The Model AI Assignments session seeks to gather and disseminate the best assignment designs of the Artificial Intelligence (AI) Education community. Recognizing that assignments form the core of student learning experience, we here present abstracts of nine AI assignments from the 2020 session that are easily adoptable, playfully engaging, and flexible for a variety of instructor needs. Assignment specifications and supporting resources may be found at http://modelai.gettysburg.edu.

Improvements in medical imaging techniques have provided clinicians the ability to obtain detailed brain images of patients at lower costs. This increased availability of rich data opens up new avenues of research that promise better understanding of common brain ailments such as Alzheimer's Disease and dementia. Improved data mining techniques, however, are required to leverage these new data sets to identify intermediate disease states (e.g., mild cognitive impairment) and perform early diagnosis. We propose a graphical model framework based on conditional random fields (CRFs) to mine MRI brain images. As a proof-of-concept, we apply CRFs to the problem of brain tissue segmentation. Experimental results show robust and accurate performance on tissue segmentation comparable to other state-of-the-art segmentation methods. In addition, results show that our algorithm generalizes well across data sets and is less susceptible to outliers. Our method relies on minimal prior knowledge unlike atlas-based techniques, which assume images map to a normal template. Our results show that CRFs are a promising model for tissue segmentation, as well as other MRI data mining problems such as anatomical segmentation and disease diagnosis where atlas assumptions are unreliable in abnormal brain images.

In line with institutions across the United States, the Computer Science Department at Swarthmore College has faced the challenge of maintaining a demographic composition of students that matches the student body as a whole. To combat this trend, our department has made a concerted effort to revamp our introductory course sequence to both attract and retain more women and minority students.

An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. Previous work by some of this paper's authors [1] describes an automated approach to this otherwise time-consuming process. An important step in the previous method requires searching the density map for many small template protein-fragments. This previous approach uses Fourier convolution to quickly match some rotation of the template to the entire density map. This paper proposes an alternate approach that makes use of the spherical-harmonic decomposition of the template and of some region in the density map. This new framework allows us to mask specific regions of the map, enabling a first-pass filter to eliminate a majority of the density map without requiring an expensive rotational search. We show our new template matching method improves accuracy and reduces running time, compared to our previous approach. Protein models constructed using this matching also show significant accuracy improvement.

MOTIVATION: One bottleneck in high-throughput protein crystallography is interpreting an electron-density map, that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed ACMI (Automatic Crystallographic Map Interpreter), an algorithm that uses a probabilistic model to infer an accurate protein backbone layout. Here, we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of ACMI to guide the particle filter's sampling, producing an accurate, physically feasible set of structures. RESULTS: We test our algorithm on 10 poor-quality experimental density maps. We show that particle filtering produces accurate all-atom models, resulting in fewer chains, lower sidechain RMS error and reduced R factor, compared to simply placing the best-matching sidechains on ACMI's trace. We show that our approach produces a more accurate model than three leading methods--Textal, Resolve and ARP/WARP--in terms of main chain completeness, sidechain identification and crystallographic R factor. AVAILABILITY: Source code and experimental density maps available at http://ftp.cs.wisc.edu/machine-learning/shavlik-group/programs/acmi/