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Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in…
The advantages for the presence of an XML schema for XML documents are numerous. However, many XML documents in practice are not accompanied by a schema or by a valid schema. Relax NG is a popular and powerful schema language, which…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Sequential Recommendation (SeqRec) aims to predict the next item by capturing sequential patterns from users' historical interactions, playing a crucial role in many real-world recommender systems. However, existing approaches predominantly…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
In differential expression (DE) analysis of RNA-seq count data, it is known that genes with a larger read number are more likely to be differentially expressed. This bias has a profound effect on the subsequent Gene Ontology (GO) analysis…
Direct preference optimization methods have emerged as a computationally efficient alternative to Reinforcement Learning from Human Feedback (RLHF) for aligning Large Language Models (LLMs). Latest approaches have streamlined the alignment…
Spectrum sharing allows different protocols of the same standard (e.g., 802.11 family) or different standards (e.g., LTE and DVB) to coexist in overlapping frequency bands. As this paradigm continues to spread, wireless systems must also…
Data leakage remains a recurrent source of optimistic bias in biomedical machine learning studies. Standard row-wise cross-validation and globally estimated preprocessing steps are often inappropriate for data with repeated measurements,…
Recent recommender systems started to use rating elicitation, which asks new users to rate a small seed itemset for inferring their preferences, to improve the quality of initial recommendations. The key challenge of the rating elicitation…
The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…
Matched case-control studies are commonly employed in epidemiological research for their convenience and efficiency. Analysis of secondary outcomes can yield valuable insights into biological pathways and help identify genetic variants of…
Specialized reasoning language models (RLMs) have demonstrated that scaling test-time computation through detailed reasoning traces significantly enhances performance. Although these traces effectively facilitate knowledge distillation into…
Protocol reverse engineering (PRE) aims to infer the specification of network protocols when the source code is not available. Specifically, field inference is one crucial step in PRE to infer the field formats and semantics. To perform…
The fields of therapeutic application and drug research and development (R&D) both face substantial challenges, i.e., the therapeutic domain calls for more treatment alternatives, while numerous promising pre-clinical drugs have failed in…
This paper proposes a new evaluation protocol for cross-media retrieval which better fits the real-word applications. Both image-text and text-image retrieval modes are considered. Traditionally, class labels in the training and testing…
Natural Language Inference (NLI) or Recognizing Textual Entailment (RTE) aims at predicting the relation between a pair of sentences (premise and hypothesis) as entailment, contradiction or semantic independence. Although deep learning…
Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…
Rare diseases affect hundreds of millions worldwide, yet diagnosis often spans years. Convectional pipelines decouple noisy evidence extraction from downstream inferential diagnosis, and general/medical large language models (LLMs) face…