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Targeting Aging-Related Diseases by Integrating Machine Learning, Biophysical and Cellular Tools

Research

Dec 20th, 2022
Targeting Aging-Related Diseases by Integrating Machine Learning, Biophysical

Researchers: Prof. Haim Wolfson (Computer Science), Dr. Maayan Gal (Dental Medicine) and Dr. Daniel Bar (Dental Medicine)

  • Health-Biomedicine

At the heart of modern drug discovery lies the ability to modulate a defined cellular pathway in order to achieve the desired therapeutic effect. Protein-protein interactions (PPIs) are the main achineries regulating such pathways, and as such are promising therapeutic targets.

 

Unfortunately, the generic physico-chemical characteristics of PPIs greatly complicates the identification of small molecule drugs capable of disrupting the interactions and PPIs are thus often considered undruggable. A promising path towards the discovery of PPI modulators is to design binding peptides.

 

Here, we propose to develop and integrate three specific and complementary AI-based approaches towards the discovery of new peptides that bind a prescribed region of a target protein: (i) Mining and reverse-engineering of binding peptides extracted from native protein substrates using sequence generative models. (ii) Fast screening of complementary binding motifs of the targeted region via geometric deep learning. (iii) De novo complex structure prediction of protein-peptides complexes using the state-of-the-art AlphaFold multimer model.

 

These tools will identify high affinity peptides that can then be validated experimentally, thus providing a unique discovery engine for PPI interface modulators.

Real time Augmented Reality Registration of Stretchable Structures for Needle Navigation through the Gluteus Muscles

Research

Feb 24th, 2022
Real time Augmented Reality Registration of Stretchable Structures for Needle

Researchers: Dr. Dan Raviv, (Electrical Engineering), Shai Tejman-Yarden, M.D., Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center & Sackler Faculty of Medicine

  • Vision
  • Health-Biomedicine
  • AI for social good

Virtual Reality (VR) and Augmented Reality (AR) are two popular platforms to enhance human vision by providing additional layers of information not visible to the naked eye. The gaming industry is blooming using this technology, and the tech giants have recently manufactured high accuracy VR/AR glasses.

 

In this proposal, we claim that we can use the same hardware but add improved AI algorithms of alignment between stretchable domains and project pre-scanned CT images on top of the soft tissues. The current alignment done in a virtual scenario is not sufficient for surgical procedures, especially where there is a movement of the skin and fat tissues between the CT scans and the 3D positioning of the body during the medical procedure. While brain surgery navigation is accurate enough for computer assistance, it is built for hard tissues (bones) and requires heavy preparation per patient. Here we focus on a quick solution for soft tissues with minimal resource requirements.

 

Using state-of-the-art rigid and non-rigid geometric deep learning alignment algorithms developed recently in Dr. Raviv’s lab and the medical expertise from Dr. Tejman-Yarden’s lab, we believe we can solve a fundamental medical task. Using superior algorithms, we plan to provide a robust real-time data fusion tool of soft tissues for surgical needs. We plan to focus first on needle insertion through the Gluteus Muscles, but the same approach can be used for multiple organs and multiple treatments.

 

 

General Falsification Tests for Instrumental Variables

Research

Feb 24th, 2022
General Falsification Tests for Instrumental Variables

Researchers: Dr. Oren Danieli (Economics), Dr. Daniel Nevo (Statistics & Operations Research), Dr. Dan Zeltzer (Economics)

  • Fundamentals of AI and DS
  • Economy and Finance
  • AI for social good

Instrumental variable (IV) estimation is a widely used method that supports high stakes government policies and business decisions, when controlled experiments are not feasible or when a treatment is not successfully delivered to every unit in a randomized experiment.

 

In this research project, we will develop statistical methods for assessing the validity of such designs. IV designs rely on exclusion restriction assumptions that are not directly testable and that are therefore challenging to assess empirically. In this context, this project aims to formalize the logic of falsification tests, a set of tests that leverage contextual knowledge about the absence of causal links (for example, from future to past outcomes) to test the validity of candidate instruments.

 

We will establish that IV falsification tests can be mapped to a class of prediction problems that can leverage current machine learning methods. Based on this conceptualization, we will develop general methods that would both improve falsification test efficiency and help guide the construction of such tests.

 

These methods will be particularly applicable to research using large datasets with many candidate variables that can be used for falsification, an increasingly common situation for which no formal methods currently exist. Developing methods for evaluating and improving the validity of these common research designs entails clear societal benefits.

 

 

 

Photo: Leon Levy Dead Sea Scrolls Digital Library, Israel Antiquities Authority; color photographer Shai Halevi, infrared by Najib Anton Albina

Research

Feb 24th, 2022
Opening the Dead Sea Scrolls to the World

Researchers: Prof. Nachum Dershowitz (Computer Science), Prof. Jonathan Ben-Dov (Biblical Studies)

  • NLP
  • Digital Humanities
  • AI for social good

Our goal in this collaborative project is to adapt various algorithms in computer vision and machine learning (segmentation, registration, and alignment), turning them into practical methods that can be applied to the whole photographic collection of Dead Sea Scrolls (DSS), including even very fragmentary ones from Qumran.

 

The resulting tools are already active in the website of Scripta Qumranica Electronica (https://sqe.deadseascrolls.org.il), operated by the Israel Antiquities Authority (IAA), and are improved as the project advances. The algorithms thus greatly enhance the usability of the DSS collection, which enjoys enormous interest in the public sphere due to its overwhelming cultural and historical importance abd the open access granted by the IAA.

 

With such highly fragmentary scrolls, the registration and alignment of the rich photographic log is a significant asset for improving the reconstruction of scrolls and expose hitherto unknown texts. The website – augmented by our advanced algorithms - brings multiple images and texts together for the benefit of scholars and laypersons alike, as well as enables a new wave of scholarly editions of this highly difficult and fragmentary material.

 

The figure shows examples of recent color images on the left and an old IR image on the right. The two arrows indicate matches.

 

 

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