Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning

Copyright © 2022 Walker, Tucker and Nicolson. The mobilization of large-scale datasets of specimen images and metadata through herbarium digitization provide a rich environment for the application and development of machine learning techniques. However, limited access to computational resources and uneven progress in digitization, especially for small herbaria, still present barriers to the wide adoption of these new technologies. Using deep learning to extract representations of herbarium specimens useful for a wide variety of applications, so-called “representation learning,” could help remove these barriers. Despite its recent popularity for camera trap and natural world images, representation learning is not yet as popular for herbarium specimen images. We investigated the potential of representation learning with specimen images by building three neural networks using a publicly available dataset of over 2 million specimen images spanning multiple continents and institutions. We compared the extracted representations and tested their performance in application tasks relevant to research carried out with herbarium specimens. We found a triplet network, a type of neural network that learns distances between images, produced representations that transferred the best across all applications investigated. Our results demonstrate that it is possible to learn representations of specimen images useful in different applications, and we identify some further steps that we believe are necessary for representation learning to harness the rich information held in the worlds’ herbaria.Research/Scientific Computing teams at the James Hutton Institute and NIAB for providing computational resources and technical support for the “UK’s Crop Diversity Bioinformatics HPC” (BBSRC grant BB/S019669/1)

A relativistic helical jet in the gamma-ray AGN 1156+295

We present the results of a number of high resolution radio observations of the AGN 1156+295. These include multi-epoch and multi-frequency VLBI, VSOP, MERLIN and VLA observations made over a period of 50 months. The 5 GHz MERLIN images trace a straight jet extending to 2 arcsec at P.A. -18 degrees. Extended low brightness emission was detected in the MERLIN observation at 1.6 GHz and the VLA observation at 8.5 GHz with a bend of about 90 degrees at the end of the 2 arcsecond jet. A region of similar diffuse emission is also seen about 2 arcseconds south of the radio core. The VLBI images of the blazar reveal a core-jet structure with an oscillating jet on a milli-arcsecond (mas) scale which aligns with the arcsecond jet at a distance of several tens of milli-arcseconds from the core. This probably indicates that the orientation of the jet structure is close to the line of sight, with the northern jet being relativistically beamed toward us. In this scenario the diffuse emission to the north and south is not beamed and appears symmetrical. For the northern jet at the mas scale, proper motions of 13.7 +/-3.5, 10.6 +/- 2.8, and 11.8 +/- 2.8 c are measured in three distinct components of the jet (q_0=0.5, H_0=65 km /s /Mpc are used through out this paper). Highly polarised emission is detected on VLBI scales in the region in which the jet bends sharply to the north-west. The spectral index distribution of the source shows that the strongest compact component has a flat spectrum, and the extended jet has a steep spectrum. A helical trajectory along the surface of a cone was proposed based on the conservation laws for kinetic energy and momentum to explain the observed phenomena, which is in a good agreement with the observed results on scales of 1 mas to 1 arcsec.Comment: 19 pages with 18 figures. Accepted for publication in the A&

The first resolved imaging of milliarcsecond-scale jets in Circinus X-1

We present the first resolved imaging of the milliarcsecond-scale jets in the neutron star X-ray binary Circinus X-1, made using the Australian Long Baseline Array. The angular extent of the resolved jets is ~20 milliarcseconds, corresponding to a physical scale of ~150 au at the assumed distance of 7.8 kpc. The jet position angle is relatively consistent with previous arcsecond-scale imaging with the Australia Telescope Compact Array. The radio emission is symmetric about the peak, and is unresolved along the minor axis, constraining the opening angle to be less than 20 degrees. We observe evidence for outward motion of the components between the two halves of the observation. Constraints on the proper motion of the radio-emitting components suggest that they are only mildly relativistic, although we cannot definitively rule out the presence of the unseen, ultra-relativistic (Lorentz factor >15) flow previously inferred to exist in this system.Comment: Accepted for publication in MNRAS Letters. 6 pages, 4 figure

4-(1-Naphth­yl)benzoic acid

In the title mol­ecule, C17H12O2, the dihedral angle between the mean plane of the benzene ring and that of the naphthalene ring system is 49.09 (6)°. In the crystal structure, mol­ecules are linked to form centrosymmetric dimers via inter­molecular O—H⋯O hydrogen bonds. The hydr­oxy H atom is disordered over two sites with refined occupancies of 0.62 (3) and 0.38 (3)

