Extending the reach of uncertainty quantification in nuclear theory

The theory of the strong interaction—quantum chromodynamics (QCD)—is unsuited to practical calculations of nuclear observables and approximate models for nuclear interaction potentials are required. In contrast to phenomenological models, chiral effective field theories (χEFTs) of QCD grant a handle on the theoretical uncertainty arising from the truncation of the chiral expansion. Uncertainties in χEFT are preferably quantified using Bayesian inference, but quantifying reliable posterior predictive distributions for nuclear observables presents several challenges. First, χEFT is parametrized by unknown low-energy constants (LECs) whose values must be inferred from low-energy data of nuclear structure and reaction observables. There are 31 LECs at fourth order in Weinberg power counting, leading to a high-dimensional inference problem which I approach by developing an advanced sampling protocol using Hamiltonian Monte Carlo (HMC). This allows me to quantify LEC posteriors up to and including fourth chiral order. Second, the χEFT truncation error is correlated across independent variables such as scattering energies and angles; I model correlations using a Gaussian process. Third, the computational cost of computing few- and many-nucleon observables typically precludes their direct use in Bayesian parameter estimation as each observable must be computed in excess of 100,000 times during HMC sampling. The one exception is nucleon-nucleon scattering observables, but even these incur a substantial computational cost in the present applications. I sidestep such issues using eigenvector-continuation emulators, which accurately mimic exact calculations while dramatically reducing the computational cost. Equipped with Bayesian posteriors for the LECs, and a model for the truncation error, I explore the predictive ability of χEFT, presenting the results as the probability distributions they always were

Efficient sampling of Bayesian posteriors and predictive distributions in χEFT

In this thesis I employ Bayesian statistics to quantify parametric and epistemic uncertainties in chiral effective field theories (χEFT) and propagate these forward to predictions of observables in low-energy nuclear physics. Two primary sources of uncertainty---experimental errors and the theoretical error induced by the truncation of the EFT at up to next-to-next-to-leading-order---are modelled and accounted for in the posterior distributions of the unknown low-energy constants (LECs) that govern interaction strengths in χEFT. These posteriors are computationally challenging to extract and I therefore introduce an advanced Markov chain Monte Carlo (MCMC) algorithm, known as Hamiltonian Monte Carlo, and investigate its performance. I compare its sampling efficiency to standard MCMC algorithms and find reductions in computation time by factors around 3-6 in the present work. I exploit the extracted posteriors to produce predictive distributions for neutron-proton and proton-proton scattering cross sections below and above the pion production threshold and check the consistency of the model predictions against empirical data and higher-order point estimates. I find that the predictive distributions provide reliable credibility intervals as long as the size of the truncation error is estimated from expansion coefficients at next-to-leading-order and above. The LEC posteriors are also central to uncertainty quantification in few- and manybody systems, and as part of a larger collaboration I explore constraints on three-nucleon forces imposed by light-nuclei observables

Research on Bias in Mediation: Policy Implications

One of the most important and disputed questions within the field of international mediation concerns the issue of bias. The question of bias cuts to the core of what mediation is and the ways in which mediators can help the parties reach peace. Focusing on research on the role of neutrality and bias in international peace diplomacy in civil wars, this article draws out the policy implications of my own empirically-based work on the role of bias in the mediation of internal armed conflicts. This article suggests that neutrality should not be part of the definition of mediators, and that instead type and degree of bias should be treated as independent variables. In fact, my research has shown that biased mediators, under some conditions, outperform neutral mediators, and also importantly, that it matters in civil wars to which side the mediator is biased: for the government or for the rebel-side. This does not imply that neutral mediators have no role to play in peacemaking processes around the globe: this article discusses explicitly the implications of my research on how neutral mediators should engage themselves in order to bring about peace in civil wars. The article also discusses the notion of “insider-partial”, that is, third party actors within the conflict societies and it suggested that it is important to tap these domestic resources for peace

Research on Bias in Mediation: Policy Implications

One of the most important and disputed questions within the field of international mediation concerns the issue of bias. The question of bias cuts to the core of what mediation is and the ways in which mediators can help the parties reach peace. Focusing on research on the role of neutrality and bias in international peace diplomacy in civil wars, this article draws out the policy implications of my own empirically-based work on the role of bias in the mediation of internal armed conflicts. This article suggests that neutrality should not be part of the definition of mediators, and that instead type and degree of bias should be treated as independent variables. In fact, my research has shown that biased mediators, under some conditions, outperform neutral mediators, and also importantly, that it matters in civil wars to which side the mediator is biased: for the government or for the rebel-side. This does not imply that neutral mediators have no role to play in peacemaking processes around the globe: this article discusses explicitly the implications of my research on how neutral mediators should engage themselves in order to bring about peace in civil wars. The article also discusses the notion of “insider-partial”, that is, third party actors within the conflict societies and it suggested that it is important to tap these domestic resources for peace

