arXiv subjects

Paul Smyth

Publications and source records attributed to Paul Smyth.

At least 19 recordsLinked to original sources

arXiv2024

Fine-tuning Protein Language Models with Deep Mutational Scanning improves Variant Effect Prediction

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

q-bio.GN↗

arXiv2021

A Mask R-CNN approach to counting bacterial colony forming units in pharmaceutical development

We present an application of the well-known Mask R-CNN approach to the counting of different types of bacterial colony forming units that were cultured in Petri dishes. Our model was made available to lab technicians in a modern SPA (Single-Page Application). Users can upload images of dishes, after which the Mask R-CNN model that was trained and tuned specifically for this task detects the number of BVG- and BVG+ colonies and displays these in an interactive interface for the user to verify. Users can then check the model's predictions, correct them if deemed necessary, and finally validate them. Our adapted Mask R-CNN model achieves a mean average precision (mAP) of 94\% at an intersection-over-union (IoU) threshold of 50\%. With these encouraging results, we see opportunities to bring the benefits of improved accuracy and time saved to related problems, such as generalising to other bacteria types and viral foci counting.

cs.LG↗

arXiv2020

Deep Learning to Detect Bacterial Colonies for the Production of Vaccines

During the development of vaccines, bacterial colony forming units (CFUs) are counted in order to quantify the yield in the fermentation process. This manual task is time-consuming and error-prone. In this work we test multiple segmentation algorithms based on the U-Net CNN architecture and show that these offer robust, automated CFU counting. We show that the multiclass generalisation with a bespoke loss function allows distinguishing virulent and avirulent colonies with acceptable accuracy. While many possibilities are left to explore, our results show the potential of deep learning for separating and classifying bacterial colonies.

cs.CV↗

arXiv2014

Scalar masses in general N=2 gauged supergravity theories

We readdress the question of whether any universal upper bound exists on the square mass m^2 of the lightest scalar around a supersymmetry breaking vacuum in generic N=2 gauged supergravity theories for a given gravitino mass m_3/2 and cosmological constant V. We review the known bounds which apply to theories with restricted matter content from a new perspective. We then extend these results to theories with both hyper and vector multiplets and a gauging involving only one generator, for which we show that such a bound exists for both V>0 and V<0. We finally argue that there is no bound for the same theories with a gauging involving two or more generators. These results imply that in N=2 supergravity theories metastable de Sitter vacua with V< >m^2_3/2 can also arise when a single isometry is gauged.

hep-th↗

arXiv2013

The rigid limit of N=2 supergravity

In this paper we review the rigid limit of N=2 supergravity coupled to vector and hypermultiplets. In particular we show how the respective scalar field spaces reduce to their global counterparts. In the hypermultiplet sector we focus on the relation between the local and rigid c-map.

hep-th↗

arXiv2013

Simple metastable de Sitter vacua in N=2 gauged supergravity

We construct a simple class of N=2 gauged supergravity theories that admit metastable de Sitter vacua, generalizing the recent work done in the context of rigid supersymmetry. The setup involves one hypermultiplet and one vector multiplet spanning suitably curved quaternionic-Kahler and special-Kahler geometries, with an Abelian gauging based on a single triholomorphic isometry, but neither Fayet-Iliopoulos terms nor non-Abelian gauge symmetries. We construct the most general model of this type and show that in such a situation the possibility of achieving metastable supersymmetry breaking vacua crucially depends on the value of the cosmological constant V relative to the gravitino mass squared m_{3/2}^2 in Planck units. In particular, focusing on de Sitter vacua with positive V, we show that metastability is only possible when V >= 2.17 m_{3/2}^2. We also derive an upper bound on the lightest scalar mass in this kind of model relative to the gravitino mass m_{3/2} as a function of the cosmological constant V, and discuss its physical implications.

hep-th↗

arXiv2013

Metastable spontaneous breaking of N=2 supersymmetry

We show that contrary to the common lore it is possible to spontaneously break N=2 supersymmetry even in simple theories without constant Fayet-Iliopoulos terms. We consider the most general N=2 supersymmetric theory with one hypermultiplet and one vector multiplet without Fayet-Iliopoulos terms, and show that metastable supersymmetry breaking vacua can arise if both the hyper-Kahler and the special-Kahler geometries are suitably curved. We then also prove that while all the scalars can be massive, the lightest one is always lighter than the vector boson. Finally, we argue that these results also directly imply that metastable de Sitter vacua can exist in N=2 supergravity theories with Abelian gaugings and no Fayet-Iliopoulos terms, again contrary to common lore, at least if the cosmological constant is sufficiently large.

