@phdthesis{22258, abstract = {Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures. First, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. Second, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times. Collectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification.}, author = {Depope, Al}, issn = {2663-337X}, keywords = {Approximate Message Passing, GWAS, Genomics, Proteomics, Survival modeling}, pages = {169}, publisher = {Institute of Science and Technology Austria}, title = {{From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics}}, doi = {10.15479/AT-ISTA-22258}, year = {2026}, } @phdthesis{22667, author = {Vijatovic, David}, isbn = {978-3-99078-082-4}, issn = {2663-337X}, pages = {172}, publisher = {Institute of Science and Technology Austria}, title = {{Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis}}, doi = {10.15479/AT-ISTA-22667}, year = {2026}, } @phdthesis{22399, author = {Spasić, Aleksa}, issn = {2791-4585}, pages = {32}, publisher = {Institute of Science and Technology Austria}, title = {{Studying the evolutionary systems biology of the lac operon}}, doi = {10.15479/AT-ISTA-22399}, year = {2026}, } @phdthesis{22281, abstract = {In this thesis, we took a look at networks, and more specifically, at networks that change over time, whether those are networks in the distributed algorithms sense of the word, or the graph algorithm sense. In distributed algorithms, we looked at two main problems. First, the broadcast problem: given n agents, each agent is tasked to forward a (unique) message to every other agent. Agents collaborate and can copy and forward all messages they have received up until that point. Broadcast is achieved when one agent has successfully broadcast its message to everyone else. We studied the case where the communication network is controlled by an adversary, under the condition that the graph is rooted in every round of communication. We show that the adversary can delay broadcast for at most l (1 + √ 2)n m rounds, improving on the $O(n\log\log n)$ previous upper bound~\cite{fugger2020radius}, and asymptotically matching the $\sim 1.5n$ lower bound~\cite{schwarz2017linear}. We then looked at the stochastic version of the problem: here, the adversary -- parametrized by $k$ where $k=0$ signifies that the adversary has no control, and $k=n$ that the adversary has full control -- can choose parts of the graph, and the graph is then completed stochastically. Here, we are able to look at a stronger version of broadcast: instead of having $n$ messages trying to be broadcast in parallel, we can assume that only one message needs to be broadcasted. We show the bound $\Theta(k+\log n)$. Then, we looked at undecided states dynamics in population protocols: given a population of $n$ agents, where each initially holds an opinion among $k$ different ones. In each round, two agents are chosen uniformly at random, and can interact. If they have different opinions, they forget their opinions and become undecided. If one of them is undecided while the other has an opinion, they undecided agent copies they opinion of the decided one. The question is then, how many interactions does it take for the whole population to share the same opinion? We show a $\Omega(kn\log \frac {\sqrt n} {k \log n})$ lower bound for any $k = o\left(\frac {\sqrt n}{\log n}\right)$. This is tight for any $ k \le n^{\frac 1 2 - \epsilon}$, where $\epsilon >0$ can be any small constant, matching the known $O(kn\log n)$ upper bound for $k = O\left(\frac {\sqrt n} {\log ^2 n}\right)$~\cite{DBLP:conf/podc/AmirABBHKL23}. Finally, in dynamic algorithms, we study the minimum cut problem: we are given a graph, whose vertex set we want to partition into two subsets such that the number of edges crossing from one subset to the other is minimized. Then, the graph can be updated via edge insertions or deletions, and we must update the solution without recomputing everything from scratch. We present an exact fully-dynamic minimum cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum cut size is at most $2^{\Theta(\log^{3/4-c}n)}$ for any $c>0$, improving on the previous algorithm~\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit is $(\log n)^{o(1)}$. Using sparsification and randomization techniques, we are able to extend this to all values of the minimum cut in weighted graphs, at the cost of a $(1+o(1))$-approximation ratio.}, author = {El-Hayek, Antoine}, issn = {2663-337X}, pages = {244}, publisher = {Institute of Science and Technology Austria}, title = {{Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks}}, doi = {10.15479/AT-ISTA-22281}, year = {2026}, } @phdthesis{20991, abstract = {Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments. In Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation. A major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses. Collectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms.}, author = {Garcia Castillo, Diego Fernando}, isbn = {978-3-99078-077-0}, issn = {2663-337X}, pages = {199}, publisher = {Institute of Science and Technology Austria}, title = {{The genomic architecture of local adaptation in introduced populations}}, doi = {10.15479/AT-ISTA-20991}, year = {2026}, } @phdthesis{22684, abstract = {Contact electrification (CE) is a simple yet elusive phenomenon that occurs when two materials come into contact and separate, leaving behind net electrical charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In this thesis, we investigate CE from three complementary perspectives: developing a quantitative method to measure charge at the nanoscale, exploring the dynamic behavior of charge on insulating surfaces, and uncovering the role of mechanical history in forming a triboelectric series. In the first part, we establish a rigorous framework for converting qualitative Kelvin probe force microscopy (KPFM) voltage maps into quantitative charge density distributions. Using finite element method (FEM) simulations, we determine the point-spread function of the KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed by numerical deconvolution. This procedure enables the recovery of both the magnitude and sign of charge density with high fidelity, resolving nanoscale features that are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces, we show that existing analytical approximations, such as parallel plate or spherical models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM approach therefore provides a fast and general method to convert qualitative KPFM signals into quantitative charge data, enabling nanoscale charge mapping under realistic experimental conditions. In the second part, we study the temporal stability of CE-induced charges and identify the key material factors that determine whether KPFM can capture meaningful charge patterns. Through time-resolved experiments combining a custom-built transfer system with both microscopic and macroscopic measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve CE charge long enough for stationary imaging. For less conductive polymers, such as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction. Using a simple capacitor-based model, we reproduce the observed decay dynamics and confirm that the transferred charge decays characteristic to the sample's bulk conductivity. Further, we always observe homogeneous charge transfer. In the third part, we address the question: can we form a triboelectric series with identical materials? Using controlled repetitive contact experiments, we show that nominally identical materials can progressively order themselves into a triboelectric series, where surfaces with more contact history charge negatively relative to fresher ones. By constructing a minimal model based on this ``contact bias'', we replicate the evolution from random to ordered charging observed in experiments. Supporting surface analyses, including atomic force microscopy, reveal that repeated contact induces nanoscale morphological changes, suggesting a mechanism tightly coupled to mechanical strain. These results highlight the crucial role of surface history and nanoscale mechanics in dictating charge transfer, motivating further exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric polarization.}, author = {Pertl, Felix}, isbn = {978-3-99078-083-1}, issn = {2663-337X}, pages = {107}, publisher = {Institute of Science and Technology Austria}, title = {{Experimental probing of nanoscale charge features and surface morphology changes during tribocharging}}, doi = {10.15479/AT-ISTA-22684}, year = {2026}, } @article{21763, abstract = {Reactive oxygen species (ROS) have been implicated in multiple signaling processes in plants, but the underlying mechanisms and roles remain enigmatic. In this study, we developed a method of live imaging of apoplastic ROS at the root surface. Distinct signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts. Genetic and optogenetic manipulations of Arabidopsis identified calcium transients as necessary and sufficient for ROS bursts through activation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS bursts are not required, but they do limit gravity-induced root bending. Root bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH oxidase activation. The resulting ROS production stiffens cell walls to facilitate soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility and stiffness to navigate soil.}, author = {Kulich, Ivan and Vladimirtsev, Dmitrii and Randuch, Marek and Gao, Shiqiang and Citterico, Matteo and Konrad, Kai R. and Nagel, Georg and Wrzaczek, Michael and Cascaro, Léa and Vinet, Pauline and Durand, Pauline and Asnacios, Atef and Verma, Lokesh and Bennett, Malcolm J. and Pandey, Bipin K. and Friml, Jiří}, issn = {1095-9203}, journal = {Science}, number = {6795}, pages = {296--300}, publisher = {AAAS}, title = {{Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation}}, doi = {10.1126/science.adu8197}, volume = {392}, year = {2026}, } @phdthesis{23145, author = {Randuch, Marek}, issn = {2663-337X}, pages = {289}, publisher = {Institute of Science and Technology Austria}, title = {{Fast growth responses in plants: Growth regulation and phospho-proteomic }}, doi = {10.15479/AT-ISTA-23145}, year = {2026}, } @article{21983, abstract = {Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology.}, author = {Mascolo, Elia and Körei, Reka E and Herrera-Álvarez, Santiago and Guet, Calin C and Crocker, Justin and Tkačik, Gašper}, issn = {1879-0380}, journal = {Current Opinion in Genetics & Development}, publisher = {Elsevier}, title = {{Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps}}, doi = {10.1016/j.gde.2026.102483}, volume = {99}, year = {2026}, } @article{18706, abstract = {We prove discrete-to-continuum convergence for dynamical optimal transport on Zd -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of 1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations.}, author = {Portinale, Lorenzo and Quattrocchi, Filippo}, issn = {1469-4425}, journal = {European Journal of Applied Mathematics}, keywords = {optimal transport, discrete-to-continuum, homogenisation, linear growth, gamma-convergence}, number = {3}, pages = {614--642}, publisher = {Cambridge University Press}, title = {{Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs}}, doi = {10.1017/s0956792524000810}, volume = {37}, year = {2026}, } @phdthesis{21423, abstract = {Biological systems, such as cytoskeletal filaments and multicellular collectives, exhibit rich self-organization driven by their intrinsic activity and physical constraints. Across scales, geometry plays a central role: the shape of active units and the structure of their environment strongly influence how order emerges in these far-from-equilibrium systems. In this thesis, we combine minimal active-matter models with bottom-up in vitro experiments to identify the principles by which geometry and activity shape collective behavior in biological matter. At the subcellular scale, we investigate how the physical properties of chiral FtsZ filaments govern their large-scale organization. Using a mesoscopic model validated by reconstituted filament assays, we show that filament shape, intrinsic curvature, and flexibility, together with activity-driven straightening, determine whether filaments form chiral rings, polar bands, or nematic-like states. Our model shows that small changes in filament mechanics produce large shifts in collective structures, revealing how the geometry of individual filaments amplifies through activity to control patterns relevant for bacterial cytokinesis. At the cellular scale, we examine how geometry of the external environment influences collective cancer cell migration. Experiments in controlled microfabricated obstacle environments demonstrate that geometric disorder alone can induce a transition from collective to single-cell invasion. A minimal model of active particles in disordered geometries reproduces these effects, demonstrating that cell dissemination results both from local geometrical constraints and a global integration of spatial disorder over time. Surprisingly, this transition is accompanied by a change in the universality class of interface dynamics, revealing that cell-environment interactions can shift the collective behavior of an invasive front purely through mechanics. In the last system, we study how cell-intrinsic geometry and chirality affect collective motion in confined and unconfined settings. Using a minimal model inspired by in vitro experiments, we analyze motile cells that exhibit persistent rotation due to intrinsic left-right asymmetry. In circular confinement, this simplified chiral model reproduces several experimentally observed features within specific parameter regimes. At high densities in unconfined environments, however, intrinsic chirality becomes masked even before the onset of the jamming transition. These results show that single-cell geometric asymmetry does not necessarily translate into large-scale chiral flows, offering new insight into how forces and symmetries shape collective motion in dense cellular systems. Overall, this work uncovers how geometric constraints – embedded in the intrinsic architecture of an active filament or encoded in the complexity of a microenvironment couple to active forces to generate different classes of complex behaviors. }, author = {Dunajova, Zuzana}, isbn = {978-3-99078-076-3}, issn = {2663-337X}, pages = {110}, publisher = {Institute of Science and Technology Austria}, title = {{Geometry-driven self-organization of migrating cells and chiral filaments}}, doi = {10.15479/AT-ISTA-21423}, year = {2026}, } @misc{21439, abstract = {These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis.}, author = {Dunajova, Zuzana}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”}}, doi = {10.15479/AT-ISTA-21439}, year = {2026}, } @misc{20842, abstract = {Probing the possibility of entanglement generation through gravity offers a path to tackle the question of whether gravitational fields possess a quantum mechanical nature. A potential realization necessitates systems with low-frequency dynamics at an optimal mass scale, for which the microgram-to-milligram range is a strong contender. Here, after refining a figure-of-merit for the problem, we present a 1-milligram torsional pendulum operating at 18 Hz. We demonstrate laser cooling its motion from room temperature to 240~microkelvins, surpassing by over 20-fold the coldest motions attained for oscillators ranging from micrograms to kilograms. We quantify and contrast the utility of the current approach with other platforms. The achieved performance and large improvement potential highlight milligram-scale torsional pendulums as a powerful platform for precision measurements relevant to future studies at the quantum-gravity interface.