Enhancing Sampling in Computational Statistics Using Modified Hamiltonians

The Hamiltonian Monte Carlo (HMC) method has been recognized as a powerful sampling tool in computational statistics. In this thesis, we show that performance of HMC can be dramatically improved by replacing Hamiltonians in the Metropolis test with modified Hamiltonians, and a complete momentum update with a partial momentum refreshment. The resulting generalized HMC importance sampler, which we called Mix & Match Hamiltonian Monte Carlo (MMHMC), arose as an extension of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method, previously proposed for molecular simulation. The MMHMC method adapts GSHMC specifically to computational statistics and enriches it with new essential features: (i) the efficient algorithms for computation of modified Hamiltonians; (ii) the implicit momentum update procedure and (iii) the two-stage splitting integration schemes specially derived for the methods sampling with modified Hamiltonians. In addition, different optional strategies for momentum update and flipping are introduced as well as algorithms for adaptive tuning of parameters and efficient sampling of multimodal distributions are developed. MMHMC has been implemented in the in-house software package HaiCS (Hamiltonians in Computational Statistics) written in C, tested on the popular statistical models and compared in sampling efficiency with HMC, Generalized Hybrid Monte Carlo, Riemann Manifold Hamiltonian Monte Carlo, Metropolis Adjusted Langevin Algorithm and Random Walk Metropolis-Hastings. The analysis of time-normalized effective sample size reveals the superiority of MMHMC over popular sampling techniques, especially in solving high-dimensional problems.FPU12/05209, MTM2013–46553–C3–1–

Pločnik: technology of metal production

Metallurgical materials recovered during the excavation campaigns of 2012 and 2013 in Pločnik show similar characteristics to samples already studied and published previously (Radivojević 2012, 2015; Radivojević and Kuzmanović Cvetković 2014; Radivojević and Rehren 2016; Radivojević et al. 2013). They include, as for Belovode (Chapter 11), predominantly malachite minerals and ores (Table 1), that occur as roughly beneficiated pieces and without a distinct spatial patterning in Trench 24. In comparison to Belovode, they occur less frequently across all five horizons, partially explained by the fact that most of Trench 24 is a large rectangular feature – a house (F1=F2=F4=F5=F6=F10), and there is very little economic area surrounding it

Modified Hamiltonian Monte Carlo for Bayesian Inference

The Hamiltonian Monte Carlo (HMC) method has been recognized as a powerful sampling tool in computational statistics. We show that performance of HMC can be significantly improved by incorporating importance sampling and an irreversible part of the dynamics into a chain. This is achieved by replacing Hamiltonians in the Metropolis test with modified Hamiltonians, and a complete momentum update with a partial momentum refreshment. We call the resulting generalized HMC importance sampler—Mix & Match Hamiltonian Monte Carlo (MMHMC). The method is irreversible by construction and further benefits from (i) the efficient algorithms for computation of modified Hamiltonians; (ii) the implicit momentum update procedure and (iii) the multi-stage splitting integrators specially derived for the methods sampling with modified Hamiltonians. MMHMC has been implemented, tested on the popular statistical models and compared in sampling efficiency with HMC, Riemann Manifold Hamiltonian Monte Carlo, Generalized Hybrid Monte Carlo, Generalized Shadow Hybrid Monte Carlo, Metropolis Adjusted Langevin Algorithm and Random Walk Metropolis-Hastings. To make a fair comparison, we propose a metric that accounts for correlations among samples and weights, and can be readily used for all methods which generate such samples. The experiments reveal the superiority of MMHMC over popular sampling techniques, especially in solving high dimensional problems.Agile BioFoundry (http://agilebiofoundry.org) supported by the U.S. Department of Energy, Energy Efficiency and Renewable Energy, Bioenergy Technologies Office, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy

Belovode: technology of metal production

Metal production evidence yielded during the excavation campaigns 2012 and 2013 in Belovode shows similar characteristic to the samples from the site studied and published previously (Radivojević 2012, 2013, 2015; Radivojević and Kuzmanović Cvetković 2014; Radivojević and Rehren 2016; Radivojević et al. 2010a). These are predominantly malachite mineral and ore samples, most likely roughly beneficiated (no samples larger than 2–3 cm in length, see Appendix B_Ch11), and very importantly, without any significant spatial pattern in the excavated area of Trench 18 or its extension (T18ext henceforth). These minerals were discovered in all areas, whether in living or economic spaces, inside the dwellings and other features, and across the excavation spits, which is why they have also been found by previous excavation campaigns (Šljivar 1993–2009)

