Atom-Density Representations for Machine Learning

The applications of machine learning techniques to chemistry and materials science become more numerous by the day. The main challenge is to devise representations of atomic systems that are at the same time complete and concise, so as to reduce the number of reference calculations that are needed to predict the properties of different types of materials reliably. This has led to a proliferation of alternative ways to convert an atomic structure into an input for a machine-learning model. We introduce an abstract definition of chemical environments that is based on a smoothed atomic density, using a bra-ket notation to emphasize basis set independence and to highlight the connections with some popular choices of representations for describing atomic systems. The correlations between the spatial distribution of atoms and their chemical identities are computed as inner products between these feature kets, which can be given an explicit representation in terms of the expansion of the atom density on orthogonal basis functions, that is equivalent to the smooth overlap of atomic positions (SOAP) power spectrum, but also in real space, corresponding to $n$-body correlations of the atom density. This formalism lays the foundations for a more systematic tuning of the behavior of the representations, by introducing operators that represent the correlations between structure, composition, and the target properties. It provides a unifying picture of recent developments in the field and indicates a way forward towards more effective and computationally affordable machine-learning schemes for molecules and materials

Understanding Kant’s architectonic method in the critique of pure reason and its role in the work of Gilles Deleuze

How we read Kant's Critique of Pure Reason has a huge influence on how convincing we find the parts of which it is composed. This thesis will argue that by taking its arguments and concepts in isolation we neglect the unifying architectonic method that Kant employed. Understanding this text as a response to a single problem, that of the possibility of synthetic a priori judgement, will allow us to evaluate it more fully. We will explore Kant's attempts to relate the a priori and the synthetic in the Introduction, Metaphysical Deduction and Analytic of Principles of the Critique of Pure Reason. Having developed this reading at length we will be able to reassess Kant's relation to the work of Gilles Deleuze. Deleuze's critique of Kant and his tendency to make selective use of his work has so far characterised their relations. However, by reading Kant's Critique of Pure Reason in terms of its unifying method we will open up a new means of relating these two thinkers. Whilst Deleuze rejects many key Kantian concerns and concepts he embraces his methodological concern with the ability of problems to unify our thought. The problem-setting and forms of argument that emerge within Kant's architectonic method will be related to Deleuze's account of experience. This thesis will contribute to both Kant and Deleuze studies on the basis of the reading of the Critique of Pure Reason it will present. By showing how Kant's text is to be read as a whole we will be able to challenge the conclusion that the arguments he makes ultimately rely upon a notion of 'subjective origin'. The problem of accounting for 'the actual' through its relation to 'the virtual' in Deleuze's thought will be re-assessed on the basis of his newly established relation with Kant. Understanding Kant's method in the Critique of Pure Reason will be shown to strengthen both his own account of experience and that offered by Deleuze

Feature Optimization for Atomistic Machine Learning Yields A Data-Driven Construction of the Periodic Table of the Elements

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes it possible to improve the accuracy of the model for a given amount of reference data. When using a description of the structures that is transparent and well-principled, optimizing the representation might reveal insights into the chemistry of the data set. Here we show how one can generalize the SOAP kernel to introduce a distance-dependent weight that accounts for the multi-scale nature of the interactions, and a description of correlations between chemical species. We show that this improves substantially the performance of ML models of molecular and materials stability, while making it easier to work with complex, multi-component systems and to extend SOAP to coarse-grained intermolecular potentials. The element correlations that give the best performing model show striking similarities with the conventional periodic table of the elements, providing an inspiring example of how machine learning can rediscover, and generalize, intuitive concepts that constitute the foundations of chemistry.Comment: 9 pages, 4 figure

The effects of amoebic dysentery as encountered in British troops from 1942 to 1946

