En masse scanning and automated surfacing of small objects using Micro-CT

Modern archaeological methods increasingly utilize 3D virtual representations of objects, computationally intensive analyses, high resolution scanning, large datasets, and machine learning. With higher resolution scans, challenges surrounding computational power, memory, and file storage quickly arise. Processing and analyzing high resolution scans often requires memory-intensive workflows, which are infeasible for most computers and increasingly necessitate the use of super-computers or innovative methods for processing on standard computers. Here we introduce a novel protocol for en-masse micro-CT scanning of small objects with a {\em mostly-automated} processing workflow that functions in memory-limited settings. We scanned 1,112 animal bone fragments using just 10 micro-CT scans, which were post-processed into individual PLY files. Notably, our methods can be applied to any object (with discernible density from the packaging material) making this method applicable to a variety of inquiries and fields including paleontology, geology, electrical engineering, and materials science. Further, our methods may immediately be adopted by scanning institutes to pool customer orders together and offer more affordable scanning. The work presented herein is part of a larger program facilitated by the international and multi-disciplinary research consortium known as Anthropological and Mathematical Analysis of Archaeological and Zooarchaeological Evidence (AMAAZE). AMAAZE unites experts in anthropology, mathematics, and computer science to develop new methods for mass-scale virtual archaeological research. Overall, our new scanning method and processing workflows lay the groundwork and set the standard for future mass-scale, high resolution scanning studies.

Convergence rates for Poisson learning to a Poisson equation with measure data

In this paper we prove discrete to continuum convergence rates for Poisson Learning, a graph-based semi-supervised learning algorithm that is based on solving the graph Poisson equation with a source term consisting of a linear combination of Dirac deltas located at labeled points and carrying label information. The corresponding continuum equation is a Poisson equation with measure data in a Euclidean domain $\Omega \subset \mathbb{R}^d$. The singular nature of these equations is challenging and requires an approach with several distinct parts: (1) We prove quantitative error estimates when convolving the measure data of a Poisson equation with (approximately) radial function supported on balls. (2) We use quantitative variational techniques to prove discrete to continuum convergence rates on random geometric graphs with bandwidth $\varepsilon>0$ for bounded source terms. (3) We show how to regularize the graph Poisson equation via mollification with the graph heat kernel, and we study fine asymptotics of the heat kernel on random geometric graphs. Combining these three pillars we obtain $L^1$ convergence rates that scale, up to logarithmic factors, like $O(\varepsilon^{\frac{1}{d+2}})$ for general data distributions, and $O(\varepsilon^{\frac{2-\sigma}{d+4}})$ for uniformly distributed data, where $\sigma>0$. These rates are valid with high probability if $\varepsilon\gg\left({\log n}/{n}\right)^q$ where $n$ denotes the number of vertices of the graph and $q \approx \frac{1}{3d}$.

Numerical solution of a PDE arising from prediction with expert advice

This work investigates the online machine learning problem of prediction with expert advice in an adversarial setting through numerical analysis of, and experiments with, a related partial differential equation. The problem is a repeated two-person game involving decision-making at each step informed by $n$ experts in an adversarial environment. The continuum limit of this game over a large number of steps is a degenerate elliptic equation whose solution encodes the optimal strategies for both players. We develop numerical methods for approximating the solution of this equation in relatively high dimensions ($n\leq 10$) by exploiting symmetries in the equation and the solution to drastically reduce the size of the computational domain. Based on our numerical results we make a number of conjectures about the optimality of various adversarial strategies, in particular about the non-optimality of the COMB strategy.

Consistency of semi-supervised learning, stochastic tug-of-war games, and the p-Laplacian

In this paper we give a broad overview of the intersection of partial differential equations (PDEs) and graph-based semi-supervised learning. The overview is focused on a large body of recent work on PDE continuum limits of graph-based learning, which have been used to prove well-posedness of semi-supervised learning algorithms in the large data limit. We highlight some interesting research directions revolving around consistency of graph-based semi-supervised learning, and present some new results on the consistency of p-Laplacian semi-supervised learning using the stochastic tug-of-war game interpretation of the p-Laplacian. We also present the results of some numerical experiments that illustrate our results and suggest directions for future work.

Novel Batch Active Learning Approach and Its Application to Synthetic Aperture Radar Datasets

Active learning improves the performance of machine learning methods by judiciously selecting a limited number of unlabeled data points to query for labels, with the aim of maximally improving the underlying classifier's performance. Recent gains have been made using sequential active learning for synthetic aperture radar (SAR) data arXiv:2204.00005. In each iteration, sequential active learning selects a query set of size one while batch active learning selects a query set of multiple datapoints. While batch active learning methods exhibit greater efficiency, the challenge lies in maintaining model accuracy relative to sequential active learning methods. We developed a novel, two-part approach for batch active learning: Dijkstra's Annulus Core-Set (DAC) for core-set generation and LocalMax for batch sampling. The batch active learning process that combines DAC and LocalMax achieves nearly identical accuracy as sequential active learning but is more efficient, proportional to the batch size. As an application, a pipeline is built based on transfer learning feature embedding, graph learning, DAC, and LocalMax to classify the FUSAR-Ship and OpenSARShip datasets. Our pipeline outperforms the state-of-the-art CNN-based methods.