A stylized model for the continuous double auction

A stylized phenomenological model for the continuous double auction is introduced. This model is equivalent to two uncoupled M/M/1 queues. The conditions for statistical equilibrium (ergodicity) are derived. The results of Monte Carlo simulations are presented on the behaviour of price differences and log-returns

Metallurgical knowledge and networks of supply in the 5th millennium BC Balkans: Belovode and Pločnik in their regional context

The recent set of excavations (campaigns 2012 and 2013) at the sites of Belovode and Pločnik (see Chapters 11 and 26) have shown the use of copper minerals and metallurgical activities to be highly consistent with results from previous analytical research (Radivojević 2007, 2012, 2013, 2015; Radivojević et al. 2010a; Radivojević and Rehren 2016). Specific aspects to emerge so far include: persistent selection of black and green manganese-rich copper ores for metal extraction; similar engineering parameters involved in the early copper smelting technology; field evidence from Belovode supporting the presence of pottery- lined hole-in-the-ground installations; consistent metal making and working technology remains at both sites; and direct absolute dating evidence that leaves no doubt for c. 5000 BC as the beginning of copper metallurgy in the Balkans. In this chapter we will synthesise the evidence for this c. 7,000 years old copper production technology within the Vinča culture, in its local and regional perspective, including data and debates on the provenance of copper ores

The Rise of Metallurgy in Eurasia: Evolution, organisation and consumption of early metal in the Balkans: an introduction to the project

The study of early metallurgy has many aspects and has, accordingly, taken many forms and foci (Rehren and Pernicka 2008 and literature therein). Some scholars have documented the morpho-typological evolution of artefact types and some have explored the role of metals in creating social hierarchies, in storing and displaying wealth, or the more transcendent role of metals in a variety of rituals. Other researchers are fascinated by the skills and technical achievements of the metalworkers and their intangible heritage as expressed in intricate castings, ingenious manufacturing methods and elaborate surface decorations. Yet others study the transformation of rocks and ores to metal as documented in the slags and furnace fragments or try to trace the geological origins of metal objects, as a proxy for the movement of people, materials, and ideas. The investigation of ancient mining extends well beyond the field of archaeometallurgy, with mines for flint, pigments, precious stones and salt all pre-dating metal smelting, and quarrying for building stone exceeding metal mining both in scale and value generation (e.g. Schauer et al. 2020). This range of interests inevitably implies the application of a multitude of methods, borrowed from a host of mother disciplines, adjusted and refined to form the interdisciplinary field of archaeometallurgy. It also makes any holistic project both a daunting prospect and an exercise in interdisciplinary diplomacy

Where do we take global early metallurgy studies next?

The results and experiences gained from the multidisciplinary and holistic approaches underlying the Rise of Metallurgy in Eurasia project provide an opportunity, not only to reflect on programmes of further research in the Balkans, but also on scholarship in early metallurgy across the world. This chapter outlines what might be usefully taken forward from this project, but also seeks to highlight gaps in our understandings that could be addressed. It is by no means a comprehensive agenda for global early metallurgy studies but is instead intended to stimulate further debate and discussions that lead to new programmes of research

Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation

Our inability to predict the behavior of biological systems severely hampers progress in bioengineering and biomedical applications. We cannot predict the effect of genotype changes on phenotype, nor extrapolate the large-scale behavior from small-scale experiments. Machine learning techniques recently reached a new level of maturity, and are capable of providing the needed predictive power without a detailed mechanistic understanding. However, they require large amounts of data to be trained. The amount and quality of data required can only be produced through a combination of synthetic biology and automation, so as to generate a large diversity of biological systems with high reproducibility. A sustained investment in the intersection of synthetic biology, machine learning, and automation will drive forward predictive biology, and produce improved machine learning algorithms

Pottery technology at the dawn of metallurgy in the Vinča culture

This chapter summarises the macroscopic and microscopic analyses of pottery sherds from the sites of Belovode and Pločnik, presented in Chapters 14 and 31, and provides insight into different technological traits in order to aid reconstruction of pottery making recipes in these two Vinča culture communities. Using a multi- pronged scientific approach, we reconstructed routines of raw material acquisition and processing, techniques of forming and finishing vessels, firing conditions and organisational aspects of pottery production. The possible non-local production identified in this research is also considered in order to understand the dynamics that shaped pottery circulation in these prehistoric communities (e.g. Quinn et al. 2010). These results also contribute significantly to the previous technological studies carried out on Neolithic pottery from sites in the central Balkans (Figure 1) (e.g. Dammers et al. 2012; Kaiser 1984, 1989, 1990; Kaiser et al. 1986; Kreiter et al. 2009, 2011, 2013, 2017a, 2017b, 2019; Spataro 2014, 2017, 2018; Szakmány et al. 2019)