1. Amoebic Dysentery has constituted a considerable problem during the War. 2. Large numbers of British troops suffered from Amoebic Dysentery for the fist time in 1942 in Bengal. Most of the patients were recent arrivals in India. 815 cases were treated in eight months in a Hospital in Calcutta in 1942. 3. The incidence of Amoebic Dysentery was greater than that of Bacillary Dysentery among British troops treated in Calcutta in 1942. 4. There was a marked rise in the incidence of Amoebic Dysentery at the time of the Monsoon, favouring a water borne spread. Bacillary Dysentery showed a similar rise in the Monsoon period. 5. The immediate mortality from fresh infections with Amoebic Dysentery was low. 6. Emetine Hydrochloride injections and Carbarsone were administered as routine treatment in 1942. The period of observation of cases following treatment was unduly short. The form of treatment and the short period of observation were dicta /ted by conditions at the time. Relapses occurred following this treatment and the proved relapse figure of 5% within eight months is a minimal one. Carbarsone appeared to be of value in eradicating Entamoeba Histolytica cysts. Kurchi Bismuth Iodide was valueless as an Amoebicidal agent and was of symptomatic use in relieving diarrhoea only. 7. Fifty chronic cases of Amoebiasis were treated in 1943 as the Hospital had become e Centre for the treatment of Chronic Amoebic Dysentery. All the cases had recieved repeated courses of Emetine injections and it is postulated that they had experienced relief from this treatment but had never been cured. The unsatisfactory nature of treatment by Emine injections and Carbarsone alone was thus displayed again. 8. Chronic Amoebic Dysentery leads to a state of invalidism with mentalapathy, intermittent diarrhoea, weaknes gross loss of weight and abdominal pain. 9. Sigmoidoscopy is an excellent method of assessing progress in Chronic Ameóbiasis but stool examinations are even more important in diagnosis. Thus 85% of cases in which the stools were positive showed Sigmoidoscopic lesions. It was interesting to observe the disappearance of ulcers in three weeks in some cases of Chronic Amoebiasis while other ulcers showed no response following Emetine Bismuth Iodide and Chiniofon. Sigmoidoscopy is a good test of cure but stool examination is even more reliable. 10. Emetine Bismuth Iodide was a drug of low toxicity in that the pulse and blood pressure were not affected following treatment. . 11. Emetine Bismuth Iodide and Chiniofon alone cured only 42% of fifty chronic cases. This consitituted an advance in that the patients had not been cured by Emetine injections The result was nevertheless disappointing. 12. 125 of the cases relapsed during observation over a period of one month, thus emphasising the importance of an adequate period of surveillance. 13. The lack of response to Emetine Bismuth Iodide and Chiniofon or Yatren was apparent to various workers when chronic refractory cases from the India and Burma Theatres returned to the United Kingdom. 14. Failure of previous methods of treatment give rise to speculation on the causes of chronicity. 15. Hargreaves contended that secondary infection was responsible for the failure of Chronic Amoebiasis to respond to treatment by Amoebici dal drugs. He therefore advocated a preliminary course of Penicillin and Sulpha-suxidine in all such cases. A few cases were personally treated in this way in the United Kingdom. Three cases of Chronic Colonic Amoebiasis have progressed well to date and are still under observation. A Haemolytic Streptococcus was cultured from the Amoebic ulcers of one case. 16. Perusal of the researches of various workers corroborate the importance of secondary infection in Amoebic Dysentery. It is considered that this is the most important factor from the therapeutic point of view. Cultures from Amoebic ulcers on Desoxycholate and bloodfiger media from a large number of Chronic cases would enable t e frequency of occurrence of some of the various secondary organisms to be assessed. 17. An adequate period of surveillance after treatment of Amoebic Dysentery is essential. Observation for three months at least is suggested as fifty chronic cases treated in 1943 averaged two and a half months between recurrences of symptoms. 18. After witnessing the effects of this disease for four years, one feels that no treatment, however prolonged, can be too thorough in the eradication of the infection

Current practice in septal surgery and adjunctive turbinate reduction: a multi-site experience in 226 consecutive cases

Septal and turbinate surgeries are often performed concurrently for nasal obstruction, yet the causative pathology for each structure becoming symptomatic can usually be attributed to structural deformity and mucosal problems respectively. This article is protected by copyright. All rights reserved

