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26 Apr 2022
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Archaeophenomics of ancient domestic plants and animals using geometric morphometrics : a review

Archaeophenomics: an up-and-coming field in bioarchaeology

Recommended by based on reviews by Stefan Schlager and 1 anonymous reviewer

Anneke H. van Heteren based on reviews by Stefan Schlager and 1 anonymous reviewer

Phenomics is the analysis of high-dimensional phenotypic data [1]. Phenomics research strategies are capable of linking genetic variation to phenotypic variation [2], but a genetic component is not absolutely necessary. The paper “Archaeophenomics of ancient domestic plants and animals using geometric morphometrics: a review” by Evin and colleagues [3] examines the use of geometric morphometrics in bioarchaeology and coins the term archaeophenomics. Archaeophenomics can be described as the large-scale phenotyping of ancient remains, and both addresses taxonomic identification, as well as infers spatio-temporal agrobiodiversity dynamics. It is a relatively new field in bioarchaeology with the first paper using this approach stemming from 2004. This study by Evin et al. [3] presents an excellent review and unquestionably demonstrates the potential of archaeophenomics.

The authors provide an exhaustive review specifically of bioarchaeological studies in international journals using geometric morphometrics to study archaeological remains of domestic species. Although geometric morphometrics lends itself well for archaeophenomics, readers should keep in mind that this is not the only method and other approaches might equally fall under archaeophenomics as long as high-dimensional phenotypic archaeological data are involved.

Distinguishing archaeophenomics from phenomics is important because of a critical difference. Archaeological remains are often altered by taphonomical processes. As such data may not be as complete as when working with modern specimens. Although this poses difficulties, morphometric analyses can usually still be performed as long as the structures presenting the relevant geometrical features are present. Even fragmented remains can be studied with a restricted version of the original landmarking/measurement protocol.

Evin et al. [3] define archaeophenomics as “phenomics of the past”. This is only partly correct. It can be deduced from their review that they really mean phenomics of our (human) past. This leaves a gap for phenomics of the non-human past, for which I suggest the term palaeophenomics. 

[1] Jin, L. (2021). Welcome to the Phenomics Journal. Phenomics, 1, 1–2. https://doi.org/10.1007/s43657-020-00009-4.
[2] Bilder, R.M., Sabb, F.W., Cannon, T.D., London, E.D., Jentsch, J.D., Stott Parker, D., Poldrack, R.A., Evans, C., Freimer, N.B. (2009). Phenomics: the systematic study of phenotypes on a genome-wide scale. Neuroscience, 164(1), 30-42. https://doi.org/10.1016/j.neuroscience.2009.01.027
[3] Evin, A., Bouby, L., Bonhomme, V., Jeanty, A., Jeanjean, M., Terral., J.-F. (2022). Archaeophenomics of ancient domestic plants and animals using geometric morphometrics: a review. Peer-reviewed and recommended by PCI Archaeology. https://doi.org/10.31219/osf.io/skeu5

 

Archaeophenomics of ancient domestic plants and animals using geometric morphometrics : a reviewAllowen Evin, Laurent Bouby, Vincent Bonhomme, Angèle Jeanty, Marine Jeanjean, Jean-Frédéric Terral<p>Geometric morphometrics revolutionized domestication studies through the precise quantification of the phenotype of ancient plant and animal remains. Geometric morphometrics allow for an increasingly detailed understanding of the past agrobiodi...Archaeobotany, Archaeometry, Bioarchaeology, ZooarchaeologyAnneke H. van Heteren2022-02-17 09:50:39 View
14 Sep 2020
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A way to break bones? The weight of intuitiveness

Breaking bones: Nature or Culture?

Recommended by and based on reviews by Terry O'Connor, Alan Outram and 1 anonymous reviewer

The nature of breaking long bones for obtaining marrow is important in Paleolithic archaeology, due to its widespread, almost universal, character. Provided that hammer-stone percussion marks can be correctly identified using experimental datasets (e.g., [1]), the anatomical location and count of the marks may be taken to reflect recurrent “cultural” traditions in the Paleolithic [2]. Were MP humans breaking bones intuitively or did they abide by a strict “protocol”, and, if the latter, was this protocol optimized for marrow retrieval or geared towards another, less obvious goal?
The new preprint by Vettese and colleagues [3] took a novel approach to this question, by conducting an experiment which involved novice butchers, relying on nothing but their intuition, and recording the way in which they broke marrow-rich bones. Some variability was noted in the “intuitive” patterns; indeed, future studies replicating this experiment and adding more variables such as more experienced butchers and non-bovid bones are warranted. Similarities in the means by which novice butchers break bones was also observed, and especially telling is the strong effect of anatomical features in most bones, except for the femur.

