arXiv subjects

Irene Font Peradejordi

Publications and source records attributed to Irene Font Peradejordi.

3 recordsLinked to original sources

arXiv2024

PhosNetVis: a web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data

Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets across multiple conditions. Researchers then must infer kinases responsible for changes in phosphosites of each substrate. However, tools that infer kinase-substrate interactions (KSIs) are not optimized to interactively explore the resulting large and complex networks, significant phosphosites, and states. There is thus an unmet need for a tool that facilitates user-friendly analysis, interactive exploration, visualization, and communication of phosphoproteomics datasets. We present PhosNetVis, a web-based tool for researchers of all computational skill levels to easily infer, generate and interactively explore KSI networks in 2D or 3D by streamlining phosphoproteomics data analysis steps within a single tool. PhostNetVis lowers barriers for researchers in rapidly generating high-quality visualizations to gain biological insights from their phosphoproteomics datasets. It is available at: https://gumuslab.github.io/PhosNetVis/

q-bio.MN↗

arXiv2023

Bound by the Bounty: Collaboratively Shaping Evaluation Processes for Queer AI Harms

Bias evaluation benchmarks and dataset and model documentation have emerged as central processes for assessing the biases and harms of artificial intelligence (AI) systems. However, these auditing processes have been criticized for their failure to integrate the knowledge of marginalized communities and consider the power dynamics between auditors and the communities. Consequently, modes of bias evaluation have been proposed that engage impacted communities in identifying and assessing the harms of AI systems (e.g., bias bounties). Even so, asking what marginalized communities want from such auditing processes has been neglected. In this paper, we ask queer communities for their positions on, and desires from, auditing processes. To this end, we organized a participatory workshop to critique and redesign bias bounties from queer perspectives. We found that when given space, the scope of feedback from workshop participants goes far beyond what bias bounties afford, with participants questioning the ownership, incentives, and efficacy of bounties. We conclude by advocating for community ownership of bounties and complementing bounties with participatory processes (e.g., co-creation).

cs.CY↗

arXiv2020

3D human pose estimation with adaptive receptive fields and dilated temporal convolutions

In this work, we demonstrate that receptive fields in 3D pose estimation can be effectively specified using optical flow. We introduce adaptive receptive fields, a simple and effective method to aid receptive field selection in pose estimation models based on optical flow inference. We contrast the performance of a benchmark state-of-the-art model running on fixed receptive fields with their adaptive field counterparts. By using a reduced receptive field, our model can process slow-motion sequences (10x longer) 23% faster than the benchmark model running at regular speed. The reduction in computational cost is achieved while producing a pose prediction accuracy to within 0.36% of the benchmark model.

cs.CV↗