@article{14654, abstract = {Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions.}, author = {Hwong, Yi-Ling and Colin, M. and Aglas, Philipp and Muller, Caroline J and Sherwood, S. C.}, issn = {1942-2466}, journal = {Journal of Advances in Modeling Earth Systems}, number = {12}, publisher = {Wiley}, title = {{Assessing memory in convection schemes using idealized tests}}, doi = {10.1029/2023MS003726}, volume = {15}, year = {2023}, } @article{14655, abstract = {The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.}, author = {Sorichetti, Valerio and Lenz, Martin}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {22}, publisher = {American Physical Society}, title = {{Transverse fluctuations control the assembly of semiflexible filaments}}, doi = {10.1103/PhysRevLett.131.228401}, volume = {131}, year = {2023}, } @article{14657, abstract = {Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.}, author = {Tkadlec, Josef and Kaveh, Kamran and Chatterjee, Krishnendu and Nowak, Martin A.}, issn = {1742-5662}, journal = {Journal of the Royal Society, Interface}, number = {208}, publisher = {The Royal Society}, title = {{Evolutionary dynamics of mutants that modify population structure}}, doi = {10.1098/rsif.2023.0355}, volume = {20}, year = {2023}, } @article{14658, abstract = {We investigate spin-charge separation of a spin- 1 2 Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom.}, author = {Becker, J. M. and Koutentakis, Georgios and Schmelcher, P.}, issn = {2643-1564}, journal = {Physical Review Research}, number = {4}, publisher = {American Physical Society}, title = {{Spin-charge correlations in finite one-dimensional multiband Fermi systems}}, doi = {10.1103/PhysRevResearch.5.043039}, volume = {5}, year = {2023}, } @article{14659, abstract = {Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment.}, author = {Salerno, Franco and Guyennon, Nicolas and Yang, Kun and Shaw, Thomas and Lin, Changgui and Colombo, Nicola and Romano, Emanuele and Gruber, Stephan and Bolch, Tobias and Alessandri, Andrea and Cristofanelli, Paolo and Putero, Davide and Diolaiuti, Guglielmina and Tartari, Gianni and Verza, Gianpietro and Thakuri, Sudeep and Balsamo, Gianpaolo and Miles, Evan S. and Pellicciotti, Francesca}, issn = {1752-0908}, journal = {Nature Geoscience}, pages = {1120--1127}, publisher = {Springer Nature}, title = {{Local cooling and drying induced by Himalayan glaciers under global warming}}, doi = {10.1038/s41561-023-01331-y}, volume = {16}, year = {2023}, } @article{14661, abstract = {This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are "close to" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit.}, author = {Carioni, Marcello and Fischer, Julian L and Schlömerkemper, Anja}, issn = {2363-6394}, journal = {Journal of Convex Analysis}, number = {1}, pages = {217--247}, publisher = {Heldermann Verlag}, title = {{External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development}}, volume = {30}, year = {2023}, } @article{14662, abstract = {We consider a class of polaron models, including the Fröhlich model, at zero total momentum, and show that at sufficiently weak coupling there are no excited eigenvalues below the essential spectrum.}, author = {Seiringer, Robert}, issn = {1664-0403}, journal = {Journal of Spectral Theory}, number = {3}, pages = {1045--1055}, publisher = {EMS Press}, title = {{Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling}}, doi = {10.4171/JST/469}, volume = {13}, year = {2023}, } @article{14663, abstract = {As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity.}, author = {Zhao, Jinyan and Yao, Zihao and Bunting, Rhys and Hu, P. and Wang, Jianguo}, issn = {2155-5435}, journal = {ACS Catalysis}, number = {22}, pages = {15054--15073}, publisher = {American Chemical Society}, title = {{Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles}}, doi = {10.1021/acscatal.3c03893}, volume = {13}, year = {2023}, } @article{14664, abstract = {The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”.}, author = {Hema, Kuntrapakam and Grommet, Angela B. and Białek, Michał J. and Wang, Jinhua and Schneider, Laura and Drechsler, Christoph and Yanshyna, Oksana and Diskin-Posner, Yael and Clever, Guido H. and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {45}, pages = {24755--24764}, publisher = {American Chemical Society}, title = {{Guest encapsulation alters the thermodynamic landscape of a coordination host}}, doi = {10.1021/jacs.3c08666}, volume = {145}, year = {2023}, } @article{14666, abstract = {So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function.