This paper provides a baseline for location analyses of percussion marks. Their dataset may therefore be regarded as a null hypothesis according to which the archaeological data could be tested. If Paleolithic patterns of percussion marks differ from Vettese et al.’s [3] “intuitive” patterns, then the null hypothesis is disproved and one can argue in favor of a learned pattern. The latter can be a result of ”culture”, as Vettese et al. [3] phrase it, in the sense of nonrandom action that draws on transmitted knowledge. Such comparisons bear a great potential for understanding the degree of technological behavior in the Paleolithic by factoring out the “natural” constraints of bone breakage patterns. Vettese et al. [3: fig. 14] started this discourse by comparing their experimental dataset to some Middle and Upper Paleolithic faunas; we are confident that many other studies will follow.

Bibliography

[1]Pickering, T.R., Egeland, C.P., 2006. Experimental patterns of hammerstone percussion damage on bones: Implications for inferences of carcass processing by humans. J. Archaeol. Sci. 33, 459–469. https://doi.org/10.1016/j.jas.2005.09.001

[2]Blasco, R., Rosell, J., Domínguez-Rodrigo, M., Lozano, S., Pastó, I., Riba, D., Vaquero, M., Peris, J.F., Arsuaga, J.L., de Castro, J.M.B., Carbonell, E., 2013. Learning by Heart: Cultural Patterns in the Faunal Processing Sequence during the Middle Pleistocene. PLoS One 8, e55863. https://doi.org/10.1371/journal.pone.0055863

[3]Vettese, D., Stavrova, T., Borel, A., Marin, J., Moncel, M.-H., Arzarello, M., Daujeard, C. (2020) A way to break bones? The weight of intuitiveness. BioRxiv, 011320, ver. 4 peer-reviewed and recommended by PCI Archaeology. https://doi.org/10.1101/2020.03.31.011320

A way to break bones? The weight of intuitivenessDelphine Vettese, Trajanka Stavrova, Antony Borel, Juan Marin, Marie-Hélène Moncel, Marta Arzarello, Camille Daujeard<p>During the Middle Paleolithic period, bone marrow extraction was an essential source of fat nutrients for hunter-gatherers especially throughout cold and dry seasons. This is attested by the recurrent findings of percussion marks in osteologica...Archaeometry, Bioarchaeology, Spatial analysis, Taphonomy, ZooarchaeologyBeatrice Demarchi2020-04-01 11:52:05 View
06 Oct 2023
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Body Mapping the Digital: Visually representing the impact of technology on archaeological practice.

Understanding archaeological documentation through a participatory, arts-based approach

Recommended by based on reviews by 2 anonymous reviewers

This paper presents the use of a participatory arts-based methodology to understand how digital and analogue tools affect individuals' participation in the process of archaeological recording and interpretation. The preliminary results of this work highlight the importance of rethinking archaeologists' relationship with different recording methods, emphasising the need to recognise the value of both approaches and to adopt a documentation strategy that exploits the strengths of both analogue and digital methods.

Although a larger group of participants with broader and more varied experience would have provided a clearer picture of the impact of technology on current archaeological practice, the article makes an important contribution in highlighting the complex and not always easy transition that archaeologists trained in analogue methods are currently experiencing when using digital technology.

 This is assessed by using arts-based methodologies to enable archaeologists to consider how digital technologies are changing the relationship between mind, body and practice.

I found the range of experiences described in the papers by the archaeologists involved in the experiment particularly interesting and very representative of the change in practice that we are all experiencing.  As the article notes, the two approaches cannot be directly compared because they offer different possibilities: if analogue methods foster a deeper connection with the archaeological material, digital documentation seems to be perceived as more effective in terms of data capture, information exchange and data sharing (Araar et al., 2023).

It seems to me that an important element to consider in such a study is the generational shift and the incredible divide between native and non-native digital.

 The critical issues highlighted in the paper are central and provide important directions for navigating this ongoing (digital) transition.

References

Araar, L., Morgan, C. and Fowler, L. (2023) Body Mapping the Digital: Visually representing the impact of technology on archaeological practice., Zenodo, 7990581, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7990581

Body Mapping the Digital: Visually representing the impact of technology on archaeological practice.Araar, Leila; Morgan, Colleen; Fowler, Louise<p>This paper uses a participatory, art-based methodology to understand how digital and analog tools impact individuals' experience and perceptions of archaeological recording. Body mapping involves the co-creation of life-sized drawings and narra...Computational archaeology, Theoretical archaeologyNicolo Dell'Unto2023-06-01 09:06:52 View
12 Dec 2022
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Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?

