arXiv AI
Human mutation field reveals an equilibrium-like structure with irreversible circulation
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arXiv Machine Learning
Aug 4
Evolutionary Curriculum Learning Improves Biological Sequence Modeling
arXiv:2608. 00697v1 Announce Type: cross Abstract: Variational autoencoders (VAEs) trained on multiple sequence alignments (MSAs) have emerged as powerful generative models for biological sequences, with applications ranging from disease variant prediction to functional RNA design.
arXiv Machine Learning
Jul 9
Trajectory Inference of Human Aging from Cross-Sectional DNA Methylation Data
arXiv:2607. 06583v1 Announce Type: cross Abstract: DNA methylation (DNAm) serves as one of the most robust molecular biomarkers of biological aging.
arXiv Machine Learning
Sep 7
When Genomic Masking Priors Fail to Transfer: Strong Variant Prediction, Weak Functional Generation
The paper introduces GenDA, a bidirectional discrete diffusion model designed for genomic sequence reconstruction, hypothesizing that entropy-guided span placement would improve variant-effect prediction and functional sequence generation. While the 202‑million‑parameter GenDA model achieves a higher ClinVar SNV AUROC (0.774) than a comparable autoregressive model, the improvement is not attributable to entropy guidance, and the model fails to outperform a shuffled‑gap baseline in zero‑shot functional inpainting across various genomic regions. The authors identify limitations such as tokenization granularity, span length caps, and the mismatch between local sequence complexity and functional importance, concluding that variant prediction, corruption priors, and functional generation are distinct tasks requiring separate validation.
arXiv Machine Learning
Jun 26
Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention
arXiv:2603. 14717v2 Announce Type: replace Abstract: Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples.
arXiv Machine Learning
Sep 1
Reproducible macroscopic dynamics in a closed-loop human-AI learning system
arXiv:2608.30946v1 Announce Type: new Abstract: Closed-loop human-AI systems generate high-dimensional behavioural trajectories whose collective dynamics remain obscure. Using 297,915 learners' adapt...
arXiv Machine Learning
Aug 27
Beyond Tokens: Probing Higher-Order Epistasis in Learned Protein Representations
The paper introduces ORBIT, a framework for probing higher‑order epistasis in protein representations. ORBIT validates Walsh‑based diagnostics on synthetic landscapes, then applies them to the GB1 fitness landscape, comparing several models including ridge regression, MLPs, and Residual Interaction Tokenization (RIT). While no architecture differences were found in overall prediction performance, RIT notably increased pairwise token‑level accessibility, and deeper MLPs improved higher‑order functional recovery, revealing representation‑level changes hidden by conventional metrics.