Haonan Zhu

Hao-Nan Zhu, Goodness Ayinmode, Cesar A. Stuardo et al.

Scalable distributed systems form the backbone of modern computing infrastructure. However, as scale grows, system complexity may lead to scalability faults. Scalability faults are challenging to uncover and diagnose, as they are often latent and only manifest at large-scale deployment. In this paper, we present the first comprehensive study on scalability faults and propose an approach for their detection. First, we systematically investigate 444 scalability issue reports from 10 large-scale distributed systems to understand the common anti-patterns and root causes of scalability faults. We found that the majority of these faults are caused by the synergy between dimensional code fragments and anti-patterns associated with them. Second, based on our findings, we design and implement ScaleLens, a novel approach to detect scalability faults. ScaleLens combines dynamic and static analyses to pinpoint dimensional code fragments and match them with anti-patterns. Our evaluation shows that ScaleLens detects 4.2x more dimensional code fragments associated with known scalability faults compared to the baseline. On the latest stable versions of Cassandra, HDFS, and Ignite, ScaleLens detects 334 dimensional code fragments with confirmed problematic behavior.

Haonan Zhu, Andre R. Goncalves, Camilo Valdes et al.

This paper proposes a hierarchical Bayesian multitask learning model that is applicable to the general multi-task binary classification learning problem where the model assumes a shared sparsity structure across different tasks. We derive a computationally efficient inference algorithm based on variational inference to approximate the posterior distribution. We demonstrate the potential of the new approach on various synthetic datasets and for predicting human health status based on microbiome profile. Our analysis incorporates data pooled from multiple microbiome studies, along with a comprehensive comparison with other benchmark methods. Results in synthetic datasets show that the proposed approach has superior support recovery property when the underlying regression coefficients share a common sparsity structure across different tasks. Our experiments on microbiome classification demonstrate the utility of the method in extracting informative taxa while providing well-calibrated predictions with uncertainty quantification and achieving competitive performance in terms of prediction metrics. Notably, despite the heterogeneity of the pooled datasets (e.g., different experimental objectives, laboratory setups, sequencing equipment, patient demographics), our method delivers robust results.

Haonan Zhu, Mary Silva, Jose Cadena et al.

Recent technological advances have introduced new high-throughput methods for studying host-virus interactions, but testing synergistic interactions between host gene pairs during infection remains relatively slow and labor intensive. Identification of multiple gene knockdowns that effectively inhibit viral replication requires a search over the combinatorial space of all possible target gene pairs and is infeasible via brute-force experiments. Although active learning methods for sequential experimental design have shown promise, existing approaches have generally been restricted to single-gene knockdowns or small-scale double knockdown datasets. In this study, we present an integrated Deep Active Learning (DeepAL) framework that incorporates information from a biological knowledge graph (SPOKE, the Scalable Precision Medicine Open Knowledge Engine) to efficiently search the configuration space of a large dataset of all pairwise knockdowns of 356 human genes in HIV infection. Through graph representation learning, the framework is able to generate task-specific representations of genes while also balancing the exploration-exploitation trade-off to pinpoint highly effective double-knockdown pairs. We additionally present an ensemble method for uncertainty quantification and an interpretation of the gene pairs selected by our algorithm via pathway analysis. To our knowledge, this is the first work to show promising results on double-gene knockdown experimental data of appreciable scale (356 by 356 matrix).