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129<div class="mobile-site-title mobile-visible"> <a href="https://samgelman.com/"> Sam Gelman</a></div><div class="menu-toggle"> <span></span> <span></span> <span></span></div><div class="lmpixels-arrows-nav">
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149<div class="item"> <h4>Machine Learning</h4></div><div class="item"> <h4>Protein Engineering</h4></div><div class="item"> <h4>Bioinformatics</h4></div></div><h1>Sam Gelman</h1>
150<p>Hi, I'm Sam! I research deep learning methods for protein design. I have a strong background in computer science, machine learning, and biology, which has allowed me to excel in this field.
151I am passionate about using deep learning to better understand protein structure and function, and I have developed innovative algorithms and models in this area.
152Let's connect!</p>
153<div class="home-buttons"> <a href="https://samgelman.com/#about" target="" class="btn btn-secondary">About Me</a> <a href="https://samgelman.com/#contact" target="" class="btn btn-secondary">Contact Me</a></div></div></div></div></div></div></div></div></div></div></div></section>
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160<div class="block-title"><h2>Featured <span>talk</span></h2></div></div></div></div></div></div></section>
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176<div class="block-title"><h2>Featured <span>preprint</span></h2></div></div></div></div></div></div></section>
177<section class="elementor-section elementor-top-section elementor-element elementor-element-82d3976 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="82d3976" data-element_type="section">
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179<div class="elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-3d83316" data-id="3d83316" data-element_type="column">
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182<div class="elementor-widget-container"> <h3><a href="https://doi.org/10.1101/2024.03.15.585128">Biophysics-based protein language models for protein engineering</a></h3><p><strong>Sam Gelman</strong>
182, Bryce Johnson, Chase Freschlin, Arnav Sharma, <span data-delta="3" data-hasqtip="2" aria-describedby="qtip-2">Sameer D&#8217;Costa</span>, John Peters, Anthony Gitter, Philip A. Romero. <em>bioRxiv</em> (2024).</p><p>Protein language models trained on evolutionary data have emerged as powerful tools for predictive problems involving protein sequence, structure, and function. However, these models overlook decades of research into biophysical factors governing protein function. We propose Mutational Effect Transfer Learning (METL), a protein language model framework that unites advanced machine learning and biophysical modeling. Using the METL framework, we pretrain transformer-based neural networks on biophysical simulation data to capture fundamental relationships between protein sequence, structure, and energetics. We finetune METL on experimental sequence-function data to harness these biophysical signals and apply them when predicting protein properties like thermostability, catalytic activity, and fluorescence. METL excels in challenging protein engineering tasks like generalizing from small training sets and position extrapolation, although existing methods that train on evolutionary signals remain powerful for many types of experimental assays. We demonstrate METL&#8217;s ability to design functional green fluorescent protein variants when trained on only 64 examples, showcasing the potential of biophysics-based protein language models for protein engineering.</p></div></div></div></div></div></section>
183<section class="elementor-section elementor-top-section elementor-element elementor-element-af26ab3 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="af26ab3" data-element_type="section">
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188<div class="elementor-widget-container">
189<div class="block-title"><h2>Featured <span>publication</span></h2></div></div></div></div></div></div></section>
190<section class="elementor-section elementor-top-section elementor-element elementor-element-ac2e873 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="ac2e873" data-element_type="section">
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194<section class="elementor-section elementor-inner-section elementor-element elementor-element-3dfb8be elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="3dfb8be" data-element_type="section">
195<div class="elementor-container elementor-column-gap-default">
196<div class="elementor-column elementor-col-100 elementor-inner-column elementor-element elementor-element-d179f7b" data-id="d179f7b" data-element_type="column">
197<div class="elementor-widget-wrap elementor-element-populated">
