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docs
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publications
Optimum Design, Manufacturing and Experiment of a Passive Walking Biped: Effects of Structural Parameters on Efficiency, Stability and Robustness on Uneven Trains
In this research, a deployed model of biped that can be built has been considered, and then its walking performance sensitivity such as efficiency, stability...
Enhanced Waddington Landscape Model with Cell-Cell Communication Can Explain Molecular Mechanisms of Self-Organization
Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principle...
Recognizing Arrow Of Time In The Short Stories
Recognizing arrow of time in short stories is a challenging task. i.e., given only two paragraphs, determining which comes first and which comes next is a di...
Bayesian optimization for ternary complex prediction (BOTCP)
Proximity-inducing compounds (PICs) are an emergent drug technology through which a protein of interest (POI), often a drug target, is brought into the vicin...
Encoding Protein-Ligand Interactions: Binding Affinity Prediction with Multigraph-based Modeling and Graph Convolutional Network
Machine learning models are employed to enhance the speed and provide novel insights in drug discovery due to their demonstrated effectiveness in predicting ...
Quantifying the hardness of bioactivity prediction tasks for transfer learning
Today, machine learning methods are widely employed in drug discovery. However, the chronic lack of data continues to hamper their further development, valid...
Evaluating Machine Learning Models for Molecular Property Prediction: Performance and Robustness on Out-of-Distribution Data
Today, machine learning models are employed extensively to predict the physicochemical and biological properties of molecules. Their performance is typically...
recipes
talks
System biology and waddington landscape
In this talk, I presented our work on pattern formation during human embryonic stem cell development. We proposed a multicellular mathematical model for pat...
Causal learning and inference
Causal learning and discovery have received significant attention in the machine learning community. Causal learning allows us to answer the question about ...
teaching
Advanced bioinformatics
I worked as the teaching assistant of “Advanced bioinformatics course”. This is a graduate level course which covers topics such as: Microaarray and RNA-Seq ...
Machine learning workshop
I am running a machine learning workshop, which I present diverse topics; from knowledge distillation and compression to causal inference and invariance.
Active learning in drug discovery
Active learning and Bayesian optimization have become important/prevalent tools in drug discovery and design. They provide a systematic way to select sample...