The supramolecular structures of oximes: an update and the crystal structure of 1,3-diphenyl-propan-2-one oxime

The crystal structure of 1,3-diphenyl-propan-2-one oxime, C15H15NO, is described. The compound crystallises in the monoclinic space group C2/c. Centrosymmetrically related molecules are linked to form R22 (6) dimers. An update, since 2003, of a systematic analysis of the hydrogen bonding patterns in oxime structures with and without competitive O-H...A type acceptors (an acceptor other than the nitrogen of the oxime) functional group is made, taking into account their moieties. The majority of these oximes form dimeric, R22 (6), structures but R33 (8) and R44 (12) were also found. C3 chains which were classically claimed as the usual oxime H-bond pattern were rarely observed. They are mostly found in aldoxime structures

Adult beginner distance language learner perceptions and use of assignment feedback

This qualitative study examines perceptions and use of assignment feedback among adult beginner modern foreign language learners on higher education distance learning courses. A survey of responses to feedback on assignments by 43 Open University students on beginner language courses in Spanish, French, and German indicated that respondents can be classified into three groups: those who use feedback strategically by integrating it into the learning process and comparing it with, for example, informal feedback from interaction with native speakers, those who take note of feedback, but seem not to use it strategically, and those who appear to take little account of either marks or feedback. The first group proved to be the most confident and most likely to maintain their motivation in the longer term. The conclusion discusses some of the pedagogical and policy implications of the findings

'Education, education, education' : legal, moral and clinical

This article brings together Professor Donald Nicolson's intellectual interest in professional legal ethics and his long-standing involvement with law clinics both as an advisor at the University of Cape Town and Director of the University of Bristol Law Clinic and the University of Strathclyde Law Clinic. In this article he looks at how legal education may help start this process of character development, arguing that the best means is through student involvement in voluntary law clinics. And here he builds upon his recent article which argues for voluntary, community service oriented law clinics over those which emphasise the education of students

James Hutton’s geological tours of Scotland : romanticism, literary strategies, and the scientific quest

This article explores a somewhat neglected part of the story of the emergence of geology as a science and discourse in the late eighteenth century – James Hutton’s posthumously published accounts of the geological tours of Scotland that he undertook in the years 1785 to 1788 in search of empirical evidence in support of his theory of the Earth and that he intended to include in the projected third volume of his Theory of the Earth of 1795. The article brings some of the assumptions and techniques of literary criticism to bear on Hutton’s scientific travel writing in order to open up new connections between geology, Romantic aesthetics and eighteenth-century travel writing about Scotland. Close analysis of Hutton’s accounts of his field trips to Glen Tilt, Galloway and Arran, supplemented by later accounts of the discoveries at Jedburgh and Siccar Point, reveals the interplay between desire, travel and the scientific quest and foregrounds the textual strategies that Hutton uses to persuade his readers that they share in the experience of geological discovery and interpretation as ‘virtual witnesses’. As well as allowing us to revisit the interrelation between scientific theory and discovery, this article concludes that Hutton was a much better writer than he has been given credit for and suggests that if these geological tours had been published in 1795 they would have made it impossible for critics to dismiss him as an armchair geologist

Collective dynamics of colloids at fluid interfaces

The evolution of an initially prepared distribution of micron sized colloidal particles, trapped at a fluid interface and under the action of their mutual capillary attraction, is analyzed by using Brownian dynamics simulations. At a separation \lambda\ given by the capillary length of typically 1 mm, the distance dependence of this attraction exhibits a crossover from a logarithmic decay, formally analogous to two-dimensional gravity, to an exponential decay. We discuss in detail the adaption of a particle-mesh algorithm, as used in cosmological simulations to study structure formation due to gravitational collapse, to the present colloidal problem. These simulations confirm the predictions, as far as available, of a mean-field theory developed previously for this problem. The evolution is monitored by quantitative characteristics which are particularly sensitive to the formation of highly inhomogeneous structures. Upon increasing \lambda\ the dynamics show a smooth transition from the spinodal decomposition expected for a simple fluid with short-ranged attraction to the self-gravitational collapse scenario.Comment: 13 pages, 12 figures, revised, matches version accepted for publication in the European Physical Journal