arXiv subjects

Andrew R. Cohen

Publications and source records attributed to Andrew R. Cohen.

7 recordsLinked to original sources

arXiv2026

Algorithmic statistics of retinal images

There has been a tremendous amount of image processing and machine learning research to measure and classify disease progression from live optical coherence tomography (OCT) imaging of the retina. The images considered here are large, complex, three-dimensional (3-D) and difficult to visualize effectively. Many current supervised machine learning approaches, \emph{e.g.} neural networks, are non-metric meaning that any features or measurements generated can introduce systematic distortion that may be correlated with underlying non-meaningful physiological differences. Here we present a metric learning approach using the normalized compression distance (NCD) combined with anisotropic structure-enhancing filters to quantify and visualize the principal differences among a collection of 3-D retinal images. We validate the NCD-measured structural differences between pairs of images against the physician-measured change in visual field function, achieving a prediction error of $\sim$ 0.5 dB, more accurate than non-metric deep learning approaches. The normalized compression vectors (NCV) are proposed as a feature set measuring visual differences among a collection of 3-D microscopy images. The utility of the NCV for visualizing and measuring patterns of change is demonstrated for a human with moderate non-progressing glaucoma and for a non-human primate model using intraocular pressure setting manipulation. We conclude with a brief simulation of non-metric embedding features, \emph{e.g.} from neural networks, introducing class-correlated statistical distortion.

eess.IV↗

arXiv2026

A Kolmogorov metric embedding for live cell microscopy signaling patterns

We present a metric embedding that captures spatiotemporal patterns of cell signaling dynamics in 5-D $(x,y,z,channel,time)$ live cell microscopy movies. The embedding uses a metric distance called the normalized information distance (NID) based on Kolmogorov complexity theory, an absolute measure of information content between digital objects. The NID uses statistics of lossless compression to compute a theoretically optimal metric distance between pairs of 5-D movies, requiring no a priori knowledge of expected pattern dynamics, and no training data. The cell signaling structure function (SSF) is defined using a class of metric 3-D image filters that compute at each spatiotemporal cell centroid the voxel intensity configuration of the nucleus w.r.t. the surrounding cytoplasm, or a functional output e.g. velocity. The only parameter is the expected cell radii ($μm$). The SSF can be optionally combined with segmentation and tracking algorithms. The resulting lossless compression pipeline represents each 5-D input movie as a single point in a metric embedding space. The utility of a metric embedding follows from Euclidean distance between any points in the embedding space approximating optimally the pattern difference, as measured by the NID, between corresponding pairs of 5-D movies. This is true throughout the embedding space, not only at points corresponding to input images. Examples are shown for synthetic data, for 2-D+time movies of ERK and AKT signaling under different oncogenic mutations in human epithelial (MCF10A) cells, for 3-D MCF10A spheroids under optogenetic manipulation of ERK, and for ERK dynamics during colony differentiation in human stem cells.

cs.CV↗

arXiv2022

The cluster structure function

For each partition of a data set into a given number of parts there is a partition such that every part is as much as possible a good model (an "algorithmic sufficient statistic") for the data in that part. Since this can be done for every number between one and the number of data, the result is a function, the cluster structure function. It maps the number of parts of a partition to values related to the deficiencies of being good models by the parts. Such a function starts with a value at least zero for no partition of the data set and descents to zero for the partition of the data set into singleton parts. The optimal clustering is the one chosen to minimize the cluster structure function. The theory behind the method is expressed in algorithmic information theory (Kolmogorov complexity). In practice the Kolmogorov complexities involved are approximated by a concrete compressor. We give examples using real data sets: the MNIST handwritten digits and the segmentation of real cells as used in stem cell research.

cs.LG↗

arXiv2022

Plagiarism deterrence for introductory programming

Plagiarism in introductory programming courses is an enormous challenge for both students and institutions. For students, relying on the work of others too early in their academic development can make it impossible to acquire necessary skills for independent success in the future. For institutions, widespread student cheating can dilute the quality of the educational experience being offered. Currently available solutions consider only pairwise comparisons between student submissions and focus on punitive deterrence. Our approach instead relies on a class-wide statistical characterization that can be clearly and securely shared with students via an intuitive new p-value representing independence of student effort. A pairwise, compression-based similarity detection algorithm captures relationships between assignments more accurately. An automated deterrence system is used to warn students that their behavior is being closely monitored. High-confidence instances are made directly available for instructor review using our open-source toolkit. An unbiased scoring system aids students and the instructor in understanding true independence of effort. Preliminary results indicate that the system can provide meaningful measurements of independence from week one, improving the efficacy of technical education.

cs.CY↗

arXiv2020

Web Similarity in Sets of Search Terms using Database Queries

Normalized web distance (NWD) is a similarity or normalized semantic distance based on the World Wide Web or another large electronic database, for instance Wikipedia, and a search engine that returns reliable aggregate page counts. For sets of search terms the NWD gives a common similarity (common semantics) on a scale from 0 (identical) to 1 (completely different). The NWD approximates the similarity of members of a set according to all (upper semi)computable properties. We develop the theory and give applications of classifying using Amazon, Wikipedia, and the NCBI website from the National Institutes of Health. The last gives new correlations between health hazards. A restriction of the NWD to a set of two yields the earlier normalized google distance (NGD) but no combination of the NGD's of pairs in a set can extract the information the NWD extracts from the set. The NWD enables a new contextual (different databases) learning approachbased on Kolmogorov complexity theory that incorporates knowledge from these databases.

cs.IR↗

arXiv2013

Normalized Google Distance of Multisets with Applications

Normalized Google distance (NGD) is a relative semantic distance based on the World Wide Web (or any other large electronic database, for instance Wikipedia) and a search engine that returns aggregate page counts. The earlier NGD between pairs of search terms (including phrases) is not sufficient for all applications. We propose an NGD of finite multisets of search terms that is better for many applications. This gives a relative semantics shared by a multiset of search terms. We give applications and compare the results with those obtained using the pairwise NGD. The derivation of NGD method is based on Kolmogorov complexity.

cs.IR↗

arXiv2013

Normalized Compression Distance of Multisets with Applications

Normalized compression distance (NCD) is a parameter-free, feature-free, alignment-free, similarity measure between a pair of finite objects based on compression. However, it is not sufficient for all applications. We propose an NCD of finite multisets (a.k.a. multiples) of finite objects that is also a metric. Previously, attempts to obtain such an NCD failed. We cover the entire trajectory from theoretical underpinning to feasible practice. The new NCD for multisets is applied to retinal progenitor cell classification questions and to related synthetically generated data that were earlier treated with the pairwise NCD. With the new method we achieved significantly better results. Similarly for questions about axonal organelle transport. We also applied the new NCD to handwritten digit recognition and improved classification accuracy significantly over that of pairwise NCD by incorporating both the pairwise and NCD for multisets. In the analysis we use the incomputable Kolmogorov complexity that for practical purposes is approximated from above by the length of the compressed version of the file involved, using a real-world compression program. Index Terms--- Normalized compression distance, multisets or multiples, pattern recognition, data mining, similarity, classification, Kolmogorov complexity, retinal progenitor cells, synthetic data, organelle transport, handwritten character recognition

cs.CV↗