Hamid Reza Hassanzadeh

Reihaneh Hassanzadeh, Anees Abrol, Hamid Reza Hassanzadeh et al.

Generative approaches for cross-modality transformation have recently gained significant attention in neuroimaging. While most previous work has focused on case-control data, the application of generative models to disorder-specific datasets and their ability to preserve diagnostic patterns remain relatively unexplored. Hence, in this study, we investigated the use of a generative adversarial network (GAN) in the context of Alzheimer's disease (AD) to generate functional network connectivity (FNC) and T1-weighted structural magnetic resonance imaging data from each other. We employed a cycle-GAN to synthesize data in an unpaired data transition and enhanced the transition by integrating weak supervision in cases where paired data were available. Our findings revealed that our model could offer remarkable capability, achieving a structural similarity index measure (SSIM) of $0.89 \pm 0.003$ for T1s and a correlation of $0.71 \pm 0.004$ for FNCs. Moreover, our qualitative analysis revealed similar patterns between generated and actual data when comparing AD to cognitively normal (CN) individuals. In particular, we observed significantly increased functional connectivity in cerebellar-sensory motor and cerebellar-visual networks and reduced connectivity in cerebellar-subcortical, auditory-sensory motor, sensory motor-visual, and cerebellar-cognitive control networks. Additionally, the T1 images generated by our model showed a similar pattern of atrophy in the hippocampal and other temporal regions of Alzheimer's patients.

Longxiang Zhang, Renato Negrinho, Arindam Ghosh et al.

Fine-tuning pretrained models for automatically summarizing doctor-patient conversation transcripts presents many challenges: limited training data, significant domain shift, long and noisy transcripts, and high target summary variability. In this paper, we explore the feasibility of using pretrained transformer models for automatically summarizing doctor-patient conversations directly from transcripts. We show that fluent and adequate summaries can be generated with limited training data by fine-tuning BART on a specially constructed dataset. The resulting models greatly surpass the performance of an average human annotator and the quality of previous published work for the task. We evaluate multiple methods for handling long conversations, comparing them to the obvious baseline of truncating the conversation to fit the pretrained model length limit. We introduce a multistage approach that tackles the task by learning two fine-tuned models: one for summarizing conversation chunks into partial summaries, followed by one for rewriting the collection of partial summaries into a complete summary. Using a carefully chosen fine-tuning dataset, this method is shown to be effective at handling longer conversations, improving the quality of generated summaries. We conduct both an automatic evaluation (through ROUGE and two concept-based metrics focusing on medical findings) and a human evaluation (through qualitative examples from literature, assessing hallucination, generalization, fluency, and general quality of the generated summaries).

Hamid Reza Hassanzadeh, Ying Sha, May D. Wang

Multiple cause-of-death data provides a valuable source of information that can be used to enhance health standards by predicting health related trajectories in societies with large populations. These data are often available in large quantities across U.S. states and require Big Data techniques to uncover complex hidden patterns. We design two different classes of models suitable for large-scale analysis of mortality data, a Hadoop-based ensemble of random forests trained over N-grams, and the DeepDeath, a deep classifier based on the recurrent neural network (RNN). We apply both classes to the mortality data provided by the National Center for Health Statistics and show that while both perform significantly better than the random classifier, the deep model that utilizes long short-term memory networks (LSTMs), surpasses the N-gram based models and is capable of learning the temporal aspect of the data without a need for building ad-hoc, expert-driven features.

Hamid Reza Hassanzadeh, Pushkar Kolhe, Charles L. Isbell et al.

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

Hamid Reza Hassanzadeh, Hadi Sadoghi Yazdi, Abedin Vahedian

In this paper we introduce a fuzzy constraint linear discriminant analysis (FC-LDA). The FC-LDA tries to minimize misclassification error based on modified perceptron criterion that benefits handling the uncertainty near the decision boundary by means of a fuzzy linear programming approach with fuzzy resources. The method proposed has low computational complexity because of its linear characteristics and the ability to deal with noisy data with different degrees of tolerance. Obtained results verify the success of the algorithm when dealing with different problems. Comparing FC-LDA and LDA shows superiority in classification task.

Hamid Reza Hassanzadeh

The concept of uncertainty is posed in almost any complex system including parallel robots as an outstanding instance of dynamical robotics systems. As suggested by the name, uncertainty, is some missing information that is beyond the knowledge of human thus we may tend to handle it properly to minimize the side-effects through the control process. Type-II fuzzy logic has shown its superiority over traditional fuzzy logic when dealing with uncertainty. Type-II fuzzy logic controllers are however newer and more promising approaches that have been recently applied to various fields due to their significant contribution especially when noise (as an important instance of uncertainty) emerges. During the design of Type-I fuzzy logic systems, we presume that we are almost certain about the fuzzy membership functions which is not true in many cases. Thus T2FLS as a more realistic approach dealing with practical applications might have a lot to offer. Type-II fuzzy logic takes into account a higher level of uncertainty, in other words, the membership grade for a type-II fuzzy variable is no longer a crisp number but rather is itself a type-I linguistic term. In this thesis the effects of uncertainty in dynamic control of a parallel robot is considered. More specifically, it is intended to incorporate the Type-II Fuzzy Logic paradigm into a model based controller, the so-called computed torque control method, and apply the result to a 3 degrees of freedom parallel manipulator. ...

Hamid Reza Hassanzadeh, John H. Phan, May D. Wang

Prediction of survival for cancer patients is an open area of research. However, many of these studies focus on datasets with a large number of patients. We present a novel method that is specifically designed to address the challenge of data scarcity, which is often the case for cancer datasets. Our method is able to use unlabeled data to improve classification by adopting a semi-supervised training approach to learn an ensemble classifier. The results of applying our method to three cancer datasets show the promise of semi-supervised learning for prediction of cancer survival.