Tootfinder

Interpolation in First-Order Logic
Balder ten Cate, Jesse Comer
https://arxiv.org/abs/2510.03822 https://arxiv.org/pdf/2510.03822

Interpolation in First-Order Logic
In this chapter we give a basic overview of known results regarding Craig interpolation for first-order logic as well as for fragments of first-order logic. Our aim is to provide an entry point into the literature on interpolation theorems for first-order logic and fragments of first-order logic, and their applications. In particular, we cover a range of known refinements of the Craig interpolation theorem, we discuss several important applications of interpolation in logic and computer science…

Full die PIC12F683 100x scan at M3 with a little bit of passivation remaining.
There's a few small particulates on the surface from my somewhat crude "rub it with a swab" cleaning to remove residual undercut glass fragments.
Plan is to give it ~10 more seconds in HF to get more glass residue off, then maybe a very brief sonication (like 2-3 seconds), then image again to see if it cleaned up at all.
Depending on how things go I might end up just continuing to e…

Langtauferer
Today, a year ago, I ventured on a dream trip I'd been researching for a long time, and which ended up being a semi-religious experience, being immersed in (and somewhat overwhelmed by) an actively changing environment, the upheaval and plethora of geological features, structures, unreal colors, layers, textures and the "wounds" exposed by the melting and disappearing glaciers... Countless waterfalls, stunning erosion features, later traversing the glacier ga…

Fast Leave-One-Out Approximation from Fragment-Target Prevalence Vectors (molFTP) : From Dummy Masking to Key-LOO for Leakage-Free Feature Construction
Guillaume Godin
https://arxiv.org/abs/2510.06029 …

Fast Leave-One-Out Approximation from Fragment-Target Prevalence Vectors (molFTP) : From Dummy Masking to Key-LOO for Leakage-Free Feature Construction
We introduce molFTP (molecular fragment-target prevalence), a compact representation that delivers strong predictive performance. To prevent feature leakage across cross-validation folds, we implement a dummy-masking procedure that removes information about fragments present in the held-out molecules. We further show that key leave-one-out (key-loo) closely approximates true molecule-level leave-one-out (LOO), with deviation below 8% on our datasets. This enables near full data training while p…

Production of spectator neutrons, protons and light fragments on fixed targets at NICA
A. O. Svetlichny (Institute for Nuclear Research, Russian Academy of Sciences, Moscow, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Russia), E. Y. Vasyagina (Institute for Nuclear Research, Russian Academy of Sciences, Moscow, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Russia), S. D. Savenkov (Institute for Nuclear Research, Russian Academy of Sciences, Mosco…

Production of spectator neutrons, protons and light fragments on fixed targets at NICA
The Ultrarelativistic Quantum Molecular Dynamics (UrQMD) model was connected to a set of models called Ablation Monte Carlo (AMC) to identify excited spectator fragments on completion of the UrQMD modeling of nucleus-nucleus collisions and then simulate spectator decays. The UrQMD-AMC approach combines the Minimum Spanning Tree (MST) clustering algorithm, which associates individual nucleons with excited clusters termed prefragments, with decay models of excited nuclei from the Geant4 toolkit. …

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
Furkan Eris, Ulysse McConnell, Can Firtina, Onur Mutlu
https://arxiv.org/abs/2510.03629

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to selectively stop sequencing a molecule before completion. Traditionally, the raw electrical signals generated during sequencing are converted into DNA sequences through a process called basecalling, which typically relies on large neural network models. Raw signal an…

Discontinuous Epitope Fragments as Sufficient Target Templates for Efficient Binder Design
Zhenfeng Deng, Ruijie Hou, Ningrui Xie, Mike Tyers, Micha{\l} Koziarski
https://arxiv.org/abs/2509.25479

Discontinuous Epitope Fragments as Sufficient Target Templates for Efficient Binder Design
Recent advances in structure-based protein design have accelerated de novo binder generation, yet interfaces on large domains or spanning multiple domains remain challenging due to high computational cost and declining success with increasing target size. We hypothesized that protein folding neural networks (PFNNs) operate in a ``local-first'' manner, prioritizing local interactions while displaying limited sensitivity to global foldability.Guided by this hypothesis, we propose an epitope-only …

🇺🇦 #NowPlaying on KEXP's #EasternEchoes
Social Club Hyangwu:
🎵 Dust Fragments (먼지조각)
#SocialClubHyangwu

Artillery shell exploded prematurely over California freeway during marines celebration;
Shrapnel fragments rained on vehicles parked on Interstate 5 including highway patrol and JD Vance’s detail
https://www.theguardian.com/us-news/2025/oct/…

MightyPPL: Verification of MITL with Past and Pnueli Modalities
Hsi-Ming Ho, Shankara Narayanan Krishna, Khushraj Madnani, Rupak Majumdar, Paritosh Pandya
https://arxiv.org/abs/2510.01490

MightyPPL: Verification of MITL with Past and Pnueli Modalities
Metric Interval Temporal Logic (MITL) is a popular formalism for specifying properties of reactive systems with timing constraints. Existing approaches to using MITL in verification tasks, however, have notable drawbacks: they either support only limited fragments of the logic or allow for only incomplete verification. This paper introduces MightyPPL, a new tool for translating formulae in Metric Interval Temporal Logic with Past and Pnueli modalities (MITPPL) over the pointwise semantics into …

Replaced article(s) found for math.LO. https://arxiv.org/list/math.LO/new
[1/1]:
- Characterizing fragments of collection principle in set theory with model theoretic properties
Junhong Chen

First passage times to T cell activation
Tony Wong, Ikchang Cho, Maria R. D'Orsogna, Tom Chou
https://arxiv.org/abs/2510.01694 https://arxiv.org/pdf/25…

