Mohamad Koohi-Moghadam

Morteza Homayounfar, Mohamad Koohi-Moghadam, Reza Rawassizadeh et al.

As deep neural networks include a high number of parameters and operations, it can be a challenge to implement these models on devices with limited computational resources. Despite the development of novel pruning methods toward resource-efficient models, it has become evident that these models are not capable of handling "imbalanced" and "limited number of data points". We proposed a novel filter pruning method by considering the input and output of filters along with the values of the filters that deal with imbalanced datasets better than others. Our pruning method considers the fact that all information about the importance of a filter may not be reflected in the value of the filter. Instead, it is reflected in the changes made to the data after the filter is applied to it. In this work, three methods are compared with the same training conditions except for the ranking values of each method, and 14 methods are compared from other papers. We demonstrated that our model performed significantly better than other methods for imbalanced medical datasets. For example, when we removed up to 58% of FLOPs for the IDRID dataset and up to 45% for the ISIC dataset, our model was able to yield an equivalent (or even superior) result to the baseline model. To evaluate FLOP and parameter reduction using our model in real-world settings, we built a smartphone app, where we demonstrated a reduction of up to 79% in memory usage and 72% in prediction time. All codes and parameters for training different models are available at https://github.com/mohofar/Beta-Rank

Mohamad Koohi-Moghadam, Hongzhe Sun, Hongyan Li et al.

The discovery of anticancer therapeutics has traditionally treated organic small molecules and metal-based coordination complexes as separate chemical domains, limiting knowledge transfer despite their shared biological objectives. This disparity is particularly pronounced in available data, with extensive screening databases for organic compounds compared to only a few thousand characterized metal complexes. Here, we introduce ChemCLIP, a dual-encoder contrastive learning framework that bridges this organic-inorganic divide by learning unified representations based on shared anticancer activities rather than structural similarity. We compiled complementary datasets comprising 44,854 unique organic compounds and 5,164 unique metal complexes, standardized across 60 cancer cell lines. By training parallel encoders with activity-aware hard negative mining, we mapped structurally distinct compounds into a shared 256-dimensional embedding space where biologically similar compounds cluster together regardless of chemical class. We systematically evaluated four molecular encoding strategies: Morgan fingerprints, ChemBERTa, MolFormer, and Chemprop, through quantitative alignment metrics, embedding visualizations, and downstream classification tasks. Morgan fingerprints achieved superior performance with an average alignment ratio of 0.899 and downstream classification AUCs of 0.859 (inorganic) and 0.817 (organic). This work establishes contrastive learning as an effective strategy for unifying disparate chemical domains and provides empirical guidance for encoder selection in multi-modal chemistry applications, with implications extending beyond anticancer drug discovery to any scenario requiring cross-domain chemical knowledge transfer.

Mohamad Koohi-Moghadam, Mohammad-Ali Nikouei Mahani, Kyongtae Tyler Bae

The development of robust artificial intelligence models for histopathology diagnosis is severely constrained by the scarcity of expert-annotated lesion data, particularly for rare pathologies and underrepresented disease subtypes. While data augmentation offers a potential solution, existing methods fail to generate sufficiently realistic lesion morphologies that preserve the complex spatial relationships and cellular architectures characteristic of histopathological tissues. Here we present PathoGen, a diffusion-based generative model that enables controllable, high-fidelity inpainting of lesions into benign histopathology images. Unlike conventional augmentation techniques, PathoGen leverages the iterative refinement process of diffusion models to synthesize lesions with natural tissue boundaries, preserved cellular structures, and authentic staining characteristics. We validate PathoGen across four diverse datasets representing distinct diagnostic challenges: kidney, skin, breast, and prostate pathology. Quantitative assessment confirms that PathoGen outperforms state-of-the-art generative baselines, including conditional GAN and Stable Diffusion, in image fidelity and distributional similarity. Crucially, we show that augmenting training sets with PathoGen-synthesized lesions enhances downstream segmentation performance compared to traditional geometric augmentations, particularly in data-scarce regimes. Besides, by simultaneously generating realistic morphology and pixel-level ground truth, PathoGen effectively overcomes the manual annotation bottleneck. This approach offers a scalable pathway for developing generalizable medical AI systems despite limited expert-labeled data.

Dariush Lotfi, Mohammad-Ali Nikouei Mahani, Mohamad Koohi-Moghadam et al.

In AI-driven medical imaging, the failure to detect out-of-distribution (OOD) data poses a severe risk to clinical reliability, potentially leading to critical diagnostic errors. Current OOD detection methods often demand impractical retraining or modifications to pre-trained models, hindering their adoption in regulated clinical environments. To address this challenge, we propose a post-hoc normalizing flow-based approach that seamlessly integrates with existing pre-trained models without altering their weights. We evaluate the approach on our in-house-curated MedOOD dataset, designed to capture clinically relevant distribution shifts, and on the MedMNIST benchmark. The proposed method achieves an AUROC of 84.61% on MedOOD, outperforming ViM (80.65%) and MDS (80.87%), and reaches 93.8% AUROC on MedMNIST, surpassing ViM (88.08%) and ReAct (87.05%). This combination of strong performance and post-hoc integration capability makes our approach a practical and effective safeguard for clinical imaging workflows. The model and code to build OOD datasets are publicly accessible at https://github.com/dlotfi/MedOODFlow.