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Shasha Lu

Publications and source records attributed to Shasha Lu.

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TARE: Tail Aware Evaluation of HPC Job Runtime Prediction

Runtime estimates affect reservation quality, backfilling opportunities, and queue delay in HPC schedulers. Under heavy tailed workloads, however, averaging over jobs can misrepresent scheduling impact because a small fraction of jobs dominates resource usage. This paper presents an empirical evaluation methodology for HPC job runtime prediction that focuses on the tail, combining GeoAccuracy weighted by resource usage with decile and split analyses. Using production traces from NREL Eagle and ALCF Mira/Intrepid, we compare XGBoost and Last2 against the user provided walltime estimate at submission (UserReq). Across all three datasets, evaluation focused on the tail changes the offline conclusion: MeanAccuracy keeps the methods relatively close, whereas GeoAccuracy reveals clearer separation and makes UserReq's strength in the upper tail visible. In the top decile, UserReq achieves the highest GeoAccuracy and lowest underestimation rate on all three datasets, and this pattern remains stable across rolling splits. We then translate this signal into a simple hybrid scheduling policy that keeps XGBoost for most jobs and routes the top decile by proxy_cost at submission to UserReq. Online replay on four production queues reduces mean wait time by up to 8% and increases backfilled jobs by 50% to 115%. These results show that offline evaluation focused on the tail better characterizes prediction quality relevant to scheduling and informs scheduling policy design.

cs.DC

In silico bioactivity prediction of proteins interacting with graphene-based nanomaterials guides rational design of biosensor

Graphene based nanomaterials have attracted significant attention for their potentials in biomedical and biotechnology applications in recent years, owing to the outstanding physical and chemical properties. However, the interaction mechanism and impact on biological activity of macro and micro biomolecules still require more concerns and further research in order to enhance their applicability in biosensors, etc. Herein, an integrated method has been developed to predict the protein bioactivity performance when interacting with nanomaterials for protein based biosensor. Molecular dynamics simulation and molecular docking technique were consolidated to investigate several nanomaterials C60 fullerene, single walled carbon nanotube, pristine graphene and graphene oxide, and their effect when interacting with protein. The adsorption behavior, secondary structure changes and protein bioactivity changes were simulated, and the results of protein activity simulation were verified in combination with atomic force spectrum, circular dichroism spectrum fluorescence and electrochemical experiments. The best quantification alignment between bioactivity obtained by simulation and experiment measurements was further explored. The two proteins, RNase A and Exonuclease III, were regarded as analysis model for the proof of concept, and the prediction accuracy of protein bioactivty could reach up to 0.98.

q-bio.BM