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199<div class="elementor-widget-container"> <h3><a href="https://www.pnas.org/doi/full/10.1073/pnas.2104878118">Neural networks to learn protein sequence–function relationships from deep mutational scanning data</a></h3><p><strong>Sam Gelman</strong>, Sarah A. Fahlberg, Pete Heinzelman, Philip A. Romero, Anthony Gitter. <em>Proceedings of the National Academy of Sciences</em> (2021).</p><p><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" fetchpriority="high" decoding="async" class="alignnone wp-image-351 size-full" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/10/overview.webp" alt="blank" width="1973" height="329"/></p><p>Understanding the relationship between protein sequence and function is necessary to design new and useful proteins with applications in bioenergy, medicine, and agriculture. The mapping from protein sequence to function is highly complex, making it challenging to predict how sequence changes will affect a protein’s behavior and properties. We show that neural networks can learn the sequence–function mapping from large protein datasets. Neural networks are appealing for this task because they can learn complicated relationships from data, make few assumptions about the nature of the sequence–function relationship, and can learn general rules that apply across the length of the protein sequence. We demonstrate that learned models can be applied to design new proteins with properties that exceed natural sequences.</p></div></div></div></div></div></section></div></div></div></section></div></div></section>
200<section data-id="about" class="animated-section">
201<div class="section-content">
202<div class="page-title"> <h1>About Me</h1></div><div data-elementor-type="wp-page" data-elementor-id="59" class="elementor elementor-59">
203<section class="elementor-section elementor-top-section elementor-element elementor-element-8853760 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="8853760" data-element_type="section">
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208<div class="elementor-widget-container">
209<div class="timeline clearfix"><div class="block-title element-title"><h2>Education</h2></div><div class="timeline-item clearfix">
210<div class="left-part"> <h5 class="item-period">2023</h5> <span class="item-company">University of Wisconsin-Madison</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,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" alt="University of Wisconsin-Madison" data-src="https://samgelman.com/wp-content/uploads/2022/09/color-center-UWlogo-print.webp" class="lazyload" data-eio-rwidth="2550" data-eio-rheight="1681"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" width="2550" height="1681" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/09/color-center-UWlogo-print.webp" alt="University of Wisconsin-Madison" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
211<h4 class="item-title">Ph.D. Computer Science</h4>
212<div><p>I earned a Ph.D. in Computer Science from the University of Wisconsin-Madison. I was advised by <a href="https://www.bi
212ostat.wisc.edu/~gitter/index.html">Anthony Gitter</a> and <a href="http://www.romerolab.org/">Philip Romero</a>. My research focused on deep learning methods for protein engineering. I was fortunate to receive two distinguished fellowships, including a pre-doctoral fellowship from the <a href="https://www.phrmafoundation.org/">PhRMA Foundation</a> and a short-term traineeship from UW-Madison's Genomic Sciences Training Program.</p></div></div></div><div class="timeline-item clearfix">
213<div class="left-part"> <h5 class="item-period">2016</h5> <span class="item-company">George Mason University</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,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" alt="George Mason University" data-src="https://samgelman.com/wp-content/uploads/2022/09/2560px-George_Mason_University_logo.svg_.webp" class="lazyload" data-eio-rwidth="2560" data-eio-rheight="1664"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/09/2560px-George_Mason_University_logo.svg_.webp" alt="George Mason University" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
214<h4 class="item-title">M.S. Computer Science</h4>
215<div><p>I obtained an M.S. in Computer Science from George Mason University in 2016. I was advised by Zoran Duric and Naomi Lynn Gerber. My research focused on methods for tracking human movement with depth cameras, and my master's thesis is titled <em><a href="http://mars.gmu.edu/handle/1920/10779">A method for estimating motions of contours with an application to gait recognition</a></em>. I received the Outstanding Graduate Teaching Assistant award for my efforts assisting the teaching of CS 321: Software Engineering.</p></div></div></div><div class="timeline-item clearfix">
216<div class="left-part"> <h5 class="item-period">2014</h5> <span class="item-company">George Mason University</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAB4AAAATgAQAAAAA+xWKsAAAAAnRSTlMAAHaTzTgAAAE6SURBVHja7cEBDQAAAMKg909tDwcUAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADwaXHAABRTMv9gAAAABJRU5ErkJggg==" alt="George Mason University" data-src="https://samgelman.com/wp-content/uploads/2022/09/2560px-George_Mason_University_logo.svg_.webp" class="lazyload" data-eio-rwidth="2560" data-eio-rheight="1664"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/09/2560px-George_Mason_University_logo.svg_.webp" alt="George Mason University" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
217<h4 class="item-title">B.S. Computer Science</h4>
218<div><p>I obtained a B.S. in Computer Science from George Mason University in 2014. I graduated from the Honors College and received several awards, including the Schwartzstein Best Freshmen Research Paper Scholarship, the Student Excellence Award, and Outstanding Undergraduate Teaching Assistant.</p></div></div></div></div></div></div><div class="elementor-element elementor-element-000e731 elementor-widget elementor-widget-spacer" data-id="000e731" data-element_type="widget" data-widget_type="spacer.default">
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222<div class="elementor-widget-container">
223<div class="timeline clearfix"><div class="block-title element-title"><h2>Experience</h2></div><div class="timeline-item clearfix">