Matsubara Dynamics and its Practical Implementation

This thesis develops a theory for approximate quantum time-correlation functions, Matsubara dynamics, that rigorously describes how to combine quantum statistics with classical dynamics. Matsubara dynamics is based on Feynman's path integral formulation of quantum mechanics and is expected to describe the physics of any system that satisfies quantum Boltzmann statistics and exhibits rapid quantum decoherence, e.g. liquid water at room temperature. Having derived the Matsubara dynamics theory and explored the symmetry properties that it shares with the quantum Kubo time-correlation function, we demonstrate that two heuristic computational methods, Centroid Molecular Dynamics and Ring Polymer Molecular Dynamics, are based on quantifiable approximations to the Matsubara dynamics time-correlation function. This provides these methods with a stronger theoretical foundation and helps to explain their strengths and shortcomings. We then apply the Matsubara dynamics theory to a recently developed computational method of Poulsen $\textit{et al}$. called the planetary model. We show that the planetary model is based on a harmonic approximation to Matsubara dynamics that is engineered to maintain the conservation of the quantum Boltzmann distribution, so quantum statistics and classical dynamics remain harmonised. By making practical modifications to the planetary model, we were able to calculate infrared absorption spectra for a point charge model of condensed-phase water over a range of thermodynamic conditions. We find that this harmonic approximation to Matsubara dynamics provides a good description of bending and vibrational motions and is expected to be a useful tool for future spectroscopic studies of more complex, polarisable models of water.Engineering and Physical Sciences Research Counci

Participación infantil en la investigación cualitativa en educación: reflexiones ético-pedagógicas desde Chile

El presente artículo reflexiona en torno a las posibilidades, los límites y desafíos éticos y pedagógicos de la participación de niños, niñas y adolescentes (NNA) en la investigación cualitativa en educación, basada en dos investigaciones realizadas en Chile en 2017 y 2020, con NNA de 7 a 13 años. A partir de una visión paradójica de la infancia y la adolescencia, que entiende a nna como sujetos vulnerables y dependientes y, al mismo tiempo, autónomos y libres, se cuestionan dos supuestos habituales implicados en los procesos de investigación y evaluación ética de la investigación: por una parte, el supuesto de que más participación significa sobreexposición y vulneración de los menores; y por otra, el supuesto de que más participación es de suyo mejor, y tanto ética como pedagógicamente deseable para la investigación y para NNA. Luego se distinguen tres modos básicos de participación. Mientras la investigación sobre NNA considera a estos solamente como “tema”, “contenido” u “objeto” de estudio (1), la investigación con NNA contempla su participación directa en alguna de las etapas de la investigación (2), y la investigación realizada por NNAse abre a la posibilidad de que estos participen plena y activamente en una o más etapas en calidad de co-investigadores (3). Así, se postula que la participación es un fenómeno multidimensional, relacional y ambivalente, que desafía posiciones dogmáticas adultocéntricas y puerocéntricas tradicionales, y exige ir más allá de aproximaciones estandarizadas al ámbito ético

Airborne investigation of quasi-specular Ku-band radar scattering for satellite altimetry over snow-covered Arctic sea ice

Surface-based Ku-band radar altimetry investigations indicate the radar signal is typically backscattered from well above the snow-sea ice interface. However, this would induce a bias in satellite altimeter sea ice thickness retrievals not reflected by buoy validation. Our study presents a mechanism to potentially explain this paradox: probabilistic quasi-specular radar scattering from the snow-ice interface. We introduce the theory for this mechanism before identifying it in airborne Ku-band radar observations collected over landfast first year Arctic sea ice near Eureka, Canada, in spring 2016. Based on SAR data, this study area likely represents level first year sea ice across the Arctic. Radar backscatter from the snow and ice interfaces were estimated by co-aligning laser scanner and radar observations with in situ measurements. On average, 4-5 times more radar power was scattered from the snow-ice than the air-snow interface over first-year ice. However, return power varied by up to 20 dB between consecutive radar echoes, particularly from the snow-ice interface, depending on local slope and roughness. Measured laser-radar snow depths were more accurate when radar returns were specular, but there was no systematic bias between airborne and in situ snow depths. The probability and strength of quasi-specular returns depend on the measuring height above and slope distribution of sea ice, so these findings have implications for satellite altimetry snow depth and freeboard estimates. This mechanism could explain the apparent differences in Ku-band radar penetration into snow on sea ice when observed from the range of a surface-, airborne- or satellite-based sensor