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Multimodal Information Retrieval
In today’s rapidly evolving digital landscape, the wealth of available information has expanded beyond the boundaries of traditional text-based...
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Retrieval Augmented Modeling
Till this point in our book, we have discussed the fundamental principles of information retrieval, exploring its key elements, and various...
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Outlook
While multimodal information retrieval has several exciting applications and a high potential for impact on important problems, there are several...
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Multimodal Content Generation
In this chapter, we will review the advances that are being made in this new field of multimodal content generation and also discuss several...
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Transformer-Driven Models for Language, Vision, and Multimodality
In this chapter, we will learn about the modeling and learning techniques that drive multimodal applications. We will focus specifically on the...
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Introduction
In this book, our emphasis is on multimodal information retrieval, specifically concentrating on text and image data. The traditional unimodal...
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Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets
Finding related individuals in genomic datasets is a necessary step in many genetic analysis workflows and has broader societal value as a tool for...
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Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA...
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Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency
DNA methylation data plays a crucial role in estimating chronological age in mammals, offering real-time insights into an individual’s aging process....
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Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts
An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes, conserved elements, and epigenetic...
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Computing Robust Optimal Factories in Metabolic Reaction Networks
Perhaps the most fundamental model in synthetic and systems biology for inferring pathways in metabolic reaction networks is a metabolic factory: a...
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SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes
Nucleosome landscapes across the genome are typically characterized using micrococcal nuclease sequencing (MNase-seq). MNase is an endo-exonuclease...
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Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape
Machine learning (ML) is revolutionizing our ability to model the fitness landscape of protein sequences. Recently, the protein language model (pLM)...
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ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation
Metagenomic Hi-C (metaHi-C) enables the recognition of relationships between contigs in terms of their physical proximity within the same cell,...
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An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks
Executable models of biological circuits offer the ability to simulate their behavior under different settings with important biomedical...
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Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics
A key challenge in cancer research is to reconstruct the somatic evolution within a tumor over time and across space. Spatially resolved...
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Disease Risk Predictions with Differentiable Mendelian Randomization
Predicting future disease onset is crucial in preventive healthcare, yet longitudinal datasets linking early risk factors to subsequent health...
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Protein Domain Embeddings for Fast and Accurate Similarity Search
Recently developed protein language models have enabled a variety of applications of the protein contextual embeddings. Per-protein representations...
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Map** the Topography of Spatial Gene Expression with Interpretable Deep Learning
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this...
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Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models
Microbiome profiling exhibits strong study- and batch-specific effects, impeding the identification of signals that are reproducible across studies...