Filtering by
- Member of: Barrett, The Honors College Thesis/Creative Project Collection
- Resource Type: Text
The aim of this project is to understand the basic algorithmic components of the transformer deep learning architecture. At a high level, a transformer is a machine learning model based off of a recurrent neural network that adopts a self-attention mechanism, which can weigh significant parts of sequential input data which is very useful for solving problems in natural language processing and computer vision. There are other approaches to solving these problems which have been implemented in the past (i.e., convolutional neural networks and recurrent neural networks), but these architectures introduce the issue of the vanishing gradient problem when an input becomes too long (which essentially means the network loses its memory and halts learning) and have a slow training time in general. The transformer architecture’s features enable a much better “memory” and a faster training time, which makes it a more optimal architecture in solving problems. Most of this project will be spent producing a survey that captures the current state of research on the transformer, and any background material to understand it. First, I will do a keyword search of the most well cited and up-to-date peer reviewed publications on transformers to understand them conceptually. Next, I will investigate any necessary programming frameworks that will be required to implement the architecture. I will use this to implement a simplified version of the architecture or follow an easy to use guide or tutorial in implementing the architecture. Once the programming aspect of the architecture is understood, I will then Implement a transformer based on the academic paper “Attention is All You Need”. I will then slightly tweak this model using my understanding of the architecture to improve performance. Once finished, the details (i.e., successes, failures, process and inner workings) of the implementation will be evaluated and reported, as well as the fundamental concepts surveyed. The motivation behind this project is to explore the rapidly growing area of AI algorithms, and the transformer algorithm in particular was chosen because it is a major milestone for engineering with AI and software. Since their introduction, transformers have provided a very effective way of solving natural language processing, which has allowed any related applications to succeed with high speed while maintaining accuracy. Since then, this type of model can be applied to more cutting edge natural language processing applications, such as extracting semantic information from a text description and generating an image to satisfy it.
(LC-MS/MS) is used to identify and quantify peptides and proteins. LC-MS/MS produces mass spectra, which must be searched by one or more engines, which employ
algorithms to match spectra to theoretical spectra derived from a reference database.
These engines identify and characterize proteins and their component peptides. By
training a convolutional neural network on a dataset of over 6 million MS/MS spectra
derived from human proteins, we aim to create a tool that can quickly and effectively
identify spectra as peptides prior to database searching. This can significantly reduce search space and thus run time for database searches, thereby accelerating LCMS/MS-based proteomics data acquisition. Additionally, by training neural networks
on labels derived from the search results of three different database search engines, we
aim to examine and compare which features are best identified by individual search
engines, a neural network, or a combination of these.