Mohammad Mahdi Ghassemi

Modern software systems are increasingly shifting from monolithic architectures to microservices to enhance scalability, maintainability, and deployment flexibility. Existing microservice extraction methods typically rely on hard clustering, assigning each software component to a single microservice. This approach often increases inter-service coupling and reduces intra-service cohesion. We propose Mo2oM (Monolithic to Overlapping Microservices), a framework that formulates microservice extraction as a soft clustering problem, allowing components to belong probabilistically to multiple microservices. This approach is inspired by expert-driven decompositions, where practitioners intentionally replicate certain software components across services to reduce communication overhead. Mo2oM combines deep semantic embeddings with structural dependencies extracted from methodcall graphs to capture both functional and architectural relationships. A graph neural network-based soft clustering algorithm then generates the final set of microservices. We evaluate Mo2oM on four open-source monolithic benchmarks and compare it against eight state-of-the-art baselines. Our results demonstrate that Mo2oM achieves improvements of up to 40.97% in structural modularity (balancing cohesion and coupling), 58% in inter-service call percentage (communication overhead), 26.16% in interface number (modularity and decoupling), and 38.96% in non-extreme distribution (service size balance) across all benchmarks.

Mechanical Ventilation (MV) is a critical life-support intervention in intensive care units (ICUs). However, optimal ventilator settings are challenging to determine because of the complexity of balancing patient-specific physiological needs with the risks of adverse outcomes that impact morbidity, mortality, and healthcare costs. This study introduces ConformalDQN, a novel distribution-free conformal deep Q-learning approach for optimizing mechanical ventilation in intensive care units. By integrating conformal prediction with deep reinforcement learning, our method provides reliable uncertainty quantification, addressing the challenges of Q-value overestimation and out-of-distribution actions in offline settings. We trained and evaluated our model using ICU patient records from the MIMIC-IV database. ConformalDQN extends the Double DQN architecture with a conformal predictor and employs a composite loss function that balances Q-learning with well-calibrated probability estimation. This enables uncertainty-aware action selection, allowing the model to avoid potentially harmful actions in unfamiliar states and handle distribution shifts by being more conservative in out-of-distribution scenarios. Evaluation against baseline models, including physician policies, policy constraint methods, and behavior cloning, demonstrates that ConformalDQN consistently makes recommendations within clinically safe and relevant ranges, outperforming other methods by increasing the 90-day survival rate. Notably, our approach provides an interpretable measure of confidence in its decisions, which is crucial for clinical adoption and potential human-in-the-loop implementations.

There has been a surge in optimizing edge Deep Neural Networks (DNNs) for accuracy and efficiency using traditional optimization techniques such as pruning, and more recently, employing automatic design methodologies. However, the focus of these design techniques has often overlooked critical metrics such as fairness, robustness, and generalization. As a result, when evaluating SOTA edge DNNs' performance in image classification using the FACET dataset, we found that they exhibit significant accuracy disparities (14.09%) across 10 different skin tones, alongside issues of non-robustness and poor generalizability. In response to these observations, we introduce Mixture-of-Experts-based Neural Architecture Search (MoENAS), an automatic design technique that navigates through a space of mixture of experts to discover accurate, fair, robust, and general edge DNNs. MoENAS improves the accuracy by 4.02% compared to SOTA edge DNNs and reduces the skin tone accuracy disparities from 14.09% to 5.60%, while enhancing robustness by 3.80% and minimizing overfitting to 0.21%, all while keeping model size close to state-of-the-art models average size (+0.4M). With these improvements, MoENAS establishes a new benchmark for edge DNN design, paving the way for the development of more inclusive and robust edge DNNs.

Vision Transformers (ViTs) have shown promise in medical image semantic segmentation (MISS) by capturing long-range correlations. However, ViTs often struggle to model local spatial information effectively, which is essential for accurately segmenting fine anatomical details, particularly when applied to small datasets without extensive pre-training. We introduce Gabor and Laplacian of Gaussian Convolutional Swin Network (GLoG-CSUnet), a novel architecture enhancing Transformer-based models by incorporating learnable radiomic features. This approach integrates dynamically adaptive Gabor and Laplacian of Gaussian (LoG) filters to capture texture, edge, and boundary information, enhancing the feature representation processed by the Transformer model. Our method uniquely combines the long-range dependency modeling of Transformers with the texture analysis capabilities of Gabor and LoG features. Evaluated on the Synapse multi-organ and ACDC cardiac segmentation datasets, GLoG-CSUnet demonstrates significant improvements over state-of-the-art models, achieving a 1.14% increase in Dice score for Synapse and 0.99% for ACDC, with minimal computational overhead (only 15 and 30 additional parameters, respectively). GLoG-CSUnet's flexible design allows integration with various base models, offering a promising approach for incorporating radiomics-inspired feature extraction in Transformer architectures for medical image analysis. The code implementation is available on GitHub at: https://github.com/HAAIL/GLoG-CSUnet.

