A graph-grammar cheminformatics workflow expands the carbon fixation reaction network, then uses integer linear programming flow queries to surface short autocatalytic pathways producing Acetyl-CoA and Malate with efficiencies approaching the CETCH cycle.
LSTNet is a deep learning framework for multivariate time series forecasting that uses convolutional layers for local dependencies, a recurrent-skip component for periodic long-term patterns, and an autoregressive component for scale robustness.
An updated description of nauty and introduction of Traces, two programs for graph isomorphism testing and canonical labeling using the individualization-refinement paradigm.
Surge is a constitutional isomer generator based on the canonical generation path method, using nauty for graph automorphism computation. Its three-stage pipeline (simple graph generation, vertex coloring for atom assignment, edge multiplicity for bond orders) generates 7-22 million molecules per second, outperforming MOLGEN 5.0 by 42-161x on natural product molecular formulas.
Lagrangian Neural Networks (LNNs) use neural networks to parameterize arbitrary Lagrangians, enabling energy-conserving learned dynamics without canonical coordinates. Unlike Hamiltonian approaches, LNNs handle relativistic systems and extend to graphs via Lagrangian Graph Networks.
Liquid-S4 extends the S4 framework by incorporating a linearized liquid time-constant formulation that introduces input-dependent state transitions. This yields an additional convolutional kernel capturing input correlations, improving generalization across long-range sequence tasks.
A graph-based genetic algorithm (GB-GA) and a graph-based generative model with Monte Carlo tree search (GB-GM-MCTS) for molecular optimization that match or outperform ML-based generative approaches while being orders of magnitude faster.
STONED introduces simple string manipulation algorithms on SELFIES for molecular design, achieving competitive results with deep generative models while requiring no training data or GPU resources.
This position paper demonstrates that genetic algorithms (GAs) perform surprisingly well on molecular generation benchmarks, often outperforming complex deep learning methods. The authors propose the GA criterion: new molecule generation algorithms should demonstrate a clear advantage over GAs.
A differentiable point-set alignment library implementing N-dimensional Kabsch, Horn quaternion, and Umeyama scaling algorithms with per-point weights, batch dimensions, and custom autograd across NumPy, PyTorch, JAX, TensorFlow, and MLX.
Presents a concise SVD-based algorithm for finding the optimal rotation and translation between two 3D point sets, with analysis of the degenerate reflection case that Umeyama later corrected.
The matrix-based companion to Horn’s 1987 quaternion method, deriving the optimal rotation as the orthonormal factor in the polar decomposition of the cross-covariance matrix via eigendecomposition of a 3x3 symmetric matrix.