Dystocia and caesarean section on guinea pigs in Sweden : an interview study on Swedish clinics’ routines regarding anaesthesia, analgesia and surgical procedure

Dystoki och dräktighetstoxikos är relativt vanligt förekommande problem hos marsvin förknippat med hög mortalitet både för modern och ungarna. Olika profylaktiska åtgärder och att para marsvinen innan blygdbensfogen sammanväxer är bästa sättet att förhindra dräktighetskomplikationer. Vid dystoki är kejsarsnitt ofta en sista utväg men om orsaken är värksvaghet kan försök med medicinsk behandling ha en effekt förutsatt att förlossningsvägarna är fria. Det finns mängder av tänkbara protokoll för analgesi och anestesi med olika för- och nackdelar. Utmaningar som uppstår med vården kring marsvin inkluderar bl.a. känslighet för stress och smärta, upprätthållandet av normotermi, intubering, kateterisering och blodprovstagning. Syftet med denna studie är att kartlägga rutiner kring anestesi och kejsarsnitt på marsvin som utförs i Sverige. Förhoppningen är att resultatet kan läggas till grund för fortbildningen av veterinärer och narkossköterskor i arbetet mot en bättre vård för marsvinen. Totalt fem intervjuer genomfördes med veterinärer varav tre medverkade på en fullständig intervju, en svarade på ett fåtal utvalda frågor och en intervjuades om rutiner kring anestesin. Resultatet av denna studie visar att rutinerna skiljer sig en del i valet av diagnostik, anestesi och analgesi medan den kirurgiska tekniken till stor del är densamma. Rutinen beror mycket på det akuta tillståndet och vikten av att inte stressa marsvinet för mycket eller åsamka onödigt lidande. Det anses ibland bättre att vänta med smärtlindring eller undvika helt för att uppnå en snabbare åtgärd och för att inte påverka ungarna via placenta eller mjölken. Respondenterna i denna studie är noga med att ge hemgångsråd till djurägaren där viktiga punkter är sårkontroll, stödmatning, att följa vikten på ungarna och att höra av sig om komplikationer tillstöter. En slutats av studien är att det även bör läggas ett större fokus på utbildning av djurägare gällande ansvaret att äga marsvin.Dystocia and toxaemia of pregnancy are relatively common problems in guinea pigs associated with high mortality both for the mother and cubs. Prophylactic interventions and to breed the guinea pig prior to the fusion of the pubic symphysis are deemed the best ways to prevent birth-related complications. In case of dystocia, caesarean section is often the last resort, but if the cause is uterine inertia, medicinal treatment may prove successful provided that the birth canal is not obstructed. There are many available protocols for anaesthesia and analgesia with different pros and cons. Challenges that arise when treating guinea pigs include inability to handle stress and pain, maintaining normothermia, intubation, catheterization and blood sampling. The aim of this study is to map the routines regarding anaesthesia and caesarean section performed on guinea pigs in Sweden. Hopefully the results can be of use in the education of veterinarians and veterinary nurses and in the improvement of the care for guinea pigs. A total of five interviews were performed with different veterinarians of which three were fullscale, one was shortened to a few selected questions and one interview was limited to routines regarding anaesthesia. The results show that the routines differ somewhat regarding the choice of diagnostics, anaesthesia and analgesia, while the surgical intervention remains mostly the same. The choice of surgical routine largely depends on the acute aspect and to avoid stressing the animal too much or to cause unnecessary pain. It is sometimes better to postpone the analgesics or even forego them completely to achieve the fastest treatment and not to influence the cubs via the placenta or milk. The respondents are meticulous in handing out postoperative advice to the owners, including wound inspection, supportive feeding, registering the weight of the cubs, and to contact the clinic if complications arise. A conclusion was that more focus should be on educating owners regarding the responsibility of owning a guinea pig