Mobility in pigs: A microanatomical perspective

Recommended by ORCID_LOGO based on reviews by Max Price and Ignacio A. Lazagabaster

Pig domestication and husbandry involved complex processes of introduction, introgression, and feralization that challenge our understanding of human/suid interactions in ancient times. This challenge is a constant stimulus for the development of novel methods and techniques to illuminate aspects of early pig husbandry, such as human-induced changes in mobility. Using geometric morphometrics, Harbers et al. (2020) have shown that the calcaneus records a plastic response to reduced mobility and hence to human management. In the present study, Cottereau et al. (2022) explore the possibility that a similar plastic response to different mobility regimes can be observed in the microanatomy of the calcaneus using CT scans. Their research utilizes a sample of calcanei obtained from Mesolithic specimens, and also from recent suids kept in natural habitat, large pen, and stall. Their results suggest that bone microanatomy is more affected by population differences than by mobility patterns, as illustrated by the similarity between Mesolitic boar calcanei and their difference from recent, free wild boar. 


This is an important negative result, and, as Max Price has remarked in his review, such results are biased against in the scientific literature. Beyond the merit of its careful planning and execution, I find the study thought-provoking, as it marks a scale threshold below which the plastic signal of mobility is lost. At the same breath, the close similarity between Mesolithic boars in the microanatomical scale opens a door to the investigation of inter-population anatomical differences beyond that threshold. 

 

References

Cottereau R, Ortiz K, Locatelli Y, Houssaye A, Cucchi T (2022), bioRxiv, 504790, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.1101/2022.08.22.504790

Harbers H, Neaux D, Ortiz K, Blanc B, Laurens F, Baly I, Callou C, Schafberg R, Haruda A, Lecompte F, Casabianca F, Studer J, Renaud S, Cornette R, Locatelli Y, Vigne J-D, Herrel A, Cucchi T (2020) The mark of captivity: plastic responses in the ankle bone of a wild ungulate (Sus scrofa). Royal Society Open Science, 7, 192039. https://doi.org/10.1098/rsos.192039

 

Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?Romain Cottereau, Katia Ortiz, Yann Locatelli, Alexandra Houssaye*, Thomas Cucchi*<p style="text-align: justify;">Reduced mobility associated with captivity induce changes in biomechanical stress on the skeleton of domesticated animals. Due to bone plasticity, the morphology and the internal structure of the bones can respond t...Neolithic, ZooarchaeologyNimrod Marom2022-08-26 20:29:01 View
08 Jan 2024
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Comparing summed probability distributions of shoreline and radiocarbon dates from the Mesolithic Skagerrak coast of Norway

Taking the Reverend Bayes to the seaside: Improving Norwegian Mesolithic shoreline dating with advanced statistical approaches

Recommended by based on reviews by 2 anonymous reviewers

The paper entitled “Comparing summed probability distributions of shoreline and radiocarbon dates from the Mesolithic Skagerrak coast of Norway” by Isak Roalkvam and Steinar Solheim (2024) sheds new light on the degree to which shoreline dating may be used as a reliable chronological and palaeodemographic proxy in the Mesolthic of southern Norway.

Based on geologically motivated investigations of eustatic and isostatic sea-level changes, shoreline dating has long been used as a method to date archaeological sites in Scandinavia, not least in Norway (e.g., Bjerck 2008; Astrup 2018). Establishing reliable sea-level curves requires much effort and variations across regions may be substantial. While this topic has seen a great deal of attention in Norway specifically, many purely geological questions remain. In addition, dating archaeological sites by linking their elevation to previously established seal-level curves relies strongly on the foundational assumption that such sites were in fact shore-bound. Given the strong contrast between terrestrial and marine productivity in high-latitude regions such as Norway, this assumption per se is not unreasonable. It is very likely that the sea has played a decisive role in the lives of Stone Age peoples throughout (Persson et al. 2017), just as it has in later periods here. However, many confounding factors relating to both taphonomy and human behaviour are also likely to have loosened the shore/site relationship. Systematic variations driven by cultural norms about settlement location, mobility, as well as factors such as shelter construction, fuel use and a range of other possible factors could variously have impacted the validity or at least the precision of shoreline dating.

By developing a new methodology for handling and assessing a large number of shoreline dated sites, Roalkvam and Solheim use state-of-the-art Bayesian statistical methods to compare shoreline and radiocarbon dates as proxies for population activity. The probabilistic treatment of shoreline dates in this way is novel, and the divergences between the two data sets are interpreted by the authors in light of specific behavioural, cultural, and demographic changes. Many of the peaks and troughs observed in these time-series may be interpreted in light of long-observed cultural transitions while others may relate to population dynamics now also visible in palaeogenomic analyses (Günther et al. 2018; Manninen et al. 2021). Overall, this paper makes an innovative and fresh contribution to the use of shoreline dating in Norwegian archaeology, specifically by articulating it with recent developments in Open Science and data-driven approaches to archaeological questions (Marwick et al. 2017).

References

Astrup, P. M. 2018. Sea-Level Change in Mesolithic Southern Scandinavia : Long- and Short-Term Effects on Society and the Environment. Aarhus: Aarhus University Press.

