Ali Ebrahimi

Ricco Noel Hansen Flyckt, Louise Sjodsholm, Margrethe Høstgaard Bang Henriksen et al.

Lung cancer (LC) remains the primary cause of cancer-related mortality, largely due to late-stage diagnoses. Effective strategies for early detection are therefore of paramount importance. In recent years, machine learning (ML) has demonstrated considerable potential in healthcare by facilitating the detection of various diseases. In this retrospective development and validation study, we developed an ML model based on dynamic ensemble selection (DES) for LC detection. The model leverages standard blood sample analysis and smoking history data from a large population at risk in Denmark. The study includes all patients examined on suspicion of LC in the Region of Southern Denmark from 2009 to 2018. We validated and compared the predictions by the DES model with diagnoses provided by five pulmonologists. Among the 38,944 patients, 9,940 had complete data of which 2,505 (25\%) had LC. The DES model achieved an area under the roc curve of 0.77$\pm$0.01, sensitivity of 76.2\%$\pm$2.4\%, specificity of 63.8\%$\pm$2.3\%, positive predictive value of 41.6\%$\pm$1.2\%, and F\textsubscript{1}-score of 53.8\%$\pm$1.1\%. The DES model outperformed all five pulmonologists, achieving a sensitivity 9\% higher than their average. The model identified smoking status, age, total calcium levels, neutrophil count, and lactate dehydrogenase as the most important factors for the detection of LC. The results highlight the successful application of the ML approach in detecting LC, surpassing pulmonologists' performance. Incorporating clinical and laboratory data in future risk assessment models can improve decision-making and facilitate timely referrals.

Amirhossein Zare, Amirhessam Zare, Parmida Sadat Pezeshki et al.

Class imbalance remains a major challenge in machine learning, especially for high-dimensional biomedical data where nonlinear manifold structures dominate. Traditional oversampling methods such as SMOTE rely on local linear interpolation, often producing implausible synthetic samples. Deep generative models like Conditional Variational Autoencoders (CVAEs) better capture nonlinear distributions, but standard variants treat all minority samples equally, neglecting the importance of uncertain, boundary-region examples emphasized by heuristic methods like Borderline-SMOTE and ADASYN. We propose Local Entropy-Guided Oversampling with a CVAE (LEO-CVAE), a generative oversampling framework that explicitly incorporates local uncertainty into both representation learning and data generation. To quantify uncertainty, we compute Shannon entropy over the class distribution in a sample's neighborhood: high entropy indicates greater class overlap, serving as a proxy for uncertainty. LEO-CVAE leverages this signal through two mechanisms: (i) a Local Entropy-Weighted Loss (LEWL) that emphasizes robust learning in uncertain regions, and (ii) an entropy-guided sampling strategy that concentrates generation in these informative, class-overlapping areas. Applied to clinical genomics datasets (ADNI and TCGA lung cancer), LEO-CVAE consistently improves classifier performance, outperforming both traditional oversampling and generative baselines. These results highlight the value of uncertainty-aware generative oversampling for imbalanced learning in domains governed by complex nonlinear structures, such as omics data.

Pardis Moradbeiki, Nasser Ghadiri, Sayed Jalal Zahabi et al.

Accurate sarcopenia diagnosis via ultrasound remains challenging due to subtle imaging cues, limited labeled data, and the absence of clinical context in most models. We propose MedVQA-TREE, a multimodal framework that integrates a hierarchical image interpretation module, a gated feature-level fusion mechanism, and a novel multi-hop, multi-query retrieval strategy. The vision module includes anatomical classification, region segmentation, and graph-based spatial reasoning to capture coarse, mid-level, and fine-grained structures. A gated fusion mechanism selectively integrates visual features with textual queries, while clinical knowledge is retrieved through a UMLS-guided pipeline accessing PubMed and a sarcopenia-specific external knowledge base. MedVQA-TREE was trained and evaluated on two public MedVQA datasets (VQA-RAD and PathVQA) and a custom sarcopenia ultrasound dataset. The model achieved up to 99% diagnostic accuracy and outperformed previous state-of-the-art methods by over 10%. These results underscore the benefit of combining structured visual understanding with guided knowledge retrieval for effective AI-assisted diagnosis in sarcopenia.

Hossein Basafa, Sajad Movahedi, Ali Ebrahimi et al.

This paper presents a technical report of our submission to the 4th task of SemEval-2021, titled: Reading Comprehension of Abstract Meaning. In this task, we want to predict the correct answer based on a question given a context. Usually, contexts are very lengthy and require a large receptive field from the model. Thus, common contextualized language models like BERT miss fine representation and performance due to the limited capacity of the input tokens. To tackle this problem, we used the Longformer model to better process the sequences. Furthermore, we utilized the method proposed in the Longformer benchmark on Wikihop dataset which improved the accuracy on our task data from 23.01% and 22.95% achieved by the baselines for subtask 1 and 2, respectively, to 70.30% and 64.38%.

Mingchuan Zhou, Jiahao Wu, Ali Ebrahimi et al.

Retinal surgery is a complex activity that can be challenging for a surgeon to perform effectively and safely. Image guided robot-assisted surgery is one of the promising solutions that bring significant surgical enhancement in treatment outcome and reduce the physical limitations of human surgeons. In this paper, we demonstrate a novel method for 3D guidance of the instrument based on the projection of spotlight in the single microscope images. The spotlight projection mechanism is firstly analyzed and modeled with a projection on both a plane and a sphere surface. To test the feasibility of the proposed method, a light fiber is integrated into the instrument which is driven by the Steady-Hand Eye Robot (SHER). The spot of light is segmented and tracked on a phantom retina using the proposed algorithm. The static calibration and dynamic test results both show that the proposed method can easily archive 0.5 mm of tip-to-surface distance which is within the clinically acceptable accuracy for intraocular visual guidance.

Ali Ebrahimi, Changyan He, Niravkumar Patel et al.

Surgeon hand tremor limits human capability during microsurgical procedures such as those that treat the eye. In contrast, elimination of hand tremor through the introduction of microsurgical robots diminishes the surgeon's tactile perception of useful and familiar tool-to-sclera forces. While the large mass and inertia of eye surgical robot prevents surgeon microtremor, loss of perception of small scleral forces may put the sclera at risk of injury. In this paper, we have applied and compared two different methods to assure the safety of sclera tissue during robot-assisted eye surgery. In the active control method, an adaptive force control strategy is implemented on the Steady-Hand Eye Robot in order to control the magnitude of scleral forces when they exceed safe boundaries. This autonomous force compensation is then compared to a passive force control method in which the surgeon performs manual adjustments in response to the provided audio feedback proportional to the magnitude of sclera force. A pilot study with three users indicate that the active control method is potentially more efficient.