# Timothy Baker > Senior Software Engineer, Applied ML @ Eikon Therapeutics Location: Mountain View, California, United States Profile: https://flows.cv/timothybaker Computer scientist at the intersection of machine learning, software engineering, and medicine. Expertise in efficient and applied machine learning. I'm currently building ML pipelines for drug discovery, focusing on leveraging AI to identify compounds with therapeutic effects. The work is an engaging mix of classical ML and deep learning with frequent coordination with scientists to ensure that we are building biologically relevant, interpretable, and useful tools. During my postdoc, I used ML to analyze radiological images with the goal of improving aortic disease treatment. I delivered three internal AI-based software tools for the lab's medical researchers, one of which has a pending patent. This work also involved frequent coordination with doctors to ensure clinical relevance and practicality. My PhD work centered on hardware-software co-design for ML, exploring quantization, approximate computing, and custom silicon (ASIC) design. These techniques enable more energy-efficient and faster ML algorithms. ## Work Experience ### Senior Software Engineer, Applied ML @ Eikon Therapeutics Jan 2024 – Present | Hayward, California, United States Developing machine learning pipelines to analyze cellular imaging and contribute to the discovery of novel therapeutics. ### Research Fellow @ Michigan Medicine Jan 2023 – Jan 2024 | Ann Arbor, Michigan, United States • Managed several concurrent computer vision and machine learning projects for aortic disease treatment planning, leading to three new software tools, a novel lab research direction, and several research abstracts and publications. • Optimized 3D medical imaging neural network pipelines using MONAI and Pytorch, achieving a 100x increase in training epoch speed via parallel GPU training and data caching strategies, reducing processing cost and time. • Developed custom data labeling tools, automated label validation methods, data augmentation strategies, and a hyperparameter search to create a 700 GB medical image dataset and train a U-Net model to segment arteries. ### Graduate Student Research Assistant @ University of Michigan College of Engineering Jan 2017 – Jan 2023 | Ann Arbor, Michigan • Designed compact, low-precision neural networks and digital filters optimized for deployment on edge devices. • Created a versatile Monte Carlo simulation codebase, enabling performance evaluation of RTL designs tailored for digital filtering and machine learning, resulting in new optimizations and higher application accuracy. • Developed neural network training pipelines that reduce model complexity and size through quantization and pruning, resulting in designs that utilize less 10% to 35% less resources while maintaining high application accuracy. • Published seven first-author papers in leading IEEE and ACM venues like DATE, ICCAD, TODAES, and BioCAS. ### Graduate Student Instructor @ University of Michigan College of Engineering Jan 2017 – Jan 2020 | Ann Arbor, Michigan I delivered weekly discussion lectures and developed homework/exam questions, among other responsibility. For these tasks, I started with clear learning objectives and worked backwards to develop course material. By putting student learning needs first, I was able to make efficient use of class time which ultimately led to emphatic student reviews and a 4.9/5.0 instructor effectiveness rating at the end of term. Following one semester of teaching, I was fortunate enough to advise two former undergraduate students in research. My advisees and I had complementary expertise which led to a productive collaboration. Ultimately, our efforts led to an IEEE BioCAS conference publication that applied stochastic circuits (my expertise) to hearing aids (my student's expertise). The importance of pedagogical techniques and philosophy extend beyond the classroom and given this belief, I regularly attended workshops targeted at improving specific aspects of teaching. Through these workshops and other programs, my teaching philosophy has evolved into one that emphasizes motivation, critical thinking, and community. Courses: Fall 2017: EECS 203: Discrete Mathematics Winter 2018: EECS 270: Introduction to Logic Design Winter 2019: EECS 478: Logic Circuit Synthesis and Optimization (Graduate Level) Winter 2020: EECS 478: Logic Circuit Synthesis and Optimization (Graduate Level) ### Tutor @ Rowan University Jan 2014 – Jan 2017 | Glassboro, NJ I worked alongside other tutors to run drop-in physics tutoring sessions. I tutored all general education physics courses as well as the physics major main track courses up to modern physics (a course that serves as an introduction to quantum mechanics). ### Learning Assistant @ Rowan University Jan 2014 – Jan 2016 | Glassboro, NJ As a learning assistant at Rowan University, I aided professors by answering questions and helping students during in-class group work. I also elected to help students outside of class when needed. During my time at Rowan, I was a learning assistant for Introduction to Mechanics, Introduction to Electricity and Magnetism, and Modern Physics ### Undergraduate Researcher @ Fermilab Jan 2016 – Jan 2016 | Batavia Illinois I worked with the MINERvA Collaboration on estimating the amount noise from one particularly prevalent source of uncertainty in the experiment. ### Undergraduate Researcher @ Kansas State University Jan 2015 – Jan 2015 | Manhattan, Kansas During Kansas State University's 10 week physics undergraduate research experience (REU), I was fortunate to acquire both hands on experimental experience and computational experience. On the experimental side of research, I manned a probe station whose purpose is to run electrical tests on token bit manager chips for the next upgrade of the large hadron collider (LHC) located in CERN, Switzerland. The purpose of these chips is to filter the enormous amount of data generated at the LHC during particle collisions. On the computational side of research where I spent most of my time, I worked with the Mu2e collaboration on their experiment set to run at Fermilab in 2019 I worked with Mu2e's simulation code repository in order to estimate possible the amount of background noise caused by a specific source in the experiment. I became familiar with common high energy physics simulation software such as ROOT, GEANT4 and Art as well as Fermilab's fcl language which is based on C++. To see more details, check out my poster or website made for this REU experience. Website I made for this experience: https://www.phys.ksu.edu/reu2015/bakert0/ ### Undergraduate Researcher @ The Ohio State University Jan 2014 – Jan 2014 | Columbus, Ohio During the summer of 2014 I worked as an undergraduate researcher through the Center for Emergent Materials's 10 week summer REU program at The Ohio State University. My project was to grow patterned cobalt iron thin films on top silicon and silicon dioxide surfaces. I also grew unpatterned films that were use for magnetic characterization of cobalt iron. I became familiar with using an ultra high vacuum sputtering system to grow the films and with a vibrating sample magnetometer to characterize the films. While researching I was also exposed to XRD and other structural characterization techniques. One of the more memorable events while in Ohio was when I accompanied my mentor to Argonne National Laboratory to experience and learn about the national lab while he ran some tests. Overall, this program was an enlightening experience. ### Caterer @ Sodexo Jan 2014 – Jan 2014 | Rowan University I worked as a caterer for special events held at Rowan University. ## Education ### Doctor of Philosophy - PhD in Computer Science and Engineering University of Michigan ### Master of Science - MS in Computer Science and Engineering University of Michigan ### Bachelor's Degree in Physics and Computer Science Rowan University ## Contact & Social - LinkedIn: https://linkedin.com/in/timothy-james-baker - Website: https://bakertim.com/recruit --- Source: https://flows.cv/timothybaker JSON Resume: https://flows.cv/timothybaker/resume.json Last updated: 2026-04-01