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Publications
Toward Debugging Deep Reinforcement Learning Programs with RLExplorer
Deep reinforcement learning (DRL) has shown success in diverse domains such as robotics, computer games, and recommendation systems. However… (see more), like any other software system, DRL-based software systems are susceptible to faults that pose unique challenges for debugging and diagnosing. These faults often result in unexpected behavior without explicit failures and error messages, making debugging difficult and time-consuming. Therefore, automating the monitoring and diagnosis of DRL systems is crucial to alleviate the burden on developers. In this paper, we propose RLExplorer, the first fault diagnosis approach for DRL-based software systems. RLExplorer automatically monitors training traces and runs diagnosis routines based on properties of the DRL learning dynamics to detect the occurrence of DRL-specific faults. It then logs the results of these diagnoses as warnings that cover theoretical concepts, recommended practices, and potential solutions to the identified faults. We conducted two sets of evaluations to assess RLExplorer. Our first evaluation of faulty DRL samples from Stack Overflow revealed that our approach can effectively diagnose real faults in 83% of the cases. Our second evaluation of RLExplorer with 15 DRL experts/developers showed that (1) RLExplorer could identify 3.6 times more defects than manual debugging and (2) RLExplorer is easily integrated into DRL applications.
Deep reinforcement learning (DRL) has shown success in diverse domains such as robotics, computer games, and recommendation systems. However… (see more), like any other software system, DRL-based software systems are susceptible to faults that pose unique challenges for debugging and diagnosing. These faults often result in unexpected behavior without explicit failures and error messages, making debugging difficult and time-consuming. Therefore, automating the monitoring and diagnosis of DRL systems is crucial to alleviate the burden on developers. In this paper, we propose RLExplorer, the first fault diagnosis approach for DRL-based software systems. RLExplorer automatically monitors training traces and runs diagnosis routines based on properties of the DRL learning dynamics to detect the occurrence of DRL-specific faults. It then logs the results of these diagnoses as warnings that cover theoretical concepts, recommended practices, and potential solutions to the identified faults. We conducted two sets of evaluations to assess RLExplorer. Our first evaluation of faulty DRL samples from Stack Overflow revealed that our approach can effectively diagnose real faults in 83% of the cases. Our second evaluation of RLExplorer with 15 DRL experts/developers showed that (1) RLExplorer could identify 3.6 times more defects than manual debugging and (2) RLExplorer is easily integrated into DRL applications.
2024-10-06
2024 IEEE International Conference on Software Maintenance and Evolution (ICSME) (published)
The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for… (see more) biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods.
The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for… (see more) biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods.
Personalized medicine based on medical images, including predicting future individualized clinical disease progression and treatment respons… (see more)e, would have an enormous impact on healthcare and drug development, particularly for diseases (e.g. multiple sclerosis (MS)) with long term, complex, heterogeneous evolutions and no cure. In this work, we present the first stochastic causal temporal framework to model the continuous temporal evolution of disease progression via Neural Stochastic Differential Equations (NSDE). The proposed causal inference model takes as input the patient's high dimensional images (MRI) and tabular data, and predicts both factual and counterfactual progression trajectories on different treatments in latent space. The NSDE permits the estimation of high-confidence personalized trajectories and treatment effects. Extensive experiments were performed on a large, multi-centre, proprietary dataset of patient 3D MRI and clinical data acquired during several randomized clinical trials for MS treatments. Our results present the first successful uncertainty-based causal Deep Learning (DL) model to: (a) accurately predict future patient MS disability evolution (e.g. EDSS) and treatment effects leveraging baseline MRI, and (b) permit the discovery of subgroups of patients for which the model has high confidence in their response to treatment even in clinical trials which did not reach their clinical endpoints.
Efficiently quantifying predictive uncertainty in medical images remains a challenge. While Bayesian neural networks (BNN) offer predictive … (see more)uncertainty, they require substantial computational resources to train. Although Bayesian approximations such as ensembles have shown promise, they still suffer from high training and inference costs. Existing approaches mainly address the costs of BNN inference post-training, with little focus on improving training efficiency and reducing parameter complexity. This study introduces a training procedure for a sparse (partial) Bayesian network. Our method selectively assigns a subset of parameters as Bayesian by assessing their deterministic saliency through gradient sensitivity analysis. The resulting network combines deterministic and Bayesian parameters, exploiting the advantages of both representations to achieve high task-specific performance and minimize predictive uncertainty. Demonstrated on multi-label ChestMNIST for classification and ISIC, LIDC-IDRI for segmentation, our approach achieves competitive performance and predictive uncertainty estimation by reducing Bayesian parameters by over 95\%, significantly reducing computational expenses compared to fully Bayesian and ensemble methods.
MiRGraph: A hybrid deep learning approach to identify microRNA-target interactions by integrating heterogeneous regulatory network and genomic sequences
MicroRNAs (miRNAs) mediates gene expression regulation by targeting specific messenger RNAs (mRNAs) in the cytoplasm. They can function as b… (see more)oth tumor suppressors and oncogenes depending on the specific miRNA and its target genes. Detecting miRNA-target interactions (MTIs) is critical for unraveling the complex mechanisms of gene regulation and promising towards RNA therapy for cancer. There is currently a lack of MTIs prediction methods that simultaneously perform feature learning from heterogeneous gene regulatory network (GRN) and genomic sequences. To improve the prediction performance of MTIs, we present a novel transformer-based multiview feature learning method – MiRGraph, which consists of two main modules for learning the sequence-based and GRN-based feature embedding. For the former, we utilize the mature miRNA sequences and the complete 3’UTR sequence of the target mRNAs to encode sequence features using a hybrid transformer and convolutional neural network (CNN) (TransCNN) architecture. For the latter, we utilize a heterogeneous graph transformer (HGT) module to extract the relational and structural information from the GRN consisting of miRNA-miRNA, gene-gene and miRNA-target interactions. The TransCNN and HGT modules can be learned end-to-end to predict experimentally validated MTIs from MiRTarBase. MiRGraph outperforms existing methods in not only recapitulating the true MTIs but also in predicting strength of the MTIs based on the in-vitro measurements of miRNA transfections. In a case study on breast cancer, we identified plausible target genes of an oncomir.