Natural language processing (NLP) is a key technique for developing medical artificial intelligence (AI) systems that leverage electronic health record data to build diagnostic and prognostic models. NLP enables the conversion of unstructured clinical text into structured data that can be fed into AI algorithms. The emergence of transformer architecture and large language models (LLMs) has led to advances in NLP for various healthcare tasks, such as entity recognition, relation extraction, sentence similarity, text summarization, and question-answering. In this article, we review the major technical innovations that underpin modern NLP models and present state-of-the-art NLP applications that employ LLMs in radiation oncology research. However, it is crucial to recognize that LLMs are prone to hallucinations, biases, and ethical violations, which necessitate rigorous evaluation and validation prior to clinical deployment. As such, we propose a comprehensive framework for assessing the NLP models based on their purpose and clinical fit, technical performance, bias and trust, legal and ethical implications, and quality assurance prior to implementation in clinical radiation oncology. Our article aims to provide guidance and insights for researchers and clinicians who are interested in developing and using NLP models in clinical radiation oncology.

Reza Khanmohammadi, Erfan Miahi, Mehrsa Mardikoraem, Simerjot Kaur, Ivan Brugere, Charese Smiley, Kundan S Thind, Mohammad M. Ghassemi. Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing. 2025.

Mechanical Ventilation (MV) is a critical life-support intervention in intensive care units (ICUs). However, optimal ventilator settings are challenging to determine because of the complexity of balancing patient-specific physiological needs with the risks of adverse outcomes that impact morbidity, mortality, and healthcare costs. This study introduces ConformalDQN, a novel distribution-free conformal deep Q-learning approach for optimizing mechanical ventilation in intensive care units. By integrating conformal prediction with deep reinforcement learning, our method provides reliable uncertainty quantification, addressing the challenges of Q-value overestimation and out-of-distribution actions in offline settings. We trained and evaluated our model using ICU patient records from the MIMIC-IV database. ConformalDQN extends the Double DQN architecture with a conformal predictor and employs a composite loss function that balances Q-learning with well-calibrated probability estimation. This enables uncertainty-aware action selection, allowing the model to avoid potentially harmful actions in unfamiliar states and handle distribution shifts by being more conservative in out-of-distribution scenarios. Evaluation against baseline models, including physician policies, policy constraint methods, and behavior cloning, demonstrates that ConformalDQN consistently makes recommendations within clinically safe and relevant ranges, outperforming other methods by increasing the 90-day survival rate. Notably, our approach provides an interpretable measure of confidence in its decisions, which is crucial for clinical adoption and potential human-in-the-loop implementations.

The relationship between scientific innovation in biomedical sciences and its impact on industrial activities is a complex and dynamic process. This article investigates the relationship between science and industrial innovation, focusing on how the historical impact and content of scientific paper abstracts are associated with future funding and innovation grant application content for small businesses. The research incorporates bibliometric analyses along with small business innovation research (SBIR) data to yield a holistic view of the science-industry interface. We quantify the temporal effects and impact latency of scientific advancements on industrial activity across 10 873 topics and take into account their taxonomic relationships, spanning from 2010 to 2021. We find that the impact of scientific advances on industrial projects across different thematic depths consistently exhibited p -values less than 0.05, underscoring the significant predictive power of contemporary scientific activities on future industrial projects. Further, we demonstrate that the semantic contents of scientific paper abstracts within a topic are associated with future industrial project description text embeddings. The frequency analysis reveals that various scientific activities significantly inform future industrial project funding across varying depths of MeSH topic categorization, highlighting the significant role of science in steering industrial innovation. This study demonstrates that the impact of scientific research on industrial innovation extends beyond the mere volume of scientific output, but is greatly influenced by its impact, the broader themes it advances, and the meaningful narratives it presents.

Large Language Models (LLMs) offer significant potential for clinical symptom extraction, but their deployment in healthcare settings is constrained by privacy concerns, computational limitations, and operational costs. This study investigates the optimization of compact LLMs for cancer toxicity symptom extraction using a novel iterative refinement approach. We employ a student-teacher architecture, utilizing Zephyr-7b-beta and Phi3-mini-128 as student models and GPT-4o as the teacher, to dynamically select between prompt refinement, Retrieval-Augmented Generation (RAG), and fine-tuning strategies. Our experiments on 294 clinical notes covering 12 post-radiotherapy toxicity symptoms demonstrate the effectiveness of this approach. The RAG method proved most efficient, improving average accuracy scores from 0.32 to 0.73 for Zephyr-7b-beta and from 0.40 to 0.87 for Phi3-mini-128 during refinement. In the test set, both models showed an approximate 0.20 increase in accuracy across symptoms. Notably, this improvement was achieved at a cost 45 times lower than GPT-4o for Zephyr and 79 times lower for Phi-3. These results highlight the potential of iterative refinement techniques in enhancing the capabilities of compact LLMs for clinical applications, offering a balance between performance, cost-effectiveness, and privacy preservation in healthcare settings.