Vibration response of long cable-stayed timber footbridge – case study

Timber footbridges with a span larger than 30 meters are sensitive to vibrations and dynamic factors must therefore be taken into considerations in the design. A case study of a cable-stayed footbridge, Älvsbacka Bridge, with a free span of 130 meters, is presented. The dynamic design of the bridge is compared, based on the old Swedish code, BRO 2004 and the Eurocode 5. Simplified force models presented in BRO 2004 and the ISO 10137 international standard are compared. Vertical and lateral accelerations are measured on the bridge with accelerometers attached to the bridge deck. According to the simplified force model, the vertical acceleration limit was met for a group of twenty pedestrians, which was regarded as a reasonable design situation. From the measured accelerations, the damping factor was calculated as 1.2% of critical damping, which is twice the value used in design

Larvterapi

Sårläkningens grundprinciper finns dokumenterat sedan flera tusen år tillbaka. Många metoder som användes då är idag föråldrade men det finns substanser som moderniserats och förfinats, som t.ex. honung. Med introduktionen av antibiotika och massframställningen av penicillin på 1940-talet glömdes många gamla sårläkningsmetoder bort. En av dessa metoder var larvterapi som finns beskrivet i detalj av en amerikansk läkare på 30-talet. Enligt läkaren verkade larverna lovande i behandlingen av nekrotiska sår men metoden hann inte få genomslag innan penicillinet stal rampljuset. Nu på senare tid har antibiotikaresistens hos bakterier uppmärksammats och man fruktar dagen då antibiotika inte längre har någon avdödande effekt. Multiresistenta bakterier är inget skämt. Nya läkemedel är komplicerat att framställa vilket gör att man försöker minska användningen av dem och på så sätt minska resistensutveckling. Alternativa behandlingar är eftersökta och larvterapi har många förutsättningar att vara en av dem. Med tanke på resistensläget och att sårläkning med konventionella metoder inte alltid är optimal väcks frågan om det finns alternativ som är bättre, exempelvis larvterapi. Forskning om verkningsmekanismer, jämförande studier och rapporter om kliniska fall stödjer resonemanget om att hydrogel, en konventionell metod, i vissa aspekter är sämre än larvterapi. Hydrogelen hjälper endast till genom att luckra upp nekrotisk vävnad och stimulera bildandet av bindväv. Larvernas utformning och utsöndring påverkar många fler ingående komponenter i sårläkningen. Debridering sker både mekaniskt med munkrokar och hårdheter längs kroppen och kemiskt med enzymer. Desinficering sker genom att larverna käkar upp patogener och avdödar de med antibakteriella substanser i magtarmkanalen. Sekretet som utsöndras minskar även inflammation och stimulerar sårläkning, där vissa beståndsdelar påvisats vara allantoin och MAE-P6. En annan fördel som larverna har är den relativt låga kostnaden och simpla framställningen. Nackdelar är det korta bäst före-datumet och ovana hos utövarna som leder till felaktig applicering eller att djur lyckas få av förbanden. Det lilla utbudet på noggranna och omfattande studier gör det svårt att med säkerhet bedöma larvernas användbarhet. Dock visar många av de studier som finns att larvterapi i mångt och mycket är bättre än konventionella metoder när det kommer till debridering och tid till såret börjar läka. Mer forskning behövs, i synnerhet på de antibakteriella och anti-inflammatoriska substanserna som är medverkande skäl till larvterapins framgång.The basic principles of wound healing can be found documented several thousand years ago. Many methods from that time are outdated today, but there are substances which have been modernized and refined, for example honey. With the introduction of antibiotics and the mass production of penicillin in the 1940’s, many old methods of wound treatment were forgotten. One of these methods was larval therapy which is described in detail by an American doctor in the 1930’s. According to the doctor, larval therapy seemed promising in the treatment of necrotic wounds, but the method didn’t quite catch on before the limelight was stolen by penicillin. In recent times, antibiotic resistance in bacteria is getting more and more attention and the fear of having no effective medication against these threats is real. Multi-resistant organisms are not to be trifled with. New drugs are hard to produce which makes reducing the usage of antibiotics and therefore the development of resistance even more important. Alternative treatments are sought after, and larval therapy might just fit the bill. Considering the current state of antibiotic resistance and that wound treatment by conventional means might not be ideal, it begs the question if there exist better alternatives, for example larval therapy. Research on mechanisms of action, comparative studies, and rapports from clinical cases supports the claim that hydrogel, a conventional method, in some respects is inferior to larval therapy. Hydrogel only softens and loosens necrotic tissue and help stimulate the formation of connective tissue. The shape and secretion of the larvae affects considerably more elements in wound healing. Debridement is both mechanical through specialized mouth hooks and minute spines on their bodies, and chemical through the release of enzymes. Disinfection is achieved when pathogens ingested by the larvae are destroyed by antibacterial substances present in the gut and intestines. The secrete also dampens inflammation and stimulates wound healing. Two important components of the secrete have been identified as allantoin and MAE-P6. Some other benefits of larval therapy are the relatively low cost and simple manufacturing process. Disadvantages are the short shelf life and practitioners’ unfamiliarity with the medium, which leads to incorrect application or enabling the treated animals getting the bandages off. The limited selection of thoroughly executed and extensive studies makes it difficult to evaluate the usefulness of larval therapy with certainty. However, many of the present studies show that larval therapy surpasses conventional means when it comes to debridement and the time it takes for the wound to start its healing process. More research is needed, especially on the antibacterial and anti-inflammatory substances which are heavy factors behind the success of larval therapy

