Tolga Cukur

Yilmaz Korkmaz, Tolga Cukur, Vishal M. Patel

Magnetic Resonance Imaging (MRI) produces excellent soft tissue contrast, albeit it is an inherently slow imaging modality. Promising deep learning methods have recently been proposed to reconstruct accelerated MRI scans. However, existing methods still suffer from various limitations regarding image fidelity, contextual sensitivity, and reliance on fully-sampled acquisitions for model training. To comprehensively address these limitations, we propose a novel self-supervised deep reconstruction model, named Self-Supervised Diffusion Reconstruction (SSDiffRecon). SSDiffRecon expresses a conditional diffusion process as an unrolled architecture that interleaves cross-attention transformers for reverse diffusion steps with data-consistency blocks for physics-driven processing. Unlike recent diffusion methods for MRI reconstruction, a self-supervision strategy is adopted to train SSDiffRecon using only undersampled k-space data. Comprehensive experiments on public brain MR datasets demonstrates the superiority of SSDiffRecon against state-of-the-art supervised, and self-supervised baselines in terms of reconstruction speed and quality. Implementation will be available at https://github.com/yilmazkorkmaz1/SSDiffRecon.

Saban Ozturk, Tolga Cukur

Melanoma is a fatal skin cancer that is curable and has dramatically increasing survival rate when diagnosed at early stages. Learning-based methods hold significant promise for the detection of melanoma from dermoscopic images. However, since melanoma is a rare disease, existing databases of skin lesions predominantly contain highly imbalanced numbers of benign versus malignant samples. In turn, this imbalance introduces substantial bias in classification models due to the statistical dominance of the majority class. To address this issue, we introduce a deep clustering approach based on the latent-space embedding of dermoscopic images. Clustering is achieved using a novel center-oriented margin-free triplet loss (COM-Triplet) enforced on image embeddings from a convolutional neural network backbone. The proposed method aims to form maximally-separated cluster centers as opposed to minimizing classification error, so it is less sensitive to class imbalance. To avoid the need for labeled data, we further propose to implement COM-Triplet based on pseudo-labels generated by a Gaussian mixture model. Comprehensive experiments show that deep clustering with COM-Triplet loss outperforms clustering with triplet loss, and competing classifiers in both supervised and unsupervised settings.

Şaban Öztürk, Emin Celik, Tolga Cukur

Broadspread use of medical imaging devices with digital storage has paved the way for curation of substantial data repositories. Fast access to image samples with similar appearance to suspected cases can help establish a consulting system for healthcare professionals, and improve diagnostic procedures while minimizing processing delays. However, manual querying of large data repositories is labor intensive. Content-based image retrieval (CBIR) offers an automated solution based on dense embedding vectors that represent image features to allow quantitative similarity assessments. Triplet learning has emerged as a powerful approach to recover embeddings in CBIR, albeit traditional loss functions ignore the dynamic relationship between opponent image classes. Here, we introduce a triplet-learning method for automated querying of medical image repositories based on a novel Opponent Class Adaptive Margin (OCAM) loss. OCAM uses a variable margin value that is updated continually during the course of training to maintain optimally discriminative representations. CBIR performance of OCAM is compared against state-of-the-art loss functions for representational learning on three public databases (gastrointestinal disease, skin lesion, lung disease). Comprehensive experiments in each application domain demonstrate the superior performance of OCAM against baselines.

Idil Aytekin, Onat Dalmaz, Kaan Gonc et al.

Monitoring of prevalent airborne diseases such as COVID-19 characteristically involves respiratory assessments. While auscultation is a mainstream method for preliminary screening of disease symptoms, its utility is hampered by the need for dedicated hospital visits. Remote monitoring based on recordings of respiratory sounds on portable devices is a promising alternative, which can assist in early assessment of COVID-19 that primarily affects the lower respiratory tract. In this study, we introduce a novel deep learning approach to distinguish patients with COVID-19 from healthy controls given audio recordings of cough or breathing sounds. The proposed approach leverages a novel hierarchical spectrogram transformer (HST) on spectrogram representations of respiratory sounds. HST embodies self-attention mechanisms over local windows in spectrograms, and window size is progressively grown over model stages to capture local to global context. HST is compared against state-of-the-art conventional and deep-learning baselines. Demonstrations on crowd-sourced multi-national datasets indicate that HST outperforms competing methods, achieving over 83% area under the receiver operating characteristic curve (AUC) in detecting COVID-19 cases.

Lutfi Kerem Senel, Ihsan Utlu, Veysel Yucesoy et al.

Dense word embeddings, which encode semantic meanings of words to low dimensional vector spaces have become very popular in natural language processing (NLP) research due to their state-of-the-art performances in many NLP tasks. Word embeddings are substantially successful in capturing semantic relations among words, so a meaningful semantic structure must be present in the respective vector spaces. However, in many cases, this semantic structure is broadly and heterogeneously distributed across the embedding dimensions, which makes interpretation a big challenge. In this study, we propose a statistical method to uncover the latent semantic structure in the dense word embeddings. To perform our analysis we introduce a new dataset (SEMCAT) that contains more than 6500 words semantically grouped under 110 categories. We further propose a method to quantify the interpretability of the word embeddings; the proposed method is a practical alternative to the classical word intrusion test that requires human intervention.