}, author = {Agafonova, Sofya}, publisher = {Institute of Science and Technology Austria}, title = {{Research Data for: 'One-milligram torsional pendulum toward experiments at the quantum-gravity interface'}}, doi = {10.15479/AT-ISTA-20842}, year = {2025}, } @inproceedings{21020, abstract = {Runtime verification offers scalable solutions to improve the safety and reliability of systems. However, systems that require verification or monitoring by a third party to ensure compliance with a specification might contain sensitive information, causing privacy concerns when usual runtime verification approaches are used. Privacy is compromised if protected information about the system, or sensitive data that is processed by the system, is revealed. In addition, revealing the specification being monitored may undermine the essence of third-party verification. In this work, we propose two novel protocols for the privacy-preserving runtime verification of systems against formal sequential specifications. In our first protocol, the monitor verifies whether the system satisfies the specification without learning anything else, though both parties are aware of the specification. Our second protocol ensures that the system remains oblivious to the monitored specification, while the monitor learns only whether the system satisfies the specification and nothing more. Our protocols adapt and improve existing techniques used in cryptography, and more specifically, multi-party computation. The sequential specification defines the observation step of the monitor, whose granularity depends on the situation (e.g., banks may be monitored on a daily basis). Our protocols exchange a single message per observation step, after an initialisation phase. This design minimises communication overhead, enabling relatively lightweight privacy-preserving monitoring. We implement our approach for monitoring specifications described by register automata and evaluate it experimentally.}, author = {Henzinger, Thomas A and Karimi, Mahyar and Thejaswini, K. S.}, booktitle = {Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security}, isbn = {9798400715259}, location = {Taipei, Taiwan}, pages = {2774--2787}, publisher = {Association for Computing Machinery}, title = {{Privacy-preserving runtime verification}}, doi = {10.1145/3719027.3765137}, year = {2025}, } @article{21136, abstract = {The plant hormone auxin regulates growth and development through at least two distinct signaling pathways. The nuclear pathway, involving TIR1/AFB receptors, mediates transcription; whereas the cell surface ABP1-TMK1 auxin perception triggers global ultrafast phosphorylation response. Here, we revisit the rich history of the disputed ABP1 auxin receptor, highlighting recent findings of the involvement of TMKs and other molecular components and focusing on their role in auxin canalization-mediated development.}, author = {Monzer, Aline and Friml, Jiří}, issn = {3005-1401}, journal = {npj Science of Plants}, number = {1}, pages = {2}, publisher = {Springer Nature}, title = {{Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin signaling.}}, doi = {10.1038/s44383-025-00002-8}, volume = {1}, year = {2025}, } @article{21248, abstract = {Camera-type eyes in vertebrates and cephalopods are striking examples of parallel evolution of a complex structure. While comparisons have focused on these two groups, camera-type eyes with likely high functionality are also found in other invertebrate phyla with simpler brains. Employing single-cell RNA sequencing, we identify neurogenic cells in the adult eyes and brain of the marine annelid worm Platynereis dumerilii. Distinct neural stem cells in the camera-type adult eyes, located at the edge of the cup-shaped retina, and adjacent to the glass body/lens, produce radial lines of cells, reminiscent of stem cells in ciliary marginal zones of vertebrate eyes exhibiting life-long growth. Normal proliferation in the eye depends on ambient light, a phenomenon that depends on the integrity of the photoreceptor gene c-opsin1, which is present in emerging rhabdomeric photoreceptors, and impacts on their differentiation. During reproductive maturation, proliferation in the eye as well as the entire brain sharply declines, while cells upregulate molecular characteristics of mammalian adult neural stem cell quiescence. Our data provide insights into the development and modulation of annelid head and brain cells, revealing similarities and differences to vertebrate eye development, neurogenesis and brain plasticity.}, author = {Milivojev, Nadja and Scaramuzza, Federico and Brum, Pedro Ozório and Velastegui Gamboa, Camila L and Andreatta, Gabriele and Raible, Florian and Tessmar-Raible, Kristin}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Light-modulated stem cells in the camera-type eye of an annelid model for adult brain plasticity}}, doi = {10.1038/s41467-025-65631-0}, volume = {16}, year = {2025}, } @inproceedings{21250, abstract = {We investigate the step complexity of the Leader Election problem (and implementing the corresponding test-and-set object) in asynchronous shared memory, where processes communicate through registers supporting atomic read and write and must coordinate so that a single process becomes the leader. Determining tight step complexity bounds for solving this problem is one of the key open problems in the theory of shared memory distributed computing. The best known algorithm is a randomized tournament-tree, which has worst-case expected step complexity O(log N) for N processes. There are provably no deterministic wait-free algorithms, and only restricted lower bounds are known for obstruction-free and randomized wait-free algorithms. We introduce a new lower bound that establishes an Ω((log N)/(log log N + log Q)) step complexity for any obstruction-free Leader Election algorithm, where N is the number of processes, and 2 ≤ Q ≤ N is a bound on the value contention, which we define as the maximum number of different values that processes can be simultaneously poised to write to the same register in any execution of the algorithm. Our result is strictly stronger than previous bounds based on write contention. In particular, it implies new lower bounds on step complexity that depend on register size.