arXiv:2602. 17162v3 Announce Type: replace Abstract: Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature".
arXiv:2511. 09026v2 Announce Type: replace-cross Abstract: Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood.
The paper introduces a comprehensive privacy evaluation framework for genomic language models (GLMs) that quantifies memorization risks using perplexity-based detection, canary sequence extraction, and membership inference. By planting canary sequences at different repetition rates in synthetic and real datasets, the authors systematically assess how repetition, model capacity, and training dynamics affect memorization across various GLM architectures. The study demonstrates that GLMs do memorize training data to varying degrees and that no single attack method fully captures this risk, highlighting the necessity of multi-vector privacy auditing for genomic AI systems.
arXiv:2606. 08945v1 Announce Type: new Abstract: We investigate whether information about time-to-event risk estimated by a Cox proportional hazards model can be transferred into a generative large language model.
The article presents a new semantic model for representing scientific evidence, specifically tailored to genetics, that extends existing standards by adding fine‑grained, domain‑specific structure. It aligns with FHIR Evidence and SEPIO, incorporates a compact vocabulary validated by SHACL, and was tested in a human‑AI annotation pilot on six genetics papers, producing 28 evidence items and 95 source‑anchored assertions. The authors argue that this model advances trustworthy, AI‑ready infrastructure for variant interpretation by providing a reference data model and validation schema for genetic evidence.
arXiv:2608. 00935v1 Announce Type: new Abstract: Electronic Health Records (EHRs) are widely used for clinical risk prediction using machine learning.
arXiv:2604. 04287v2 Announce Type: replace Abstract: Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing.
The paper introduces the General Demographic Pre-trained (GDP) model, a lightweight foundation model that learns representations from the two most common clinical attributes—age and sex. By optimizing encoding and visit‑reordering strategies, GDP embeddings are shown to improve predictive performance when concatenated with raw features across various disease and geographic cohorts. The model outperforms several state‑of‑the‑art tabular foundation models and tree‑based algorithms, demonstrating that enriched demographic embeddings can enhance classification tasks while remaining fully compatible with standard classifiers.
arXiv:2607. 05306v1 Announce Type: new Abstract: Integrating complex, multi-omics data presents significant challenges.
arXiv:2608.24688v1 Announce Type: new Abstract: Precision oncology necessitates a longitudinal model of patient state that captures cancer evolution and treatment over time, integrating multimodal ob...
We investigate whether information about time-to-event risk estimated by a Cox proportional hazards model can be transferred into a generative large language model. We propose a text-based survival modelling pipeline in which structured clinical covariates are converted into text prompts and a Qwen-based large language model is fine-tuned to generate patient-specific survival risk using Cox model predictions as a training target.
arXiv:2506. 10912v4 Announce Type: replace Abstract: Toxicity remains a leading cause of early-stage drug development failure.