Cover Image

Abundance-Aware Set Transformer for Microbiome Sample Embedding

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Yoo, Hyunwoo, Rosen, Gail
Format:	Preprint
Published:	2025
Subjects:	Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Predicting Microbial Ontology and Pathogen Risk from Environmental Metadata with Large Language Models
by: Yoo, Hyunwoo, et al.
Published: (2025)

Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinity
by: Refahi, Mohammadsaleh, et al.
Published: (2025)

Interpreting Microbiome Relative Abundance Data Using Symbolic Regression
by: Haldar, Swagatam, et al.
Published: (2024)

Spurious Correlation-Aware Embedding Regularization for Worst-Group Robustness
by: Park, Subeen, et al.
Published: (2025)

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
by: Refahi, Mohammad Saleh, et al.
Published: (2025)

Exploring Adversarial Robustness in Classification tasks using DNA Language Models
by: Yoo, Hyunwoo, et al.
Published: (2024)

I Dropped a Neural Net
by: Park, Hyunwoo
Published: (2026)

Exploring Large Action Sets with Hyperspherical Embeddings using von Mises-Fisher Sampling
by: Bendada, Walid, et al.
Published: (2025)

HOLE: Homological Observation of Latent Embeddings for Neural Network Interpretability
by: Athreya, Sudhanva Manjunath, et al.
Published: (2025)

Gaussian Weight Sampling for Scalable, Efficient and Stable Pseudo-Quantization Training
by: Ahn, Myeonghwan, et al.
Published: (2025)

Engineering Regression Without Real-Data Training: Domain Adaptation for Tabular Foundation Models Using Multi-Dataset Embeddings
by: Regenwetter, Lyle, et al.
Published: (2026)

Predicting Anti-microbial Resistance using Large Language Models
by: Yoo, Hyunwoo, et al.
Published: (2024)

Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity
by: Li, Zhufeng, et al.
Published: (2024)

Conditional neural control variates for variance reduction in Bayesian inverse problems
by: Siahkoohi, Ali, et al.
Published: (2026)

Pareto Set Identification With Posterior Sampling
by: Kone, Cyrille, et al.
Published: (2024)

SVDformer: Direction-Aware Spectral Graph Embedding Learning via SVD and Transformer
by: Fang, Jiayu, et al.
Published: (2025)

Structure-Aware Set Transformers: Temporal and Variable-Type Attention Biases for Asynchronous Clinical Time Series
by: Lee, Joohyung, et al.
Published: (2026)

Permutation-Invariant Transformer Neural Architectures for Set-Based Indoor Localization Using Learned RSSI Embeddings
by: Aristorenas, Aris J.
Published: (2025)

Deep Embedding Clustering Driven by Sample Stability
by: Cheng, Zhanwen, et al.
Published: (2024)

Predictive Coding for Decision Transformer
by: Luu, Tung M., et al.
Published: (2024)

Posterior Sampling of Probabilistic Word Embeddings
by: Yrjänäinen, Väinö, et al.
Published: (2025)

Set2Seq Transformer: Temporal and Position-Aware Set Representations for Sequential Multiple-Instance Learning
by: Efthymiou, Athanasios, et al.
Published: (2024)

STEM: Scaling Transformers with Embedding Modules
by: Sadhukhan, Ranajoy, et al.
Published: (2026)

Setting the Record Straight on Transformer Oversmoothing
by: Dovonon, Gbètondji J-S, et al.
Published: (2024)

Freeze, Diffuse, Decode: Geometry-Aware Adaptation of Pretrained Transformer Embeddings for Antimicrobial Peptide Design
by: Gawade, Pankhil, et al.
Published: (2025)

Sliding-Window Thompson Sampling for Non-Stationary Settings
by: Fiandri, Marco, et al.
Published: (2024)

Learning to Recall with Transformers Beyond Orthogonal Embeddings
by: Vural, Nuri Mert, et al.
Published: (2026)

DisEmbed: Transforming Disease Understanding through Embeddings
by: Faroz, Salman
Published: (2024)

ST-MTM: Masked Time Series Modeling with Seasonal-Trend Decomposition for Time Series Forecasting
by: Seo, Hyunwoo, et al.
Published: (2025)

Towards High-fidelity Head Blending with Chroma Keying for Industrial Applications
by: Lew, Hah Min, et al.
Published: (2024)

Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction
by: Kim, Younhun, et al.
Published: (2026)

Density-Aware Farthest Point Sampling
by: Climaco, Paolo, et al.
Published: (2025)

Integrated Subset Selection and Bandwidth Estimation Algorithm for Geographically Weighted Regression
by: Lee, Hyunwoo, et al.
Published: (2025)

Cardinality-Aware Set Prediction and Top-$k$ Classification
by: Cortes, Corinna, et al.
Published: (2024)

Training neural control variates using correlated configurations
by: Oh, Hyunwoo
Published: (2025)

Affinity Graph Connectivity in Convex Clustering
by: Rosen, Sam, et al.
Published: (2026)

WaveFormer: Wavelet Embedding Transformer for Biomedical Signals
by: Irani, Habib, et al.
Published: (2026)

SetCSE: Set Operations using Contrastive Learning of Sentence Embeddings
by: Liu, Kang
Published: (2024)

Sample Efficient Reinforcement Learning via Large Vision Language Model Distillation
by: Lee, Donghoon, et al.
Published: (2025)

Sharpness-Aware Minimization for Generalized Embedding Learning in Federated Recommendation
by: Yu, Fengyuan, et al.
Published: (2026)