SearcharxivSearch

arXiv subjects

Ka-Lok Ng

Publications and source records attributed to Ka-Lok Ng.

2 recordsLinked to original sources

Scalable Quantum Molecular Generation via GPU-Accelerated Tensor-Network Simulation

We propose Scalable Quantum Molecular Generation (SQMG), a variational quantum-circuit for sampling molecular graphs using chemical priors on atoms and bonds. SQMG assigns a fixed 3-qubit register to each heavy atom and reuses a single 2-qubit bond register to generate bonds sequentially, yielding an ''atom no-reuse, bond reuse'' architecture with linear qubit scaling. Measurement results are mapped to molecular graphs via lightweight classical decoding with structural constraints. In CUDA-Q, we benchmark the state-vector simulation (CPU/GPU) and the tensor-network simulation (GPU). At $N=8$ heavy atoms, the state-vector simulator (GPU) and the tensor-network simulator (GPU) achieve speeds of up to $4.5\times 10^{4}$ and $2.2\times 10^{3}$ over the state-vector (CPU) baseline, respectively. Crucially, tensor-network simulation extends exact simulation to $N=40$ heavy atoms, where state-vector methods become memory-limited. For training, Bayesian optimization outperforms COBYLA on a Validity$\times$Uniqueness objective, and the same architecture supports \textit{de novo} generation, scaffold decoration, and linker design. Overall, SQMG provides a scalable, reproducible testbed for evaluating accelerated tensor-network simulation and future quantum molecular generation algorithms.

quant-ph

Global Topological Study of the Protein-protein Interaction Networks

We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global topological parameters (such as node connectivity, average diameter, node connectivity correlation) were used to characterize these protein-protein interaction networks (PINs). The logarithm of the connectivity distribution vs. the logarithm of connectivity study indicated that PINs follow a power law (P(k) ~ k-γ) behavior. Using the regression analysis method we determined that γlies between 1.5 and 2.4, for the seven species. Correlation analysis provides good evidence supporting the fact that the seven PINs form a scale-free network. The average diameters of the networks and their randomized version are found to have large difference. We also demonstrated that the interaction networks are quite robust when subject to random perturbation. Average node connectivity correlation study supports the earlier results that nodes of low connectivity are correlated, whereas nodes of high connectivity are not directly linked. These results provided some evidence suggesting such correlation relations might be a general feature of the PINs across different species.

q-bio.MN