224<div class="left-part"> <h5 class="item-period">2023-Present</h5> <span class="item-company">
224Morgridge Institute</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAB4AAAAOKAQAAAABSDXAeAAAAAnRSTlMAAHaTzTgAAADqSURBVHja7cExAQAAAMKg9U9tCU+gAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAOBpVRcAAc+PJqoAAAAASUVORK5CYII=" alt="Morgridge Institute" data-src="https://samgelman.com/wp-content/uploads/2024/02/MorgridgeLogo_vertical_no-artifact.webp" class="lazyload" data-eio-rwidth="2395" data-eio-rheight="1130"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" width="2395" height="1130" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2024/02/MorgridgeLogo_vertical_no-artifact.webp" alt="Morgridge Institute" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
225<h4 class="item-title">Machine Learning Scientist</h4>
226<div>I am continuing my protein engineering research with the <a href="https://www.biostat.wisc.edu/~gitter/">Gitter Lab</a> as a machine learning scientist.</div></div></div><div class="timeline-item clearfix">
227<div class="left-part"> <h5 class="item-period">2017-2023</h5> <span class="item-company">University of Wisconsin-Madison</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,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" alt="University of Wisconsin-Madison" data-src="https://samgelman.com/wp-content/uploads/2022/09/color-center-UWlogo-print.webp" class="lazyload" data-eio-rwidth="2550" data-eio-rheight="1681"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" width="2550" height="1681" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/09/color-center-UWlogo-print.webp" alt="University of Wisconsin-Madison" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
228<h4 class="item-title">Graduate Research Assistant</h4>
229<div><div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p>I was a graduate research assistant in the <a href="https://www.biostat.wisc.edu/~gitter/">Gitter Lab</a> at the University of Wisconsin-Madison.</p><ul><li>Researched machine learning methods for protein engineering</li><li>Implemented custom algorithms, data processing pipelines, and machine learning frameworks</li><li>Utilized high-throughput computing clusters to accelerate GPU and CPU-based workflows</li><li>Communicated research to diverse audiences in talks and manuscripts</li><li>Collaborated with multi-disciplinary teams including computer scientists and chemists</li><li>Stayed current with new research in the area</li></ul></div></div></div></div></div></div><div class="timeline-item clearfix">
230<div class="left-part"> <h5 class="item-period">2015-2016</h5> <span class="item-company">U.S. Naval Research Laboratory</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAABAAAAAKvAQAAAADc/IAvAAAAAnRSTlMAAHaTzTgAAABtSURBVHja7cExAQAAAMKg9U9tDB+gAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAICzAVo+AAH0fnSfAAAAAElFTkSuQmCC" alt="U.S. Naval Research Laboratory" data-src="https://samgelman.com/wp-content/uploads/2022/10/nrl_logo2.webp" class="lazyload" data-eio-rwidth="1024" data-eio-rheight="687"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" width="1024" height="687" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/10/nrl_logo2.webp" alt="U.S. Naval Research Laboratory" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
231<h4 class="item-title">
231Student Research Scientist</h4>
232<div><div class="page" title="Page 1">
233<div class="layoutArea">
234<div class="column"> I was a student research scientist the U.S. Naval Research Laboratory while obtaining my master's degree from George Mason University. <ul> <li>Researched novel method for tracking motions of contours</li> <li>Applied method for gait recognition with depth cameras</li></ul></div></div></div></div></div></div><div class="timeline-item clearfix">
235<div class="left-part"> <h5 class="item-period">2014</h5> <span class="item-company">National Institutes of Health</span> <span class="item-logo"><img decoding="async" src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAB4AAAAaZAQAAAACFdy+MAAAAAnRSTlMAAHaTzTgAAAGhSURBVHja7cEBDQAAAMKg909tDjegAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALg0NmMAAe8LTK0AAAAASUVORK5CYII=" alt="National Institutes of Health" data-src="https://samgelman.com/wp-content/uploads/2022/10/nih_logo.webp" class="lazyload" data-eio-rwidth="2328" data-eio-rheight="2048"/><noscript><img onload="speedycachell.r(this,true);" src="https://samgelman.com/wp-content/plugins/speedycache-pro/assets/images/image-palceholder.png" width="2328" height="2048" decoding="async" data-speedycache-original-src="https://samgelman.com/wp-content/uploads/2022/10/nih_logo.webp" alt="National Institutes of Health" data-eio="l"/></noscript></span></div><div class="divider"></div><div class="right-part">
236<h4 class="item-title">Research Scientist Intern</h4>
237<div><div class="page" title="Page 1">
238<div class="layoutArea">
239<div class="column"> I interned at the NIH, National Institute of Diabetes and Digestive and Kidney Diseases, after completing my undergraduate degree. <ul> <li>Developed computer vision system for tracking lab mice</li> <li>Designed custom graphical tools for efficiently annotating video</li></ul></div></div></div></div></div></div></div></div></div></div></div></div></section></div></div></section>
240<section data-id="contact" class="animated-section">
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242<div class="page-title"> <h1>Contact</h1></div><div data-elementor-type="wp-page" data-elementor-id="108" class="elementor elementor-108">
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