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Mar 13

EXAONE Path 2.5: Pathology Foundation Model with Multi-Omics Alignment

Cancer progression arises from interactions across multiple biological layers, especially beyond morphological and across molecular layers that remain invisible to image-only models. To capture this broader biological landscape, we present EXAONE Path 2.5, a pathology foundation model that jointly models histologic, genomic, epigenetic and transcriptomic modalities, producing an integrated patient representation that reflects tumor biology more comprehensively. Our approach incorporates three key components: (1) multimodal SigLIP loss enabling all-pairwise contrastive learning across heterogeneous modalities, (2) a fragment-aware rotary positional encoding (F-RoPE) module that preserves spatial structure and tissue-fragment topology in WSI, and (3) domain-specialized internal foundation models for both WSI and RNA-seq to provide biologically grounded embeddings for robust multimodal alignment. We evaluate EXAONE Path 2.5 against six leading pathology foundation models across two complementary benchmarks: an internal real-world clinical dataset and the Patho-Bench benchmark covering 80 tasks. Our framework demonstrates high data and parameter efficiency, achieving on-par performance with state-of-the-art foundation models on Patho-Bench while exhibiting the highest adaptability in the internal clinical setting. These results highlight the value of biologically informed multimodal design and underscore the potential of integrated genotype-to-phenotype modeling for next-generation precision oncology.

  • 7 authors
·
Dec 15, 2025

EXAdam: The Power of Adaptive Cross-Moments

This paper introduces EXAdam (EXtended Adam), a novel optimization algorithm that builds upon the widely-used Adam optimizer. EXAdam incorporates three key enhancements: (1) new debiasing terms for improved moment estimation, (2) a gradient-based acceleration mechanism for increased responsiveness to the current loss landscape, and (3) a dynamic step size formula that allows for continuous growth of the learning rate throughout training. These innovations work synergistically to address limitations of the original Adam algorithm, potentially offering improved convergence properties, enhanced ability to escape saddle points, and greater robustness to hyperparameter choices. I provide a theoretical analysis of EXAdam's components and their interactions, highlighting the algorithm's potential advantages in navigating complex optimization landscapes. Empirical evaluations demonstrate EXAdam's superiority over Adam, achieving 48.07% faster convergence and yielding improvements of 4.6%, 4.13%, and 2.39% in training, validation, and testing accuracies, respectively, when applied to a CNN trained on the CIFAR-10 dataset. While these results are promising, further empirical validation across diverse tasks is essential to fully gauge EXAdam's efficacy. Nevertheless, EXAdam represents a significant advancement in adaptive optimization techniques, with promising implications for a wide range of machine learning applications. This work aims to contribute to the ongoing development of more efficient, adaptive, and universally applicable optimization methods in the field of machine learning and artificial intelligence.

  • 1 authors
·
Dec 28, 2024

ExoMiner++ on TESS with Transfer Learning from Kepler: Transit Classification and Vetting Catalog for 2-min Data

We present ExoMiner++, an enhanced deep learning model that builds on the success of ExoMiner to improve transit signal classification in 2-minute TESS data. ExoMiner++ incorporates additional diagnostic inputs, including periodogram, flux trend, difference image, unfolded flux, and spacecraft attitude control data, all of which are crucial for effectively distinguishing transit signals from more challenging sources of false positives. To further enhance performance, we leverage transfer learning from high-quality labeled data from the Kepler space telescope, mitigating the impact of TESS's noisier and more ambiguous labels. ExoMiner++ achieves high accuracy across various classification and ranking metrics, significantly narrowing the search space for follow-up investigations to confirm new planets. To serve the exoplanet community, we introduce new TESS catalogs containing ExoMiner++ classifications and confidence scores for each transit signal. Among the 147,568 unlabeled TCEs, ExoMiner++ identifies 7,330 as planet candidates, with the remainder classified as false positives. These 7,330 planet candidates correspond to 1,868 existing TESS Objects of Interest (TOIs), 69 Community TESS Objects of Interest (CTOIs), and 50 newly introduced CTOIs. 1,797 out of the 2,506 TOIs previously labeled as planet candidates in ExoFOP are classified as planet candidates by ExoMiner++. This reduction in plausible candidates combined with the excellent ranking quality of ExoMiner++ allows the follow-up efforts to be focused on the most likely candidates, increasing the overall planet yield.

  • 29 authors
·
Feb 13, 2025