Cover Image

Specialized Foundation Models Struggle to Beat Supervised Baselines

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Xu, Zongzhe, Gupta, Ritvik, Cheng, Wenduo, Shen, Alexander, Shen, Junhong, Talwalkar, Ameet, Khodak, Mikhail
Format:	Preprint
Published:	2024
Subjects:	Machine Learning Artificial Intelligence Computer Vision and Pattern Recognition Genomics
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

PanFoMa: A Lightweight Foundation Model and Benchmark for Pan-Cancer
by: Huang, Xiaoshui, et al.
Published: (2025)

ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics
by: Lin, Yuxiang, et al.
Published: (2024)

CellMaster: Collaborative Cell Type Annotation in Single-Cell Analysis
by: Wang, Zhen, et al.
Published: (2026)

CausalGeD: Blending Causality and Diffusion for Spatial Gene Expression Generation
by: Sadia, Rabeya Tus, et al.
Published: (2025)

Towards Unified Molecule-Enhanced Pathology Image Representation Learning via Integrating Spatial Transcriptomics
by: Han, Minghao, et al.
Published: (2024)

RECODE: Reasoning Through Code Generation for Visual Question Answering
by: Shen, Junhong, et al.
Published: (2025)

Deep Pathomic Learning Defines Prognostic Subtypes and Molecular Drivers in Colorectal Cancer
by: Wang, Zisong, et al.
Published: (2025)

Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching
by: Huang, Tinglin, et al.
Published: (2025)

Deep Neural Network: An Efficient and Optimized Machine Learning Paradigm for Reducing Genome Sequencing Error
by: Kartriku, Ferdinand, et al.
Published: (2020)

A Comprehensive Review on RNA Subcellular Localization Prediction
by: Zhang, Cece, et al.
Published: (2025)

CrossLLM-Mamba: Multimodal State Space Fusion of LLMs for RNA Interaction Prediction
by: Sadia, Rabeya Tus, et al.
Published: (2026)

Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction
by: Jaume, Guillaume, et al.
Published: (2023)

Leveraging State Space Models in Long Range Genomics
by: Popov, Matvei, et al.
Published: (2025)

Evaluating Deep Regression Models for WSI-Based Gene-Expression Prediction
by: Gustafsson, Fredrik K., et al.
Published: (2024)

QuST-LLM: Integrating Large Language Models for Comprehensive Spatial Transcriptomics Analysis
by: Huang, Chao Hui
Published: (2024)

Advancing Gene Selection in Oncology: A Fusion of Deep Learning and Sparsity for Precision Gene Selection
by: Krishna, Akhila, et al.
Published: (2024)

Beyond Conditional Computation: Retrieval-Augmented Genomic Foundation Models with Gengram
by: Xu, Huinan, et al.
Published: (2026)

DINOv3 Beats Specialized Detectors: A Simple Foundation Model Baseline for Image Forensics
by: Yu, Jieming, et al.
Published: (2026)

Auxiliary Gene Learning: Spatial Gene Expression Estimation by Auxiliary Gene Selection
by: Shiku, Kaito, et al.
Published: (2025)

A Deep Learning Pipeline for Epilepsy Genomic Analysis Using GPT-2 XL and NVIDIA H100
by: Latif, Muhammad Omer, et al.
Published: (2025)

Path-GPTOmic: A Balanced Multi-modal Learning Framework for Survival Outcome Prediction
by: Wang, Hongxiao, et al.
Published: (2024)

Explainable AI model reveals disease-related mechanisms in single-cell RNA-seq data
by: Usman, Mohammad, et al.
Published: (2025)

A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics
by: Gindra, Rushin H., et al.
Published: (2025)

Multi-omics Prediction from High-content Cellular Imaging with Deep Learning
by: Mehrizi, Rahil, et al.
Published: (2023)

Where Does My Model Underperform? A Human Evaluation of Slice Discovery Algorithms
by: Johnson, Nari, et al.
Published: (2023)

Learning to Relax: Setting Solver Parameters Across a Sequence of Linear System Instances
by: Khodak, Mikhail, et al.
Published: (2023)

ARFBench: Benchmarking Time Series Question Answering Ability for Software Incident Response
by: Xie, Stephan, et al.
Published: (2026)

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures
by: Larey, Ariel, et al.
Published: (2026)

PathoGen-X: A Cross-Modal Genomic Feature Trans-Align Network for Enhanced Survival Prediction from Histopathology Images
by: Krishna, Akhila, et al.
Published: (2024)

GestaltMML: Enhancing Rare Genetic Disease Diagnosis through Multimodal Machine Learning Combining Facial Images and Clinical Texts
by: Wu, Da, et al.
Published: (2023)

Is your data alignable? Principled and interpretable alignability testing and integration of single-cell data
by: Ma, Rong, et al.
Published: (2023)

NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction
by: Li, Zhongmin, et al.
Published: (2025)

UPS: Efficiently Building Foundation Models for PDE Solving via Cross-Modal Adaptation
by: Shen, Junhong, et al.
Published: (2024)

Multimodal Modeling of CRISPR-Cas12 Activity Using Foundation Models and Chromatin Accessibility Data
by: Amirabad, Azim Dehghani, et al.
Published: (2025)

A Hard-to-Beat Baseline for Training-free CLIP-based Adaptation
by: Wang, Zhengbo, et al.
Published: (2024)

EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations
by: Lin, Zekai, et al.
Published: (2025)

Are you Struggling? Dataset and Baselines for Struggle Determination in Assembly Videos
by: Feng, Shijia, et al.
Published: (2024)

FastImpute: A Baseline for Open-source, Reference-Free Genotype Imputation Methods -- A Case Study in PRS313
by: Ge, Aaron, et al.
Published: (2024)

Sparse Beats Dense: Rethinking Supervision in Radar-Camera Depth Completion
by: Li, Huadong, et al.
Published: (2023)