About Alexis

Hello! My name is Alexis, and I am a student at Georgia Institute of Technology. I will be graduating with my Master of Science in Biomedical Engineering this May. I also received my undergraduate from Georgia Tech in May 2024 with a Bachelor of Science in Biomedical Engineering, and a minor in Computing and Intelligence, graduating with highest honors. I have a strong foundation in both engineering and machine learning, and am excited to apply my interdisciplinary skills as a R&D engineer in the healthcare industry!

Photo 1 of Alexis

Relevant Coursework

Here are some (not all) courses that I have completed during my time at Georgia Tech:

Biomedical Engineering Capstone Design:

Hands-on experience with project planning, concept and prototype development, design verification testing, FDA Quality Systems Regulations, design controls, and regulatory pathways for commercialization of medical devices. Business functions such as marketing, sales, manufacturing, intellectual property and their effects on the product development process.

Microelectromechanical Systems Devices:

Design for Microelectromechanical systems (MEMS), fabrication, and modeling. Exploration of the MEMS design cycle, including system modeling, microfabrication techniques, structural mechanics, and transduction mechanisms.

Acoustics:

In-depth understanding of the principles governing the generation, propagation, reflection, and transmission of sound waves in fluids, and their applications in engineering.

Artificial Intelligence:

Foundational techniques such as uninformed and informed search algorithms, optimization such as simulated annealing and adversarial game strategies using minimax and alpha-beta pruning. Explored probabilistic reasoning through Bayesian networks and Hidden Markov Models, as well as machine learning techniques including decision trees, random forests, and neural networks. Additionally logic based AI, constraint satisfaction problems, planning under uncertainty, etc. along with theory and practical applications.

Machine Learning:

Techniques in machine learning with an emphasis on algorithms and their applications to real-world data. Key mathematical concepts like linear algebra, probability, and optimization. Unsupervised learning such as clustering and dimensionality reduction, as well as supervised learning including tree-based models, support vector machines, and neural networks. Hands on experience structuring machine learning workflows.

Biomechanics:

Application of engineering principles to biological systems. Including statics, dynamics, and solid mechanics, with applications to musculoskeletal biomechanics, biofluid mechanics, and the mechanical behavior of biological tissues. Analytical problem solving and computational modeling emphasizing real-world biomedical applications.

Image Based Tissue Modeling:

Computational modeling of tissue biosolid and biofluid mechanics, and simulation of medical device tissue interaction. Advanced constitutive models and application of continuum mechanics to account for large deformation and nonlinearity.

Computer Organization and Programming:

Fundamentals of both computer hardware and software. Translation of a program into commands for execution on hardware, and how the hardware executes those commands using electrons.

Circuit Analysis and Electronics Laboratory:

Design, analysis, and measurement of analog and digital electronic circuits and instrumentation.

Robotics and Perception:

Problems and solutions to autonomous robot behavior - how a robot can perceive the world, and using that information to effectively operate.

Physiology of Cellular and Molecular Systems:

Cellular systems including gene expression, organelles, cell signaling, the cytoskeleton, cell life cycle, and the extracellular matrix. Application of current cell and molecular biological technologies to real-world problems.

Biotransport:

Transport phenomena in biological systems, including fluid dynamics, mass transport, and heat transfer. Topics include biofluid mechanics, oscillatory flow, transvascular and interstitial transport, rheology, computational modeling, and disease-related transport processes such as atherosclerosis and thrombosis. Applied to cardiovascular, respiratory, and organ systems, with a focus on in vivo and in vitro measurement techniques

Quantitative Engineering Physiology Laboratory:

Design and conducting of human-centered biomedical experiments, the creation of bioinstrumentation, including sensors and circuits for analyzing physiological data.

Rational Design of Biomaterials:

Integrating chemistry and cellular biology principles in the rational design of new biomaterials.

Systems Physiology:

Human physiology emphasizing biomedical engineering approaches to organ function, disease states, and medical intervention. Core physiological principles such as homeostasis and structe-function relationships, building onto how regulatory systems (nervous, endocrine, etc.) impact the cardiovascular, respiratory, and renal systems.

Biomedical Systems and Modeling:

Computational systems biology - modeling framework, design of interaction diagrams, systems model design, parameter estimation, steady state analysis, stability, sensitivity and gains, numerical evaluations of transients, phase-plane analysis, and the simulation of representative biomedical scenarios.