Bjerck, H. B. 2008. Norwegian Mesolithic Trends: A Review. In Mesolithic Europe, edited by Geoff Bailey and Penny Spikins, 60–106. Cambridge: Cambridge University Press.

Günther, T., Malmström, H., Svensson, E. M., Omrak, A., Sánchez-Quinto, F., Kılınç, G. M., Krzewińska, M. et al. 2018. Population Genomics of Mesolithic Scandinavia: Investigating Early Postglacial Migration Routes and High-Latitude Adaptation. PLOS Biology 16 (1): e2003703. https://doi.org/10.1371/journal.pbio.2003703

Manninen, M. A., Damlien, H., Kleppe, J. I., Knutsson, K., Murashkin, A., Niemi, A. R., Rosenvinge, C. S. and Persson, P. 2021. First Encounters in the North: Cultural Diversity and Gene Flow in Early Mesolithic Scandinavia. Antiquity 95 (380): 310–28. https://doi.org/10.15184/aqy.2020.252

Marwick, B., d’Alpoim Guedes, J. A., Barton, C. M., Bates, L. A., Baxter, M., Bevan, A., Bollwerk, E. A. et al. 2017. Open Science in Archaeology. The SAA Archaeological Record 17 (4): 8–14. https://doi.org/10.31235/osf.io/72n8g

Persson, P., Riede, F., Skar, B., Breivik, H. M. and Jonsson, L. 2017. The Ecology of Early Settlement in Northern Europe: Conditions for Subsistence and Survival. Sheffield: Equinox.

Roalkvam, I. and Solheim, S. (2024). Comparing summed probability distributions of shoreline and radiocarbon dates from the Mesolithic Skagerrak coast of Norway, SocArXiv, 2f8ph, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.31235/osf.io/2f8ph

Comparing summed probability distributions of shoreline and radiocarbon dates from the Mesolithic Skagerrak coast of NorwayIsak Roalkvam, Steinar Solheim <p>By developing a new methodology for handling and assessing a large number of shoreline dated sites, this paper compares the summed probability distribution of radiocarbon dates and shoreline dates along the Skagerrak coast of south-eastern Norw...Computational archaeology, Dating, Europe, Mesolithic, PaleoenvironmentFelix Riede2023-09-26 16:43:29 View
08 Feb 2024
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CORPUS NUMMORUM – A Digital Research Infrastructure for Ancient Coins

The valuable Corpus Nummorum: a not so Little Minion

Recommended by ORCID_LOGO based on reviews by Fleur Kemmers and 1 anonymous reviewer

The paper under review/recommendation deals with Corpus Nummorum (Peter et al. 2024). The Corpus Nummorum (CN) is web portal for ancient Greek coins from various collections (https://www.corpus-nummorum.eu/). The CN is a database and research tool for Greek coins dating between 600 BCE to 300 CE. While many traditional collection databases aim at collecting coins, CN also includes coin dies, coin types and issues. It aims at achieving a complete online coin type catalogue. The paper is not a paper in a traditional sense, but presents the CN as a tool and shows the functionalities in the system. The relevance and the possibilities of the CN for numismatists is made clear in the paper and the merits are clear even for me as a Roman archaeologist and non-numismatist.

The CN was presented as a poster at the CAA 2023 in Amsterdam during “S03. Our Little Minions pt. V: small tools with major impact”, organized by Moritz Mennenga, Florian Thiery, Brigit Danthine and myself (Mennenga et al. 2023). Little Minions help us significantly in our daily work as small self-made scripts, home-grown small applications and small hardware devices. They often reduce our workload or optimize our workflows, but are generally under-represented during conferences and not often presented to the outside world. Therefore, the Little Minions form a platform that enables researchers and software engineers to share these tools (Thiery, Visser and Mennenga 2021). Little Minions have become a well known happening within the CAA-community since we started this in 2018, also because we do not only allow 10-minute lightning talks, but also spontaneous stand-up presentations during the conference. A full list of all minions presented in the past, can be found online: https://caa-minions.github.io/minions/. In a strict sense the CN would not count as a Little Minion, because it is a large project consisting of many minions that help a numismatist in his/her daily work. The CN seems a very Big Minion in that sense.

Personally, I am very happy to see the database being developed as a fully open system and that code can be found on Github (https://github.com/telota/corpus-nummorum-editor), and also made citable with citation information in GitHub (see https://citation-file-format.github.io/) and a version deposited in Zenodo with DOI (Köster and Franke 2024). In addition, the authors claim that the CN will be shared based on the FAIR-principles (Wilkinson et al. 2016, 2019). These guidelines are developed to improve the Findability, Accessibility, Interoperability, and Reuse of digital data. I feel that CN will be a way forward in open numismatics and open archaeology.