}, author = {Alistarh, Dan-Adrian and Ellen, Faith and Fedorov, Alexander}, booktitle = {39th International Symposium on Distributed Computing}, location = {Berlin, Germany}, pages = {3:1--3:16}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{An almost-logarithmic lower bound for leader election with bounded value contention}}, doi = {10.4230/LIPIcs.DISC.2025.3}, volume = {356}, year = {2025}, } @inbook{21257, abstract = {We investigate the problem of accurate sparse fine-tuning of large language models (LLMs), that is, fine-tuning pre-trained LLMs on specialized tasks, while inducing sparsity in their weights. Our work is motivated by experiments showing that standard loss-based fine-tuning methods are not able to achieve high accuracy in this setting, especially at high sparsity targets. To address this issue, we perform a detailed study of knowledge distillation losses for fine-tuning of sparse models. We determine an L2-based distillation approach that we term ‘SquareHead’, which enables accurate recovery even at higher sparsities. Investigating the question of efficient inference, we show that sparse LLMs can be executed faster by taking advantage of sparsity. Specifically, we exhibit end-to-end results showing speedups enabled by sparsity, while recovering accuracy, on the following models and tasks, respectively: T5 for language translation, Whisper for speech translation, and open GPT-type models such as the Mosaic Pre-Trained Transformer (MPT) and Llama-2 models for text generation. In particular, for popular generative tasks, we show for the first time that sparse fine-tuning can reach 75% sparsity without drops in accuracy, and provide notable end-to-end speedups for inference on CPUs. Moreover, we also highlight that sparsity is compatible with other compression approaches, such as quantization.}, author = {Kurtic, Eldar and Kuznedelev, Denis and Frantar, Elias and Goinv, Michael and Pandit, Shubhra and Agarwalla, Abhinav and Nguyen, Tuan and Marques, Alexandre and Kurtz, Mark and Alistarh, Dan-Adrian}, booktitle = {Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques}, editor = {Passban, Peyman and Way, Andy and Rezagholizadeh, Mehdi}, isbn = {9783031857461}, issn = {2522-803X}, pages = {83--97}, publisher = {Springer Nature}, title = {{Sparse Fine-Tuning for Inference Acceleration of Large Language Models}}, doi = {10.1007/978-3-031-85747-8_6}, year = {2025}, } @inproceedings{21327, abstract = {Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational heterogeneity revealed by diverse experimental modalities. Here, we present a framework for building experiment-grounded protein structure generative models that infer conformational ensembles consistent with measured experimental data. The key idea is to treat stateof-the-art protein structure predictors (e.g., AlphaFold3) as sequence-conditioned structural priors, and cast ensemble modeling as posterior inference of protein structures given experimental measurements. Through extensive real-data experiments, we demonstrate the generality of our method to incorporate a variety of experimental measurements. In particular, our framework uncovers previously unmodeled conformational heterogeneity from crystallographic densities, and generates high-accuracy NMR ensembles orders of magnitude faster than the status quo. Notably, we demonstrate that our ensembles outperform AlphaFold3 (Abramson et al., 2024) and sometimes better fit experimental data than publicly deposited structures to the Protein Data Bank (PDB, Burley et al. (2017)). We believe that this approach will unlock building predictive models that fully embrace experimentally observed conformational diversity.}, author = {Maddipatla, Sai A and Sellam, Nadav E and Bojan, Meital I and Vedula, Sanketh and Schanda, Paul and Marx, Ailie and Bronstein, Alexander}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, issn = {2640-3498}, location = {Vancouver, Canada}, pages = {42366 -- 42393}, publisher = {ML Research Press}, title = {{Inverse problems with experiment-guided AlphaFold}}, volume = {267}, year = {2025}, } @article{15128, abstract = {We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\zeta)$ and a general class of related quantities involving two resolvents at nearby spectral parameters.}, author = {Riabov, Volodymyr}, issn = {0246-0203}, journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics}, number = {1}, pages = {129--154}, publisher = {Institute of Mathematical Statistics}, title = {{Mesoscopic eigenvalue statistics for Wigner-type matrices}}, doi = {10.1214/23-AIHP1438}, volume = {61}, year = {2025}, }