Poisson Reweighted Laplacian Uncertainty Sampling for Graph-based Active Learning

We show that uncertainty sampling is sufficient to achieve exploration versus exploitation in graph-based active learning, as long as the measure of uncertainty properly aligns with the underlying model and the model properly reflects uncertainty in unexplored regions. In particular, we use a recently developed algorithm, Poisson ReWeighted Laplace Learning (PWLL) for the classifier and we introduce an acquisition function designed to measure uncertainty in this graph-based classifier that identifies unexplored regions of the data. We introduce a diagonal perturbation in PWLL which produces exponential localization of solutions, and controls the exploration versus exploitation tradeoff in active learning. We use the well-posed continuum limit of PWLL to rigorously analyze our method, and present experimental results on a number of graph-based image classification problems.

Use and Misuse of Machine Learning in Anthropology

Machine learning (ML), being now widely accessible to the research community at large, has fostered a proliferation of new and striking applications of these emergent mathematical techniques across a wide range of disciplines. In this paper, we will focus on a particular case study: the field of paleoanthropology, which seeks to understand the evolution of the human species based on biological and cultural evidence. As we will show, the easy availability of ML algorithms and lack of expertise on their proper use among the anthropological research community has led to foundational misapplications that have appeared throughout the literature. The resulting unreliable results not only undermine efforts to legitimately incorporate ML into anthropological research, but produce potentially faulty understandings about our human evolutionary and behavioral past. The aim of this paper is to provide a brief introduction to some of the ways in which ML has been applied within paleoanthropology; we also include a survey of some basic ML algorithms for those who are not fully conversant with the field, which remains under active development. We discuss a series of missteps, errors, and violations of correct protocols of ML methods that appear disconcertingly often within the accumulating body of anthropological literature. These mistakes include use of outdated algorithms and practices; inappropriate train/test splits, sample composition, and textual explanations; as well as an absence of transparency due to the lack of data/code sharing, and the subsequent limitations imposed on independent replication. We assert that expanding samples, sharing data and code, re-evaluating approaches to peer review, and, most importantly, developing interdisciplinary teams that include experts in ML are all necessary for progress in future research incorporating ML within anthropology.

Using machine learning on new feature sets extracted from 3D models of broken animal bones to classify fragments according to break agent

Distinguishing agents of bone modification at paleoanthropological sites is at the root of much of the research directed at understanding early hominin exploitation of large animal resources and the effects those subsistence behaviors had on early hominin evolution. However, current methods, particularly in the area of fracture pattern analysis as a signal of marrow exploitation, have failed to overcome equifinality. Furthermore, researchers debate the replicability and validity of current and emerging methods for analyzing bone modifications. Here we present a new approach to fracture pattern analysis aimed at distinguishing bone fragments resulting from hominin bone breakage and those produced by carnivores. This new method uses 3D models of fragmentary bone to extract a much richer dataset that is more transparent and replicable than feature sets previously used in fracture pattern analysis. Supervised machine learning algorithms are properly used to classify bone fragments according to agent of breakage with average mean accuracy of 77% across tests.

The Batch Artifact Scanning Protocol: A new method using computed tomography to rapidly create three-dimensional models of objects from large collections en masse

Within anthropology, the use of three-dimensional (3D) imaging has become increasingly standard and widespread since it broadens the available avenues for addressing a wide range of key issues. The ease with which 3D models can be shared has had major impacts for research, cultural heritage, education, science communication, and public engagement, as well as contributing to the preservation of the physical specimens and archiving collections in widely accessible data bases. Current scanning protocols have the ability to create the required research quality 3D models; however, they tend to be time and labor intensive and not practical when working with large collections. Here we describe a streamlined, Batch Artifact Scanning Protocol we have developed to rapidly create 3D models using a medical CT scanner. Though this method can be used on a variety of material types, we use a large collection of experimentally broken ungulate limb bones. Using the Batch Artifact Scanning Protocol, we were able to efficiently create 3D models of 2,474 bone fragments at a rate of less than $3$ minutes per specimen, as opposed to an average of 50 minutes per specimen using structured light scanning.

Graph-based Active Learning for Semi-supervised Classification of SAR Data

We present a novel method for classification of Synthetic Aperture Radar (SAR) data by combining ideas from graph-based learning and neural network methods within an active learning framework. Graph-based methods in machine learning are based on a similarity graph constructed from the data. When the data consists of raw images composed of scenes, extraneous information can make the classification task more difficult. In recent years, neural network methods have been shown to provide a promising framework for extracting patterns from SAR images. These methods, however, require ample training data to avoid overfitting. At the same time, such training data are often unavailable for applications of interest, such as automatic target recognition (ATR) and SAR data. We use a Convolutional Neural Network Variational Autoencoder (CNNVAE) to embed SAR data into a feature space, and then construct a similarity graph from the embedded data and apply graph-based semi-supervised learning techniques. The CNNVAE feature embedding and graph construction requires no labeled data, which reduces overfitting and improves the generalization performance of graph learning at low label rates. Furthermore, the method easily incorporates a human-in-the-loop for active learning in the data-labeling process. We present promising results and compare them to other standard machine learning methods on the Moving and Stationary Target Acquisition and Recognition (MSTAR) dataset for ATR with small amounts of labeled data.