6 Papers

LGMar 9, 2024
PR-NET: Leveraging Pathway Refined Network Structures for Prostate Cancer Patient Condition Prediction

R. Li, J. Liu, X. L. Deng et al.

The diagnosis and monitoring of Castrate Resistant Prostate Cancer (CRPC) are crucial for cancer patients, but the current models (such as P-NET) have limitations in terms of parameter count, generalization, and cost. To address the issue, we develop a more accurate and efficient Prostate Cancer patient condition prediction model, named PR-NET. By compressing and optimizing the network structure of P-NET, the model complexity is reduced while maintaining high accuracy and interpretability. The PR-NET demonstrated superior performance in predicting prostate cancer patient outcomes, outshining P-NET and six other traditional models with a significant margin. In our rigorous evaluation, PR-NET not only achieved impressive average AUC and Recall scores of 0.94 and 0.83, respectively, on known data but also maintained robust generalizability on five unknown datasets with a higher average AUC of 0.73 and Recall of 0.72, compared to P-NET's 0.68 and 0.5. PR-NET's efficiency was evidenced by its shorter average training and inference times, and its gene-level analysis revealed 46 key genes, demonstrating its enhanced predictive power and efficiency in identifying critical biomarkers for prostate cancer. Future research can further expand its application domains and optimize the model's performance and reliability.

LGJul 6, 2021
DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations

J. Wang, X. Liu, S. Shen et al.

Drug combination therapy has become a increasingly promising method in the treatment of cancer. However, the number of possible drug combinations is so huge that it is hard to screen synergistic drug combinations through wet-lab experiments. Therefore, computational screening has become an important way to prioritize drug combinations. Graph neural network have recently shown remarkable performance in the prediction of compound-protein interactions, but it has not been applied to the screening of drug combinations. In this paper, we proposed a deep learning model based on graph neural networks and attention mechanism to identify drug combinations that can effectively inhibit the viability of specific cancer cells. The feature embeddings of drug molecule structure and gene expression profiles were taken as input to multi-layer feedforward neural network to identify the synergistic drug combinations. We compared DeepDDS with classical machine learning methods and other deep learning-based methods on benchmark data set, and the leave-one-out experimental results showed that DeepDDS achieved better performance than competitive methods. Also, on an independent test set released by well-known pharmaceutical enterprise AstraZeneca, DeepDDS was superior to competitive methods by more than 16\% predictive precision. Furthermore, we explored the interpretability of the graph attention network, and found the correlation matrix of atomic features revealed important chemical substructures of drugs. We believed that DeepDDS is an effective tool that prioritized synergistic drug combinations for further wet-lab experiment validation.

CRDec 11, 2020
FLEAM: A Federated Learning Empowered Architecture to Mitigate DDoS in Industrial IoT

J. Li, L. Lyu, X. Liu et al.

The distributed denial of service (DDoS) attack is detrimental to the industrial Internet of things (IIoT) as it triggers severe resource starvation on networked objects. Recent dynamics demonstrate that it is a highly profitable business for attackers using botnets. Current centralized mitigation solutions concentrate on detection and mitigation at a victim's side, paying inadequate attention to hacking costs and the collaboration of defenders. Thus, we propose the federated learning empowered mitigation architecture (FLEAM) to advocate joint defense, incurring a higher hacking expense. FLEAM combines FL and fog computing to reduce mitigation time and improve detection accuracy, enabling defenders to jointly combatting botnets. Our comprehensive evaluations showcase that the attacking expense incurred is 2.5 times higher, the mitigation delay is about 72% lower, and the accuracy is 47% greater on average than classic solutions.

CYSep 18, 2020
Making Sense of the Robotized Pandemic Response: A Comparison of Global and Canadian Robot Deployments and Success Factors

T. Barfoot, J. Burgner-Kahrs, E. Diller et al.

From disinfection and remote triage, to logistics and delivery, countries around the world are making use of robots to address the unique challenges presented by the COVID-19 pandemic. Robots are being used to manage the pandemic in Canada too, but relative to other regions, we have been more cautious in our adoption -- this despite the important role that robots of Canadian origin are now playing on the global stage. This white paper discusses why this is the case, and argues that strategic investment and support for the Canadian robotics industry are urgently needed to bring the benefits of robotics home, where we have more control in shaping the future of this game-changing technology. Such investments will not only serve to support Canada's current pandemic response and post pandemic recovery, but will also prepare this country to weather future crises. Without such support, Canada risks falling behind other developed nations that are investing heavily in hardware automation at this time.

HCMay 4, 2020
Building Proactive Voice Assistants: When and How (not) to Interact

O. Miksik, I. Munasinghe, J. Asensio-Cubero et al.

Voice assistants have recently achieved remarkable commercial success. However, the current generation of these devices is typically capable of only reactive interactions. In other words, interactions have to be initiated by the user, which somewhat limits their usability and user experience. We propose, that the next generation of such devices should be able to proactively provide the right information in the right way at the right time, without being prompted by the user. However, achieving this is not straightforward, since there is the danger it could interrupt what the user is doing too much, resulting in it being distracting or even annoying. Furthermore, it could unwittingly, reveal sensitive/private information to third parties. In this report, we discuss the challenges of developing proactively initiated interactions, and suggest a framework for when it is appropriate for the device to intervene. To validate our design assumptions, we describe firstly, how we built a functioning prototype and secondly, a user study that was conducted to assess users' reactions and reflections when in the presence of a proactive voice assistant. This pre-print summarises the state, ideas and progress towards a proactive device as of autumn 2018.

ITFeb 3, 2017
Robust Phase Retrieval via ADMM with Outliers

Xue Jiang, H. C. So, X. Liu

An outlier-resistance phase retrieval algorithm based on alternating direction method of multipliers (ADMM) is devised in this letter. Instead of the widely used least squares criterion that is only optimal for Gaussian noise environment, we adopt the least absolute deviation criterion to enhance the robustness against outliers. Considering both intensity- and amplitude-based observation models, the framework of ADMM is developed to solve the resulting non-differentiable optimization problems. It is demonstrated that the core subproblem of ADMM is the proximity operator of the L1-norm, which can be computed efficiently by soft-thresholding in each iteration. Simulation results are provided to validate the accuracy and efficiency of the proposed approach compared to the existing schemes.