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Advancing Nuclei Detection in Drug Discovery: A Hybrid CNN+LSTM Approach with Curved Gaussian Distribution

Published: 13 May 2024 Publication History

Abstract

In the field of drug discovery, the automated detection and analysis of cell nuclei within biological images play a pivotal role in understanding cellular responses to potential drug compounds. Leveraging the capabilities of DL techniques, this research presents a novel hybrid approach for nuclei detection, combining Convolutional Neural Networks (CNNs) with Long Short-Term Memory (LSTM) networks, enhanced by a curved Gaussian distribution model. The objective is to achieve accurate and efficient nuclei detection to facilitate drug discovery processes. Utilizing the Broad Bioimage Benchmark Collection (BBBC) datasets, this study proposes a multi-stage detection pipeline. In the initial stage, a CNN is employed to capture intricate spatial features within the images, enabling the precise localization of nuclei. Subsequently, an LSTM network is introduced to exploit temporal dependencies in time-lapse microscopy images, aiding in tracking nuclei across consecutive frames. To further improve detection accuracy, a curved Gaussian distribution model is integrated to refine the predictions, considering the inherent curvature of nuclei boundaries. The proposed hybrid approach demonstrates exceptional performance, achieving an impressive accuracy of 98.87% on BBBC datasets. The combination of CNN and LSTM networks capitalizes on the complementary strengths of both architectures, resulting in accurate detection and tracking of nuclei over time. The incorporation of the curved Gaussian distribution model enhances the precision of localization, particularly at challenging boundaries. These results underscore the potential of DL techniques for nuclei detection in drug discovery and contribute to advancing the understanding of cellular dynamics under the influence of various drug compounds. This research not only provides a robust solution for nuclei detection but also paves the way for further innovations in automating cellular analysis within drug discovery pipelines. The hybrid approach's high accuracy and adaptability to diverse biological imaging scenarios underscore its potential to accelerate drug development processes and streamline the identification of potential therapeutic candidates.

References

[1]
S. Nag, “Deep learning tools for advancing drug discovery and development,” 3 Biotech, vol. 12, no. 5, pp. 1–21, 2022.
[2]
Y. Jing, Y. Bian, Z. Hu, L. Wang, and X. Q. S. Xie, “Deep Learning for Drug Design: an Artificial Intelligence Paradigm for Drug Discovery in the Big Data Era,” AAPS J., vol. 20, no. 3, pp. 1–10, 2018.
[3]
H. Kim, E. Kim, I. Lee, B. Bae, M. Park, and H. Nam, “Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches,” Biotechnol. Bioprocess Eng., vol. 25, no. 6, pp. 895–930, 2020.
[4]
V. Khetani, Y. Gandhi, S. Bhattacharya, S. N. Ajani, and S. Limkar, “INTELLIGENT SYSTEMS AND APPLICATIONS IN ENGINEERING Cross-Domain Analysis of ML and DL: Evaluating their Impact in Diverse Domains,” vol. 11, pp. 253–262, 2023.
[5]
R. Finally, “Predicting Multi-Class Nuclei Phenotypes for Drug Testing Using Deep Learning.”
[6]
R. B. Tokime, H. Elassady, and M. A. Akhloufi, “Identifying the cells’ nuclei using deep learning,” 2018 IEEE Life Sci. Conf. LSC 2018, pp. 61–64, 2018.
[7]
S. S. Alahmari, D. Goldgof, L. O. Hall, and P. R. Mouton, “A Review of Nuclei Detection and Segmentation on Microscopy Images Using Deep Learning With Applications to Unbiased Stereology Counting,” IEEE Trans. Neural Networks Learn. Syst., vol. PP, pp. 1–20, 2022.
[8]
C. Bendtsen, A. Degasperi, E. Ahlberg, and L. Carlsson, “Improving machine learning in early drug discovery,” Ann. Math. Artif. Intell., vol. 81, no. 1–2, pp. 155–166, 2017.
[9]
H. Askr, E. Elgeldawi, H. Aboul Ella, Y. A. M. M. Elshaier, M. M. Gomaa, and A. E. Hassanien, Deep learning in drug discovery: an integrative review and future challenges, vol. 56, no. 7. Springer Netherlands, 2023.
[10]
J. Xu, “Stacked sparse autoencoder (SSAE) for nuclei detection on breast cancer histopathology images,” IEEE Trans. Med. Imaging, vol. 35, no. 1, pp. 119–130, 2016.
[11]
V. Gautam, A. Gaurav, N. Masand, V. S. Lee, and V. M. Patil, “Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system,” Mol. Divers., vol. 27, no. 2, pp. 959–985, 2023.
[12]
C. Selvaraj, I. Chandra, and S. K. Singh, “Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries,” Mol. Divers., vol. 26, no. 3, pp. 1893–1913, 2022.
[13]
M. Tofighi, T. Guo, J. K. P. Vanamala, and V. Monga, “Prior Information Guided Regularized Deep Learning for Cell Nucleus Detection,” IEEE Trans. Med. Imaging, vol. 38, no. 9, pp. 2047–2058, 2019.
[14]
P. Naylor, M. Lae, F. Reyal, and T. Walter, “Nuclei segmentation in histopathology images using deep neural networks,” Proc. - Int. Symp. Biomed. Imaging, pp. 933–936, 2017.
[15]
K. Sirinukunwattana, S. E. A. Raza, Y. W. Tsang, D. R. J. Snead, I. A. Cree, and N. M. Rajpoot, “Locality Sensitive Deep Learning for Detection and Classification of Nuclei in Routine Colon Cancer Histology Images,” IEEE Trans. Med. Imaging, vol. 35, no. 5, pp. 1196–1206, 2016.
[16]
D. Jimenez-Carretero, “Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening,” PLoS Comput. Biol., vol. 14, no. 11, pp. 1–23, 2018.
[17]
K. Chen, N. Zhang, L. Powers, and J. Roveda, “Cell nuclei detection and segmentation for computational pathology using deep learning,” Simul. Ser., vol. 51, no. 5, pp. 1–6, 2019.
[18]
N. A. Koohababni, M. Jahanifar, A. Gooya, and N. Rajpoot, Nuclei detection using mixture density networks, vol. 11046 LNCS. Springer International Publishing, 2018.
[19]
A. L. Barbieri, O. Fadare, L. Fan, H. Singh, and V. Parkash, “Challenges in communication from referring clinicians to pathologists in the electronic health record era,” J. Pathol. Inform., vol. 9, no. 1, p. 5, 2018.
[20]
J. Vamathevan, “Applications of machine learning in drug discovery and development,” Nat. Rev. Drug Discov., vol. 18, no. 6, pp. 463–477, 2019.
[21]
E. Braz and R. Lotufo, “Nuclei Detection Using Deep Learning,” pp. 1059–1063, 2017.
[22]
“Image Sets _ Broad Bioimage Benchmark Collection.” .

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ICIMMI '23: Proceedings of the 5th International Conference on Information Management & Machine Intelligence
November 2023
1215 pages
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Published: 13 May 2024

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Author Tags

  1. Curved Gaussian Distribution
  2. Deep Learning (DL)
  3. Drug Discovery
  4. Image Analysis
  5. Machine Learning (ML)
  6. Nuclei Detection

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