Bayesian parameter estimation in chiral effective field theory using the Hamiltonian Monte Carlo method

The number of low-energy constants (LECs) in chiral effective field theory (chi EFT) grows rapidly with increasing chiral order, necessitating the use of Markov chain Monte Carlo techniques for sampling their posterior probability density function. For this we introduce a Hamiltonian Monte Carlo (HMC) algorithm and sample the LEC posterior up to next-to-next-to-leading order (NNLO) in the two-nucleon sector of chi EFT. We find that the sampling efficiency of HMC is three to six times higher compared to an affine-invariant sampling algorithm. We analyze the empirical coverage probability and validate that the NNLO model yields predictions for two-nucleon scattering data with largely reliable credible intervals, provided that one ignores the leading-order EFT expansion parameter when inferring the variance of the truncation error. We also find that the NNLO truncation error dominates the error budget

Bayesian estimation of the low-energy constants up to fourth order in the nucleon-nucleon sector of chiral effective field theory

We use Bayesian methods and Hamiltonian Monte Carlo (HMC) sampling to infer the posterior probability density function (PDF) for the low-energy constants (LECs) up to next-to-next-to-next-to-leading order (N3LO) in a chiral effective field theory (χEFT) description of the nucleon-nucleon interaction. In a first step, we condition the inference on neutron-proton and proton-proton scattering data and account for uncorrelated χEFT truncation errors. We demonstrate how to successfully sample the 31-dimensional space of LECs at N3LO using a revised HMC inference protocol. In a second step we extend the analysis by means of importance sampling and an empirical determination of the neutron-neutron scattering length to infer the posterior PDF for the leading charge-dependent contact LEC in the S01 neutron-neutron interaction channel. While doing so we account for the χEFT truncation error via a conjugate prior. We use the resulting posterior PDF to sample the posterior predictive distributions for the effective range parameters in the S01 wave as well as the strengths of charge-symmetry breaking and charge-independence breaking. We conclude that empirical point-estimate results of isospin breaking in the S01 channel are consistent with the PDFs obtained in our Bayesian analysis and that, when accounting for χEFT truncation errors, one must go to next-to-next-to-leading order to confidently detect isospin breaking effects

You can have your ensemble and run it too -- Deep Ensembles Spread Over Time

Ensembles of independently trained deep neural networks yield uncertainty estimates that rival Bayesian networks in performance. They also offer sizable improvements in terms of predictive performance over single models. However, deep ensembles are not commonly used in environments with limited computational budget -- such as autonomous driving -- since the complexity grows linearly with the number of ensemble members. An important observation that can be made for robotics applications, such as autonomous driving, is that data is typically sequential. For instance, when an object is to be recognized, an autonomous vehicle typically observes a sequence of images, rather than a single image. This raises the question, could the deep ensemble be spread over time? In this work, we propose and analyze Deep Ensembles Spread Over Time (DESOT). The idea is to apply only a single ensemble member to each data point in the sequence, and fuse the predictions over a sequence of data points. We implement and experiment with DESOT for traffic sign classification, where sequences of tracked image patches are to be classified. We find that DESOT obtains the benefits of deep ensembles, in terms of predictive and uncertainty estimation performance, while avoiding the added computational cost. Moreover, DESOT is simple to implement and does not require sequences during training. Finally, we find that DESOT, like deep ensembles, outperform single models for out-of-distribution detection