The CN is well known within the numismatist community and it was hard to find reviewers in this close community, because many potential reviewers work together with one or more of the authors, or are involved in the project. This also proves the relevance of the CN to the research community and beyond. Luckily, a Roman numismatist and a specialist in digital/computational archaeology were able to provide valuable feedback on the current paper. The reviewers only submitted feedback on the first version of the paper (Peter et al. 2023).

The numismatist was positive on the content and the usefulness of CN for the discipline in general. However, she pointed out some important points that need to be addressed. The digital specialist was positive is various aspects, but also raised some important issues in relation to technical aspects and the explanation thereof. While both were positive on the project and the paper in general, both reviewers pointed out some issues that were largely addressed in the second version of this paper. The revised version was edited throughout and the paper was strongly improved.

The Corpus Nummorum is well presented in this easy to read paper, although the explanations can sometimes be slightly technical. This paper gives a good introduction to the CN and I recommend this for publication. I sincerely hope that the CN will contribute and keep on contributing to the domains of numismatics, (digital) archaeology and open science in general.

References

Köster, J and Franke, C. 2024 Corpus Nummorum Editor. https://doi.org/10.5281/zenodo.10458195

Mennenga, M, Visser, RM, Thiery, F and Danthine, B. 2023 S03. Our Little Minions pt. V: small tools with major impact. In:. Book of Abstracts. CAA 2023: 50 Years of Synergy. Amsterdam: Zenodo. pp. 249–251. https://doi.org/10.5281/ZENODO.7930991

Peter, U, Franke, C, Köster, J, Tolle, K, Gampe, S and Stolba, VF. 2023 CORPUS NUMMORUM – A Digital Research Infrastructure for Ancient Coins. https://doi.org/10.5281/ZENODO.8263518

Peter, U., Franke, C., Köster, J., Tolle, K., Gampe, S. and Stolba, V. F. (2024). CORPUS NUMMORUM – A Digital Research Infrastructure for Ancient Coins, Zenodo, 8263517, ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.8263517

Thiery, F, Visser, RM and Mennenga, M. 2021 Little Minions in Archaeology An open space for RSE software and small scripts in digital archaeology. https://doi.org/10.5281/ZENODO.4575167

Wilkinson, MD, Dumontier, M, Aalbersberg, IjJ, Appleton, G, Axton, M, Baak, A, Blomberg, N, Boiten, J-W, da Silva Santos, LB, Bourne, PE, Bouwman, J, Brookes, AJ, Clark, T, Crosas, M, Dillo, I, Dumon, O, Edmunds, S, Evelo, CT, Finkers, R, Gonzalez-Beltran, A, Gray, AJG, Groth, P, Goble, C, Grethe, JS, Heringa, J, ’t Hoen, PAC, Hooft, R, Kuhn, T, Kok, R, Kok, J, Lusher, SJ, Martone, ME, Mons, A, Packer, AL, Persson, B, Rocca-Serra, P, Roos, M, van Schaik, R, Sansone, S-A, Schultes, E, Sengstag, T, Slater, T, Strawn, G, Swertz, MA, Thompson, M, van der Lei, J, van Mulligen, E, Velterop, J, Waagmeester, A, Wittenburg, P, Wolstencroft, K, Zhao, J and Mons, B. 2016 The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3(1): 160018. https://doi.org/10.1038/sdata.2016.18

Wilkinson, MD, Dumontier, M, Jan Aalbersberg, I, Appleton, G, Axton, M, Baak, A, Blomberg, N, Boiten, J-W, da Silva Santos, LB, Bourne, PE, Bouwman, J, Brookes, AJ, Clark, T, Crosas, M, Dillo, I, Dumon, O, Edmunds, S, Evelo, CT, Finkers, R, Gonzalez-Beltran, A, Gray, AJG, Groth, P, Goble, C, Grethe, JS, Heringa, J, Hoen, PAC ’t, Hooft, R, Kuhn, T, Kok, R, Kok, J, Lusher, SJ, Martone, ME, Mons, A, Packer, AL, Persson, B, Rocca-Serra, P, Roos, M, van Schaik, R, Sansone, S-A, Schultes, E, Sengstag, T, Slater, T, Strawn, G, Swertz, MA, Thompson, M, van der Lei, J, van Mulligen, E, Jan Velterop, Waagmeester, A, Wittenburg, P, Wolstencroft, K, Zhao, J and Mons, B. 2019 Addendum: The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 6(1): 6. https://doi.org/10.1038/s41597-019-0009-6

CORPUS NUMMORUM – A Digital Research Infrastructure for Ancient CoinsUlrike Peter, Claus Franke, Jan Köster, Karsten Tolle, Sebastian Gampe, Vladimir F. Stolba<p>CORPUS NUMMORUM indexes ancient Greek coins from various landscapes and develops typologies. The coins and coin types are published on the multilingual website www.corpus-nummorum.eu utilizing numismatic authority data and adhering to FAIR prin...Antiquity, ClassicRonald Visser2023-08-18 17:37:51 View
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Creating an Additional Class Layer with Machine Learning to counter Overfitting in an Unbalanced Ancient Coin Dataset