SolidWorks

I have taken on many projects for medical device development, and am a Certified SolidWorks Associate in Mechanical Design. Here are a few parts and assemblies that I have made in SolidWorks using parametric modeling:

Simple Radial Engine

Bench Vise

Wooden Ferris Wheel

Breedlove Acoustic Guitar

Projects

Below are some projects that I have done throughout my career:

Capstone Design: Mayo Clinic Convergence Science Program
For my senior engineering design class, I worked in a team of 5 biomedical engineers and neurosurgeons sponsored by the Mayo Clinic to improve the cranial drilling experience in awake patient brain surgeries. In this project, we were able to prevent mechanical and sonic discomfort due to neurosurgical drills during awake patient brain surgeries. Throughout the process, we conducted patient and surgeon interviews to better understand the problem. We translated patient needs into design inputs, and built an active noise cancellation device to dampen the bone conducted vibrations. In doing this, we built a wave propagation model with the utilization of a control loop to dynamically assess the input and output waves. The document to the right shows our final report, which includes everything from the design inputs and IP landscape investigation, to the testing and validation of the prototype.

Poster for Georgia Tech's Fall 2023 Capstone Expo
Showcase at Georgia Tech's Fall 2023 Capstone Expo Mayo Clinic Invention Disclosure Presentation

Image 1: Poster for Georgia Tech's Fall 2023 Capstone Expo.
Image 2: Showcase at Georgia Tech's Fall 2023 Capstone Expo. Among 120+ teams, our project won the honorable mention.
Image 3: Invention Disclosure Presentation at the Mayo Clinic in Jacksonville, FL.



The Effect of Surface Type and Incline on Gastrocnemius Activation
For this project, I worked in a team of 3 to measure gastrocnemius (calf muscle) activation when walking on various types of surfaces (hard or soft), and incline (declined, flat, or inclined).

We built an EMG sensor to measure gastrocnemius action on a cohort of 13 people aged 19-25 years old. Data was recorded at a sampling rate of 1200Hz, and using a bandpass filter between 20Hz and 450Hz to remove noise. By knowing the length of the trial and number of steps each participant took, we were able to calculate the frequency of their steps and used a digital band-stop filter in MATLAB to attenuate signals 5% above and below this frequency.

We found that there is an increase in activation for both inclined and declined surface in comparison to a flat surface. We also found a significant increase in muscle activation when walking on a hard surface in comparison to a soft surface. The information found in this project could be used for those who enjoy walking as a daily exercise and would like to avoid overuse injuries.

Quantitative Engineering Physiology Lab Poster

The Effects of Caffeine and Capsaicin on OE33 Cell Line Proliferation
For this project, I worked in a group of 4 to determine the effects of caffine, capsaicin, and their combination on the proliferation of the OE33 (esophageal) cancer cell line.

We had 6 treatment groups for caffeine and capsaicin separately, and then 5 treatment groups with various concentrations of the two in combination, along with a control group. Once treated and incubated, a CCK-8 assay measured absorbance on all treatment groups and a MUSE annexin V assay was run to measure apoptosis effects in the 3 treatment types.

Analyzing the reults with a Tukey's multiple comparisons test and and ANOVA, we found that both caffeine and capsaicin affect OE-33 cell line proliferation at a more significant amount than the chemicals alone. In addition to capsaicin alone affecting cell proliferation, it was also found that caffeine affects proliferation, which was not expected.

Quantitative Engineering Physiology Lab Poster

AI and Machine Learning

Here are some projects that I've worked on involving machine learning:

Game AI: Minimax Tree with Alpha Beta Pruning for Impact Isolation

I implemented a minimax tree along with alpha beta pruning to create a custom AI player to play against in a game of impact isolation. Impact Isolation is similar to the original isolation game, where there are 2 players on a 9-by-9 grid of squares. Each player takes turns placing their piece around the board, moving in a way like a queen in chess. When the piece is moved, the square that was previous occupied, along with the 4 blocks around it, is blocked off. The first player who is unable to move their piece loses. The custom AI opponent utilizes a minimax tree with alpha beta pruning. When playing against a random player, it has a win ratio of 95%. When playing against another AI player that utilizes a minimax tree of level 2, its win ratio is 75%. When it is playing against another AI player that utilizes alphabeta pruning of level 4, its win ratio is 70%.

Path Planning: Rapidly Exploring Random Tree (RRT) Algorithm

This is a demo of the implementation and testing of robot path planning capabilities, specifically using an RRT algorithm for exploration. First, the RRT algoriuthm is implemented. The robot initially is only away of the start position, and the end position. As it creates its path to the goal, it becomes aware of the obstacles and navigates around them. The main loop of the RRT algorithm is by generating random nodes, and assembling them into a tree, adding new edges until the goal is found. Since RRT algorithm can return very convoluted paths, the performance is improved by implementing path smoothing, optimizing the path by reducing the number of nodes in the path. After undergoing smoothing, the path is returned.