hep-th↗

arXiv2013

Electrically gauged N=4 supergravities in D=4 with N=2 vacua

We study N=2 vacua in spontaneously broken N=4 electrically gauged supergravities in four space-time dimensions. We argue that the classification of all such solutions amounts to solving a system of purely algebraic equations. We then explicitly construct a special class of consistent N=2 solutions and study their properties. In particular we find that the spectrum assembles in N=2 massless or BPS supermultiplets. We show that (modulo U(1) factors) arbitrary unbroken gauge groups can be realized provided that the number of N=4 vector multiplets is large enough. Below the scale of partial supersymmetry breaking we calculate the relevant terms of the low-energy effective action and argue that the special Kahler manifold for vector multiplets is completely determined, up to its dimension, and lies in the unique series of special Kahler product manifolds.

hep-th↗

arXiv2012

Supersymmetric Vacua in N=2 Supergravity

We use the embedding tensor formalism to analyse maximally symmetric backgrounds of N=2 gauged supergravities which have the full N=2 supersymmetry. We state the condition for N=2 vacua and discuss some of their general properties. We show that if the gauged isometries leave the SU(2) R-symmetry invariant, then the N=2 vacuum must be Minkowski. This implies that there are no AdS backgrounds with eight unbroken supercharges in the effective N=2 supergravity of six-dimensional SU(3) x SU(3) structure compactifications of type II string theory and M-theory. Combined with previous results on N=1 vacua, we show that there exist N=2 supergravities with a given set of gauged Abelian isometries that have both N=2 and N=1 vacua. We also argue that an analogue of our analysis holds in five and six spacetime dimensions.

hep-th↗

arXiv2012

Metastable de Sitter vacua in N=2 to N=1 truncated supergravity

We study the possibility of achieving metastable de Sitter vacua in general N=2 to N=1 truncated supergravities without vector multiplets, and compare with the situations arising in N=2 theories with only hypermultiplets and N=1 theories with only chiral multiplets. In N=2 theories based on a quaternionic manifold and a graviphoton gauging, de Sitter vacua are necessarily unstable, as a result of the peculiar properties of the geometry. In N=1 theories based on a Kahler manifold and a superpotential, de Sitter vacua can instead be metastable provided the geometry satisfies some constraint and the superpotential can be freely adjusted. In N=2 to N=1 truncations, the crucial requirement is then that the tachyon of the mother theory be projected out from the daughter theory, so that the original unstable vacuum is projected to a metastable vacuum. We study the circumstances under which this may happen and derive general constraints for metastability on the geometry and the gauging. We then study in full detail the simplest case of quaternionic manifolds of dimension four with at least one isometry, for which there exists a general parametrization, and study two types of truncations defining Kahler submanifolds of dimension two. As an application, we finally discuss the case of the universal hypermultiplet of N=2 superstrings and its truncations to the dilaton chiral multiplet of N=1 superstrings. We argue that de Sitter vacua in such theories are necessarily unstable in weakly coupled situations, while they can in principle be metastable in strongly coupled regimes.

hep-th↗

arXiv2010

The N=1 Low-Energy Effective Action of Spontaneously Broken N=2 Supergravities

We consider the class of four-dimensional N=2 gauged supergravities whose maximally symmetric ground states leave only one of the two supersymmetries intact. For these theories we derive the low-energy effective action below the scale of partial supersymmetry breaking and compute the N=1 couplings in terms of the N=2 'input data'. We show that this effective action satisfies the constraints of N=1 supergravity in that its sigma-model metric is Kahler, while the superpotential and the gauge kinetic functions are holomorphic. As an example we discuss the N=1 effective supergravity of type II compactifications.

hep-th↗

arXiv2010

Spontaneous N=2 to N=1 Supersymmetry Breaking in Supergravity and Type II String Theory

Using the embedding tensor formalism we give the general conditions for the existence of N=1 vacua in spontaneously broken N=2 supergravities. Our results confirm the necessity of having both electrically and magnetically charged multiplets in the spectrum, but also show that no further constraints on the special Kahler geometry of the vector multiplets arise. The quaternionic field space of the hypermultiplets must have two commuting isometries, and as an example we discuss the special quaternionic-Kahler geometries which appear in the low-energy limit of type II string theories. For these cases we find the general solution for stable Minkowski and AdS N=1 vacua, and determine the charges in terms of the holomorphic prepotentials. We find that the string theory realisation of the N=1 Minkowski vacua requires the presence of non-geometric fluxes, whereas they are not needed for the AdS vacua. We also argue that our results should hold in the presence of spacetime and worldsheet instanton corrections.