A significant contribution to the problem of unbalanced data in machine learning research in archaeology

Recommended by ORCID_LOGO based on reviews by Simon Carrignon, Joel Santos and 1 anonymous reviewer

This paper [1] presents an innovative approach to address the prevalent challenge of unbalanced datasets in coin type recognition, shifting the focus from coin class type recognition to coin mint recognition. Despite this shift, the issue of unbalanced data persists. To mitigate this, the authors introduce a method to split larger classes into smaller ones, integrating them into an 'additional class layer'.

Three distinct machine learning (ML) methodologies were employed to identify new possible classes, with one approach utilising unsupervised clustering alongside manual intervention, while the others leverage object detection, and Natural Language Processing (NLP) techniques. However, despite these efforts, overfitting remained a persistent issue, prompting the authors to explore alternative methods such as dataset improvement and Generative Adversarial Networks (GANs).

The paper contributes significantly to the intersection of ML techniques and archaeology, particularly in addressing overfitting challenges. Furthermore, the authors' candid acknowledgment of the limitations of their approaches serves as a valuable resource for researchers encountering similar obstacles.

This study stems from the D4N4 project, aimed at developing a machine learning-based coin recognition model for the extensive "Corpus Nummorum" dataset, comprising over 19,600 coin types and 49,000 coins from various ancient landscapes. Despite encountering challenges with overfitting due to the dataset's imbalance, the authors' exploration of multiple methodologies and transparent documentation of their limitations enriches the academic discourse and provides a foundation for future research in this field.

Reference

[1] Gampe, S. and Tolle, K. (2024). Creating an Additional Class Layer with Machine Learning to counter Overfitting in an Unbalanced Ancient Coin Dataset. Zenodo, 8298077, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.8298077

Creating an Additional Class Layer with Machine Learning to counter Overfitting in an Unbalanced Ancient Coin DatasetSebastian Gampe, Karsten Tolle<p>We have implemented an approach based on Convolutional Neural Networks (CNN) for mint recognition for our Corpus Nummorum (CN) coin dataset as an alternative to coin type recognition, since we had too few instances for most of the types (classe...Computational archaeologyAlex Brandsen2023-08-29 16:26:41 View
13 Jan 2024
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Dealing with post-excavation data: the Omeka S TiMMA web-database

Managing Archaeological Data with Omeka S

Recommended by ORCID_LOGO based on reviews by Electra Tsaknaki and 1 anonymous reviewer

Managing data in archaeology is a perennial problem. As the adage goes, every day in the field equates to several days in the lab (and beyond). For better or worse, past archaeologists did all their organizing and synthesis manually, by hand, but since the 1970s ways of digitizing data for long term management and analysis have gained increasing attention [1]. It is debatable whether this ever actually made things easier, particularly given the associated problem of sustainable maintenance and accessibility of the data. Many older archaeologists, for instance, still have reels and tapes full of data that now require a new form of archaeology to excavate (see [2] for an unrealized idea on how to solve this).

Today, the options for managing digital archaeological data are limited only by one’s imagination. There are systems built specifically for archaeology, such as Arches [3], Ark [4], Codifi [5], Heurist [6], InTerris Registries [7], OpenAtlas [8], S-Archeo [9], and Wild Note [10], as well as those geared towards museum collections like PastPerfect [11] and CatalogIt [12], among others. There are also mainstream databases that can be adapted to archaeological needs like MS Access [13] and Claris FileMaker [14], as well as various web database apps that function in much the same way (e.g., Caspio [15], dbBee [16], Amazon's Simpledb [17], Sci-Note [18], etc.) — all with their own limitations in size, price, and utility. One could also write the code for specific database needs using pre-built frameworks like those in Ruby-On-Rails [19] or similar languages. And of course, recent advances in machine-learning and AI will undoubtedly bring new solutions in the near future.

But let’s be honest — most archaeologists probably just use Excel. That's partly because, given all the options, it is hard to decide the best tool and whether its worth changing from your current system, especially given few real-world examples in the literature. Bastien Rueff’s new paper [20] is therefore a welcomed presentation on the use of Omeka S [21] to manage data collected for the Timbers in Minoan and Mycenaean Architecture (TiMMA) project. Omeka S is an open-source web-database that is based in PHP and MySQL, and although it was built with the goal of connecting digital cultural heritage collections with other resources online, it has been rarely used in archaeology. Part of the issue is that Omeka Classic was built for use on individual sites, but this has now been scaled-up in Omeka S to accommodate a plurality of sites. 

