The paper introduces a learning algorithm for threshold Boolean networks (TBNs) that can infer networks with a specified set of fixed points. The method uses a custom differentiable loss function to enforce fixed point preservation, penalize spurious attractors, encourage binary outputs, and promote sparsity via L1 regularization. When applied to the FOS-GRN model of Arabidopsis thaliana, the algorithm perfectly reconstructed all 10 desired fixed points in 5 of 30 runs and on average recovered 8.53 ± 0.90 correct fixed points without any spurious attractors, outperforming standard approaches such as the Perceptron and Logistic Regression.
By Gonzalo A. Ruz
arXiv:2606. 19623v1 Announce Type: new Abstract: Graph neural networks (GNNs) provide a flexible framework for learning from scientific data linked through physical, biological, or functional relationships.
By Antriksh Srivastava, Soumyashree Kar
arXiv:2607. 19426v1 Announce Type: cross Abstract: Single-cell datasets are increasingly costly to store, audit, and reuse for model training.
By Yaodi Luo, Peize He, Bowen Han, Lingbei Mengg
arXiv:2607. 07425v1 Announce Type: cross Abstract: Many biological processes are governed by complex dynamical mechanisms that remain incompletely understood despite increasing volumes of experimental data.
By Rebecca M. Crossley, Yuan Yin, Sarah L. Waters, Ruth E. Baker
arXiv:2606. 23880v1 Announce Type: new Abstract: From climate teleconnections to gene regulation, modern time-series datasets encompass tens or hundreds of interacting variables, making causal discovery increasingly challenging.
By Mohammad Fesanghary, Abhinav Havaldar
arXiv:2608. 06824v1 Announce Type: cross Abstract: A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships.
By Quanquan Li, Yihe Chi, Liuyang Song, Hongbo Zhang, Jingyu Li, Xidong Xi, Conghua Wei, Yijie Sun, Yu Chen, Xin Liu, Qi Hu, Jing Ke, Guitao Cao