Daniela Ruiz

Musica ex machina: Towards AI-supported research into mechanisms of music-based therapies and interventions

King-Chi Yau, Mark Ettenberger, Alejandra Perez, Martina de Witte et autres

Background: The expanding literature on music-based therapies and interventions makes it increasingly difficult for clinicians and researchers to identify relevant evidence on treatment mechanisms, moderators, mediators, and outcomes. Objective: This study explored whether artificial intelligence (AI) and natural language processing (NLP) methods …

Musica ex machina: Towards AI-supported research into mechanisms of music-based therapies and interventions

Daniela Ruiz, Alejandra Perez, King-Chi Yau, Mok Che Ling Michelle et autres

Background: The expanding literature on music-based therapies and interventions makes it increasingly difficult for clinicians and researchers to identify relevant evidence on treatment mechanisms, moderators, mediators, and outcomes. Objective: This study explored whether artificial intelligence (AI) and natural language processing (NLP) methods …

PteroSet

Daniela Ruiz, Juan Sebastián Ulloa, Zhongqi Miao, Nicolas Betancourt et autres

This release provides a curated passive acoustic monitoring dataset of Neotropical bird vocalizations recorded in Colombia (Puerto Asís, Putumayo; Pijavay, Magdalena) between 2023 and 2025. Audio was collected using autonomous AudioMoth recorders and stored as time-lapse WAV recordings, distributed across the five …

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Adaptive acoustic monitoring for endangered Cook Inlet beluga whales in complex soundscapes

Manuel Castellote, Rahul Dodhia, Daniela Ruiz, Zhongqi Miao et autres

This repository accompanies the publication Adaptive acoustic monitoring for endangered Cook Inlet beluga whales in complex soundscapes. The work is part of the long-term Cook Inlet Beluga Acoustics (CIBA) Program, a collaborative effort led by the Marine Mammal Laboratory, Alaska Fisheries Science …

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PteroSet

Daniela Ruiz, Juan Sebastián Ulloa, Zhongqi Miao, Nicolas Betancourt et autres

This release provides a curated passive acoustic monitoring dataset of Neotropical bird vocalizations recorded in Colombia (Puerto Asís, Putumayo; Pijavay, Magdalena) between 2023 and 2025. Audio was collected using autonomous AudioMoth recorders and stored in WAV format, distributed across the five project …

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Latent Gene Diffusion for Spatial Transcriptomics Completion

Paula Cárdenas, Leonardo Manrique, Daniela Vega, Daniela Ruiz et autres

Computer Vision has proven to be a powerful tool for analyzing Spatial Transcriptomics (ST) data. However, current models that predict spatially resolved gene expression from histopathology images suffer from significant limitations due to data dropout. Most existing approaches rely on single-cell RNA …

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Completing spatial transcriptomics data for gene expression prediction benchmarking

Daniela Ruiz, Paula Cárdenas, Leonardo Manrique, Daniela Vega et autres

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SpaRED benchmark: Enhancing Gene Expression Prediction from Histology Images with Spatial Transcriptomics Completion

Gabriel Mejia, Daniela Ruiz, Paula Cárdenas, Leonardo Manrique et autres

Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential applications, recent efforts have focused on predicting transcriptomic profiles solely from …

Enhancing Gene Expression Prediction from Histology Images with Spatial Transcriptomics Completion

Gabriel Mejia, Daniela Ruiz, Paula Cárdenas, Leonardo Manrique et autres

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SEPAL: Spatial Gene Expression Prediction from Local Graphs

Gabriel Mejia, Paula Cárdenas, Daniela Ruiz, Angela Castillo et autres

Spatial transcriptomics is an emerging technology that aligns histopathology images with spatially resolved gene expression profiling. It holds the potential for understanding many diseases but faces significant bottlenecks such as specialized equipment and domain expertise. In this work, we present SEPAL, a …

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SEPAL: Spatial Gene Expression Prediction from Local Graphs

Gabriel Mejia, Paula Cárdenas, Daniela Ruiz, Angela Castillo et autres

Spatial transcriptomics is an emerging technology that aligns histopathology images with spatially resolved gene expression profiling. It holds the potential for understanding many diseases but faces significant bottlenecks such as specialized equipment and domain expertise. In this work, we present SEPAL, a …

CNN for Breast Cancer Metastases Classification

Nicolás Aparicio, Isai Daniel Chacón, Daniela Ruiz

We present a Deep Convolutional Neural Network based on VGG16 for the classification of patch images from the benchmark of PatchCamelyon 2016. This dataset consists of 327680 color images from histopathologic scans of lymph node sections. The images were originally acquired at …

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