Some of the strengths of Omeka S include its open-source availability (accessible regardless of budget), the way it links data stored elsewhere on the web (keeping the database itself lean), its ability to import data from common file types, and its multi-lingual support. The latter feature was particularly important to the TiMAA project because it allowed members of the team (ranging from English, Greek, French, and Italian, among others) to enter data into the system in whatever language they felt most comfortable.

However, there are several limitations specific to Omeka S that will limit widespread adoption. Among these, Omeka S apparently lacks the ability to export metadata, auto-fill forms, produce summations or reports, or provide basic statistical analysis. Its internal search capabilities also appear extremely limited. And that is not to mention the barriers typical of any new software, such as onerous technical training, questionable long-term sustainability, or the need for the initial digitization and formatting of data. But given the rather restricted use-case for Omeka S, it appears that this is not a comprehensive tool but one merely for data entry and storage that requires complementary software to carry out common tasks.

As such, Rueff has provided a review of a program that most archaeologists will likely not want or need. But if one was considering adopting Omeka S for a project, then this paper offers critical information for how to go about that. It is a thorough overview of the software package and offers an excellent example of its use in archaeological practice.


NOTES

[1] Doran, J. E., and F. R. Hodson (1975) Mathematics and Computers in Archaeology. Harvard University Press.

[2] Snow, Dean R., Mark Gahegan, C. Lee Giles, Kenneth G. Hirth, George R. Milner, Prasenjit Mitra, and James Z. Wang (2006) Cybertools and Archaeology. Science 311(5763):958–959.

[3] https://www.archesproject.org/

[4] https://ark.lparchaeology.com/

[5] https://codifi.com/

[6] https://heuristnetwork.org/

[7] https://www.interrisreg.org/

[8] https://openatlas.eu/

[9] https://www.skinsoft-lab.com/software/archaelogy-collection-management

[10] https://wildnoteapp.com/

[11] https://museumsoftware.com/

[12] https://www.catalogit.app/

[13] https://www.microsoft.com/en-us/microsoft-365/access

[14] https://www.claris.com/filemaker/

[15] https://www.caspio.com/

[16] https://www.dbbee.com/

[17] https://aws.amazon.com/simpledb/

[18] https://www.scinote.net/

[19] https://rubyonrails.org/

[20] Rueff, Bastien (2023) Dealing with Post-Excavation Data: The Omeka S TiMMA Web-Database. peer-reviewed and recommended by Peer Community in Archaeology. https://zenodo.org/records/7989905

[21] https://omeka.org/

 

Dealing with post-excavation data: the Omeka S TiMMA web-databaseBastien Rueff<p>This paper reports on the creation and use of a web database designed as part of the TiMMA project with the Content Management System Omeka S. Rather than resulting in a technical manual, its goal is to analyze the relevance of using Omeka S in...Buildings archaeology, Computational archaeologyJonathan Hanna2023-05-31 12:16:25 View
29 Aug 2023
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Designing Stories from the Grave: Reviving the History of a City through Human Remains and Serious Games

AR and VR Gamification as a proof-of-concept

Recommended by ORCID_LOGO based on reviews by Sophie C. Schmidt and Tine Rassalle

Tsaknaki et al. (2023) discuss a work-in-progress project in which the presentation of Cultural Heritage is communicated using Serious Games techniques in a story-centric immersive narration instead of an exhibit-centered presentation with the use of Gamification, Augmented and Virtual Reality technologies. In the introduction the authors present the project called ECHOES, in which knowledge about the past of Thessaloniki, Greece is planned to be processed as an immersive and interactive experience. After presenting related work and the methodology, the authors describe the proposed design of the Serious Game and close the article with a discussion and conclusions.

The paper is interesting because it highlights an ongoing process in the realm of the visualization of Cultural Heritage (see for example Champion 2016). The process described by the authors on how to accomplish this by using Serious Games, Gamification, Augmented and Virtual Reality is promising, although still hypothetical as the project is ongoing. It remains to be seen if the proposed visuals and interactive elements will work in the way intended and offer users an immersive experience after all. A preliminary questionnaire already showed that most of the respondents were not familiar with these technologies (AR, VR) and in my experience these numbers only change slowly. One way to overcome the technological barrier however might be the gamification of the experience, which the authors are planning to implement.

I decided to recommend this article based on the remarks of the two reviewers, which the authors implemented perfectly, as well as my own evaluation of the paper. Although still in progress it seems worthwhile to have this article as a basis for discussion and comparison to similar projects. However, the article did not mention the possible longevity of data and in which ways the usability of the Serious Game will be secured for long-term storage. One eminent problem in these endeavors is, that we can read about these projects, but never find them anywhere to test them ourselves (see for example Gabellone et al. 2016). It is my intention with this review and the recommendation, that the ECHOES project will find a solution for this problem and that we are not only able to read this (and forthcoming) article(s) about the ECHOES project, but also play the Serious Game they are proposing in the near and distant future.