Frontier Exploration for Warehouse Automation

In this demo, the robot is tasked with automating a warehouse. There are 2 phases: an exploration phase and a task phase. In phase I, the robot maps out its environment with a frontier-based exploration implementation. In this implementation, a rapidly exploring random tree (RRT) was used. The robot is a differential drive robot, so as it explores, the speed of the left and right wheels are set accordingly to achieve the desired velocity. To achieve this, I utilized a tuned PID controller to adjust motion updates. The algorithm terminates when all 5 landmarks are detected.

In phase II, the robot will collect packages (landmarks) while avoiding obstacles. Using the knowledge of the map from phase I, the robot navigates to the markers, and 'picks them up' by spinning around them, facing the top to grab them. As the robot drives around the map, different kinds of noise are injected into the robot's wheel velocities such as drift, offset, and random walk noise. To control the robot's motion, another PID controller is used to maintain the correct wheel velocities in the robot's differential drive.

Particle Filter (Monte Carlo Localization)

With the implementation of a Monte Carlo Localization, the robot performs localization to estimate the its position and orientation within a known map. Each particle on the map represents a potential robot pose with an associated weight indicating its liklihood of being correct. These particles move based on the robot's motion with added noise to simulate real-world conditions. The robot is equipped with a front facing camera with a 45 degree FOV which can see markers. Based on these sensor measurements, the particle weights are adjusted, using observation of localization markers. The algorithm keeps particles with higher weights while discarding lower weight particles to focus computational resources on probable solutions. When the particles cluster around the true robot's pose (red), the algorithm considers the position estimate reliable, turning the gray estimated robot on the simulation to a green triangle.

Viterbi Trellis and Hidden Markov Models

The Viterbi algorithm is a dynamic programming algorithm that finds the most likely sequence of hidden states that results in a sequence of observed events in the context of Hidden Markov Models (HMM). In this project, I built a word recognizer for American Sign Language video sequences. It employs hidden Markov models to analyze a series of measurements from ASL videos collected for research. Using the Y coordinates of the right thumb and right hand, I encoded a HMM and built a viterbi trellis, which returns the most likely sequence of states that generated teh evidence and the probability of that sequence being correct. From this, I was able to accurately distinguish between 3 given words in ASL, 'Alligator', 'Sleep', and 'Nuts'. The gif to the right shows the signer signing the word "Alligator."

Biomedical Simulations and Modeling

I have thorough experience creating simulations through computational modeling with various software (MATLAB, Python, PLAS, FEBio, SolidWorks, Pymol, etc.). Much of my simulation experience is in modeling biomolecular systems, predictive health models, biomedical systems, physiology, acoustics, biochemistry, and medical device tissue interaction. Here are some examples of the computational modeling I have done:

PLAS (Power Law Analysis and Simulation):

PLAS is a tool for modeling integrative systems in which the dynamics of change can be approximated with power law differential equations (have the mathematical structure \(\frac{dX_i}{dt} = \sum_{j=1}^{p_i} \alpha_{ij} \prod_{k=1}^{n} X_{k}^{g_{IJK}} \)). I've use Power Law Analysis and Simulation to model biomedical and biomolecular systems ranging from protein cascade models, to building predictive models of disease outcomes, all the way to predator/prey environment models.

FEBio Simulations:

From segmenting and generating STL models from medical image data, I have used FEBio to create constitutive models including solid and fluid modeling. Biological tissues require advanced constitutive models to account for large deformation and nonlinearity. This requires the study of continuum mechanics to create such models. With FEBio, I've performed nonlinear finite element analysis of tissues including large deformation, nonlinear elastic, nonlinear viscoelastic, contact analysis, and biphasic analysis.

MATLAB Simulations:

I've used MATLAB for various reasons all throughout my studies, but most recently, I have used MATLAB to create acoustic simulations to replicate real life propagation, reflection, and transmission of sound waves in fluids using acoustic theory principles. With these simulations, I have been able to analyze the effects of transmission through different mediums for engineering applications, along with comparing theories of bidirectional by analyzing interaural time differences and interaural level differences in waves.

Medical Device Design and Prototyping

Out of all, my favorite part of BME is medical device development. I truly enjoy being involved with different phases of device development and being able to see an idea become a device over time. I have a very high amount of experience with device development, and want to show some of the prototypes that me and the various teams I've been on have made throughout my undergraduate. Below are some prototypes that my team and I have made:

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