}, author = {Chintaluri, Chaitanya and Vogels, Tim P}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {48}, publisher = {National Academy of Sciences}, title = {{Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species}}, doi = {10.1073/pnas.2306525120}, volume = {120}, year = {2023}, } @article{14667, abstract = {For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. }, author = {Erdös, László and Ji, Hong Chang}, issn = {0246-0203}, journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics}, number = {4}, pages = {2083--2105}, publisher = {Institute of Mathematical Statistics}, title = {{Functional CLT for non-Hermitian random matrices}}, doi = {10.1214/22-AIHP1304}, volume = {59}, year = {2023}, } @article{14689, author = {Ing-Simmons, Elizabeth and Machnik, Nick N and Vaquerizas, Juan M.}, issn = {1546-1718}, journal = {Nature Genetics}, number = {12}, pages = {2053--2055}, publisher = {Springer Nature}, title = {{Reply to: Revisiting the use of structural similarity index in Hi-C}}, doi = {10.1038/s41588-023-01595-5}, volume = {55}, year = {2023}, } @article{14690, abstract = {Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction.}, author = {Babkin, Serafim and Burmistrov, I}, issn = {2469-9969}, journal = {Physical Review B}, number = {20}, publisher = {American Physical Society}, title = {{Boundary multifractality in the spin quantum Hall symmetry class with interaction}}, doi = {10.1103/PhysRevB.108.205429}, volume = {108}, year = {2023}, } @inproceedings{14691, abstract = {Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20]. The recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting. In this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k. We prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al. Our lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper.}, author = {Auerbach, Benedikt and Cueto Noval, Miguel and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z}, booktitle = {21st International Conference on Theory of Cryptography}, isbn = {9783031486203}, issn = {1611-3349}, location = {Taipei, Taiwan}, pages = {271--300}, publisher = {Springer Nature}, title = {{On the cost of post-compromise security in concurrent Continuous Group-Key Agreement}}, doi = {10.1007/978-3-031-48621-0_10}, volume = {14371}, year = {2023}, } @inproceedings{14692, abstract = {The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions. In this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach. The main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach.}, author = {Auerbach, Benedikt and Hoffmann, Charlotte and Pascual Perez, Guillermo}, booktitle = {21st International Conference on Theory of Cryptography}, isbn = {9783031486203}, issn = {1611-3349}, pages = {301--330}, publisher = {Springer Nature}, title = {{Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing}}, doi = {10.1007/978-3-031-48621-0_11}, volume = {14371}, year = {2023}, } @inproceedings{14693, abstract = {Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus. First, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring. Second, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.}, author = {Hoffmann, Charlotte and Hubáček, Pavel and Kamath, Chethan and Krňák, Tomáš}, booktitle = {21st International Conference on Theory of Cryptography}, isbn = {9783031486234}, issn = {1611-3349}, location = {Taipei, Taiwan}, pages = {336--362}, publisher = {Springer Nature}, title = {{(Verifiable) delay functions from Lucas sequences}}, doi = {10.1007/978-3-031-48624-1_13}, volume = {14372}, year = {2023}, } @article{14709, abstract = {Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.}, author = {Del Bianco, Marta and Friml, Jiří and Strader, Lucia and Kepinski, Stefan}, issn = {1460-2431}, journal = {Journal of Experimental Botany}, number = {22}, pages = {6889--6892}, publisher = {Oxford University Press}, title = {{Auxin research: Creating tools for a greener future}}, doi = {10.1093/jxb/erad420}, volume = {74}, year = {2023}, } @article{14710, abstract = {The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.}, author = {Curatolo, Agnese I. and Kimchi, Ofer and Goodrich, Carl Peter and Krueger, Ryan K. and Brenner, Michael P.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{A computational toolbox for the assembly yield of complex and heterogeneous structures}}, doi = {10.1038/s41467-023-43168-4}, volume = {14}, year = {2023}, } @article{14715, abstract = {We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ.}, author = {Mitrouskas, David Johannes and Pickl, Peter}, issn = {1089-7658}, journal = {Journal of Mathematical Physics}, number = {12}, publisher = {AIP Publishing}, title = {{Exponential decay of the number of excitations in the weakly interacting Bose gas}}, doi = {10.1063/5.0172199}, volume = {64}, year = {2023}, } @article{14716, abstract = {Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. Results: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. Conclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.}, author = {Yurtseven, Alper and Buyanova, Sofia and Agrawal, Amay Ajaykumar A. and Bochkareva, Olga and Kalinina, Olga V V.}, issn = {1471-2180}, journal = {BMC Microbiology}, number = {1}, publisher = {Springer Nature}, title = {{Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis}}, doi = {10.1186/s12866-023-03147-7}, volume = {23}, year = {2023}, }