References


Champion, Erik Malcolm. 2016. „Entertaining the Similarities and Distinctions between Serious Games and Virtual Heritage Projects“. Entertainment Computing 14 (Mai): 67–74. https://doi.org/10.1016/j.entcom.2015.11.003

Gabellone, Francesco, Antonio Lanorte, Nicola Masini, und Rosa Lasaponara. 2016. „From Remote Sensing to a Serious Game: Digital Reconstruction of an Abandoned Medieval Village in Southern Italy“. Journal of Cultural Heritage. https://doi.org/10.1016/j.culher.2016.01.012

Tsaknaki, Electra, Anastasovitis, Eleftherios, Georgiou, Georgia, Alagialoglou, Kleopatra, Mavrokostidou, Maria, Kartsiakli, Vasiliki, Aidonis, Asterios, Protopsalti, Tania, Nikolopoulos, Spiros, and Kompatsiaris, Ioannis. (2023). Designing Stories from the Grave: Reviving the History of a City through Human Remains and Serious Games, Zenodo, 7981323, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7981323

Designing Stories from the Grave: Reviving the History of a City through Human Remains and Serious GamesTsaknaki, Electra; Anastasovitis, Eleftherios; Georgiou, Georgia; Alagialoglou, Kleopatra; Mavrokostidou, Maria; Kartsiakli, Vasiliki; Aidonis, Asterios; Protopsalti, Tania; Nikolopoulos, Spiros; Kompatsiaris, Ioannis<p>The main challenge of the current digital transition is to utilize computing media and cutting-edge technologyin a more meaningful way, which would make the archaeological and anthropological research outcomes relevant to a heterogeneous audien...Bioarchaeology, Computational archaeology, EuropeSebastian Hageneuer2023-05-29 13:19:46 View
03 Feb 2024
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Digital surface models of crops used in archaeological feature detection – a case study of Late Neolithic site Tomašanci-Dubrava in Eastern Croatia

What lies on top lies also beneath? Connecting crop surface modelling to buried archaeology mapping.

Recommended by ORCID_LOGO based on reviews by Ian Moffat and Geert Verhoeven

This paper (Sosic et al. 2024) explores the Neolithic landscape of the Sopot culture in Đakovština, Eastern Slavonija, revealing a network of settlements through a multi-faceted approach that combines aerial archaeology, magnetometry, excavation, and field survey. This strategy facilitates scalable research tailored to the particularities of each site and allows for improved representations of buried archaeology with minimal intrusion. 

Using the site of Tomašanci-Dubrava as an example of the overall approach, the study further explores the use of drone imagery for 3D surface modeling, revealing a consistent correlation between crop surface elevation during full plant growth and ground terrain after ploughing, attributed to subsurface archaeological features. Results are correlated with magnetic survey and test-pitting data to validate the micro-topography and clarify the relationship between different subsurface structures.

The results obtained are presented in a comprehensive way, including their source data, and are contextualized in relation to conventional cropmark detection approaches and expectations. I found this aspect very interesting, since the crop surface and terrain models contradict typical or textbook examples of cropmark detection, where the vegetation is projected to appear higher in ditches and lower in areas with buried archaeology (Renfrew & Bahn 2016, 82). Regardless, the findings suggest the potential for broader applications of crop surface or canopy height modelling in landscape wide surveys, utilizing ALS data or aerial photographs.  

It seems then that the authors make a valid argument for a layered approach in landscape-based site detection, where aerial imagery can be used to accurately map the topography of areas of interest, which can then be further examined at site scale using more demanding methods, such as geophysical survey and excavation. This scalability enhances the research's relevance in broader archaeological and geographical contexts and renders it a useful example in site detection and landscape-scale mapping.

References

Renfrew, C. and Bahn, P. (2016). Archaeology: theories, methods and practice. Thames and Hudson. 

Sosic Klindzic, R., Vuković, M., Kalafatić, H. and Šiljeg, B. (2024). Digital surface models of crops used in archaeological feature detection – a case study of Late Neolithic site Tomašanci-Dubrava in Eastern Croatia, Zenodo, 7970703, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7970703

Digital surface models of crops used in archaeological feature detection – a case study of Late Neolithic site Tomašanci-Dubrava in Eastern CroatiaSosic Klindzic Rajna; Vuković Miroslav; Kalafatić Hrvoje; Šiljeg Bartul<p>This paper presents the results of a study on the neolithic landscape of the Sopot culture in the area of Đakovština in Eastern Slavonija. A vast network of settlements was uncovered using aerial archaeology, which was further confirmed and chr...Landscape archaeology, Neolithic, Remote sensing, Spatial analysisMarkos Katsianis2023-09-01 12:57:04 View