paved a new pathway for pharmacology, focusing on drug development that targets miRNAs. However, traditional wet lab experiments are limited by efficiency and cost constraints, making it…

The lack of well-structured metadata annotations complicates there-usability and interpretation of the growing amount of publicly available RNA expression data. The machine learning-based prediction of metadata(data augmentation) can…

Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to…

Nonsense-mediated mRNA decay (NMD) is a critical post-transcriptional surveillance mechanism that degrades transcripts with premature termination codons, safeguarding transcriptome integrity and shaping disease phenotypes. However,…

Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…

Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…

Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). These feature sets used by current tools for pre-miRNA recognition differ in construction and dimension. Some…

Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare…

RNA protein Interactions (RPIs) play an important role in biological systems. Recently, we have enumerated the RPIs at the residue level and have elucidated the minimum structural unit (MSU) in these interactions to be a stretch of five…

Spiking neural networks are emerging as a promising energy-efficient alternative to traditional artificial neural networks due to their spike-driven paradigm. However, recent research in the SNN domain has mainly focused on enhancing…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…

In various statistical settings, the goal is to estimate a function which is restricted by the statistical model only through a conditional moment restriction. Prominent examples include the nonparametric instrumental variable framework for…

Direct Preference Optimization (DPO) has emerged as a predominant alignment method for diffusion models, facilitating off-policy training without explicit reward modeling. However, its reliance on large-scale, high-quality human preference…