hep-th↗

arXiv2009

Domain wall flow equations and SU(3)xSU(3) structure compactifications

We study supersymmetric domain wall solutions in four dimensions arising from the compactification of type II supergravity on a SU(3)xSU(3) structure manifold. Using a pure spinor approach, we show that the supersymmetry variations can be reinterpreted as a generalisation of the Hitchin flow equations and describe the embedding of a SU(3)xSU(3) structure manifold into a G_2xG_2 structure manifold. We find a precise agreement between the four- and ten-dimensional supergravity results. The flow equations derived here should have applications in constructing the gravity duals of Chern-Simons-matter conformal field theories.

hep-th↗

arXiv2009

Black holes, first-order flow equations and geodesics on symmetric spaces

For both extremal and non-extremal spherically symmetric black holes in theories with massless scalars and vectors coupled to gravity, we derive a general form of first-order gradient flow equations, equivalent to the equations of motion. For theories that have a symmetric moduli space after a dimensional reduction over the timelike direction, we discuss the condition for such a gradient flow to exist. This note reviews the results of arXiv:0810.1528 [hep-th].

hep-th↗

arXiv2009

First-order flow equations for extremal and non-extremal black holes

We derive a general form of first-order flow equations for extremal and non-extremal, static, spherically symmetric black holes in theories with massless scalars and vectors coupled to gravity. By rewriting the action as a sum of squares a la Bogomol'nyi, we identify the function governing the first-order gradient flow, the `generalised superpotential', which reduces to the `fake superpotential' for non-supersymmetric extremal black holes and to the central charge for supersymmetric black holes. For theories whose scalar manifold is a symmetric space after a timelike dimensional reduction, we present the condition for the existence of a generalised superpotential. We provide examples to illustrate the formalism in four and five spacetime dimensions.

hep-th↗

arXiv2008

A first-order formalism for timelike and spacelike brane solutions

We show that the construction of BPS-type equations for non-extremal black holes due to Miller et. al. can be extended to branes of arbitrary dimension and, more importantly, to time-dependent solutions. We call these first-order equations fake- or pseudo-BPS equations in light of the formalism that has been developed for domain wall and cosmological solutions of gravity coupled to scalar fields. We present the fake/pseudo-BPS equations for all stationary branes (timelike branes) and all time-dependent branes (spacelike branes) of an Einstein-dilaton-p-form system in arbitrary dimensions.

hep-th↗

arXiv2007

Kaluza-Klein Induced Supersymmetry Breaking for Braneworlds in Type IIB Supergravity

We consider Z_2-symmetric braneworlds arising from 5-sphere compactifications with 5-form flux in type IIB supergravity. This Kaluza-Klein reduction produces a D=5 theory which supports 1/2-supersymmetric Z_2-symmetric domain-wall solutions. However, upon lifting such solutions back to D=10, one finds that supersymmetry is broken by 5-sphere Kaluza-Klein effects. This happens owing to the action on the Killing spinor of the Z_2 \subset SO(1,9) symmetry, which requires an orientation-reversing transformation in the 5-sphere directions together with the flip of the orbifold coordinate. We study the consequences of this supersymmetry breaking for the masses of fermion fluctuation modes about the brane background and find a natural two-scale hierarchy: some bulk modes have characteristic masses of order 1/L_5 but other modes more closely associated to the branes have an additional factor exp(-ρ/L_5), where L_5 is the AdS_5 length parameter and ρis the orbifold size.

hep-th↗

arXiv2007

The energy and stability of D-term strings

Cosmic strings derived from string theory, supergravity or any theory of choice should be stable if we hope to observe them. In this paper we consider D-term strings in D=4, N=1 supergravity with a constant Fayet-Iliopoulos term. We show that the positive deficit angle supersymmetric D-term string is non-perturbatively stable by using standard Witten-Nester techniques to prove a positive energy theorem. Particular attention is paid to the negative deficit angle D-term string, which is known to violate the dominant energy condition. Within the class of string solutions we consider, this violation implies that the negative deficit angle D-term string must have a naked pathology and therefore the positive energy theorem we prove does not apply to it. As an interesting aside, we show that the Witten-Nester charge calculates the total gravitational energy of the D-term string without the need for a cut-off, which may not have been expected.

hep-th↗