First passage times to T cell activation
Effective recognition of foreign antigens by the adaptive immune system relies on T cells being activated by antigen-presenting cells (APCs) in lymph nodes. Here, diffusing T cells may encounter cognate APCs that present matching antigen fragments or non-cognate ones that do not; they are also subject to degradation. We develop a stochastic model in which T cell-APCs interact via a sequence of recognition steps, represented as a multistage Markov chain. T cells are successfully activated only i…

Unresolved Feeling, Fragments of Belonging: Emotion Across Text and Screen
https://ift.tt/Yt9QTyS
updated: Monday, September 1, 2025 - 3:07pmfull name / name of organization: ACLA 2026contact…
via Input 4 RELCFP

The depletion of the asteroid belt and the impact history of the Earth
Julio A. Fernandez
https://arxiv.org/abs/2509.21194 https://arxiv.org/pdf/2509.21194…

The depletion of the asteroid belt and the impact history of the Earth
We have evaluated the rate at which the asteroid belt is losing material, and how it splits between macroscopic bodies and meteoritic dust. The mass loss process is due to the injection of asteroid fragments into unstable dynamical regions, associated to mean-motion resonances with Jupiter, Saturn and Mars or secular resonances, from where they are scattered either to the region of the terrestrial planets or to the vicinity of Jupiter's orbit. Asteroid fragments that do not escape from the belt…

Replaced article(s) found for cs.AI. https://arxiv.org/list/cs.AI/new
[4/6]:
- Date Fragments: A Hidden Bottleneck of Tokenization for Temporal Reasoning
Gagan Bhatia, Maxime Peyrard, Wei Zhao

Eigen-1: Adaptive Multi-Agent Refinement with Monitor-Based RAG for Scientific Reasoning
Xiangru Tang, Wanghan Xu, Yujie Wang, Zijie Guo, Daniel Shao, Jiapeng Chen, Cixuan Zhang, Ziyi Wang, Lixin Zhang, Guancheng Wan, Wenlong Zhang, Lei Bai, Zhenfei Yin, Philip Torr, Hanrui Wang, Di Jin
https://arxiv.org/abs/2509.21193

Eigen-1: Adaptive Multi-Agent Refinement with Monitor-Based RAG for Scientific Reasoning
Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates…

Les dev front m'impressionnent.
Apparemment, il faut faire des Single Page Applications, mais avec des URLs différentes par page (non basées sur les fragments) et utiliser du Server Side Rendering pour le SEO. Mais c'est une SPA, hein 🤣
#frontend

Fragments of 2003 Cable Detail Torture in a Secret C.I.A. Prison (Carol Rosenberg/New York Times)
https://www.nytimes.com/2025/10/13/us/politics/cia-torture-black-sites.html
http://www.memeorandum.com/251013/p57#a251013p57

Fast Methods For Multisite Charge Transfer Processes I: Constrained, State Averaged CASSCF(1,M) and CASSCF(2M-1,M) Simulations
Tian Qiu, Joseph E. Subotnik
https://arxiv.org/abs/2508.21136

Fast Methods For Multisite Charge Transfer Processes I: Constrained, State Averaged CASSCF(1,M) and CASSCF(2M-1,M) Simulations
We design a dynamically-weighted state-averaged constrained CASSCF to treat \ul{e}lectrons or \ul{h}oles moving between $n$ molecular fragments (where $n$ can be larger than 2). Within such a so-called eDSCn/hDSCn approach, we consider configurations that are mutually single excitations of each other, and we apply a generalized set of constraints to tailor the method for studying charge transfer problems. The constrained optimization problem is efficiently solved using a DIIS-SQP algorithm, thu…

GraphMend: Code Transformations for Fixing Graph Breaks in PyTorch 2
Savini Kashmira, Jayanaka Dantanarayana, Thamirawaran Sathiyalogeswaran, Yichao Yuan, Nishil Talati, Krisztian Flautner, Lingjia Tang, Jason Mars
https://arxiv.org/abs/2509.16248

GraphMend: Code Transformations for Fixing Graph Breaks in PyTorch 2
This paper presents GraphMend, a high-level compiler that eliminates FX graph breaks in PyTorch 2 programs. Although PyTorch 2 introduced TorchDynamo and TorchInductor to enable just-in-time graph compilation, unresolved dynamic control flow and unsupported Python constructs often fragment models into multiple FX graphs. These fragments force frequent fallbacks to eager mode, incur costly CPU-to-GPU synchronizations, and reduce optimization opportunities. GraphMend addresses this limitation by …

The ideas that finally bubbled up to the surface in The Point of No Return last night have been festering in the back of my brain for months. Because, although it's a bit inchoate, it's only saying out loud what most of us already know.
The job now is no longer to turn the ship around. We don't have the wheel, and those who do will not listen.
The task now is to build lifeboats. To build resilient spaces in which fragments of humanity can survive.

The Point of No Return
I can't stop climate change by myself. I can't create a sustainable future for my village by myself. To do either of these things, everyone else needs to work together. But badgering people, being frustrated with people, being angry with people (and yes, I am angry — very angry — with people I know, and like, and respect, very much) doesn't motivate them to work together. My very frustration, my very sense of urgency, makes me a liability. I should stop.

Generalization of Variadic Structures with Binders: A Tool for Structural Code Comparison
Alexander Baumgartner, Temur Kutsia
https://arxiv.org/abs/2509.25023 https://

Generalization of Variadic Structures with Binders: A Tool for Structural Code Comparison
This paper introduces a novel anti-unification algorithm for the generalization of variadic structures with binders, designed as a flexible tool for structural code comparison. By combining nominal techniques for handling variable binding with support for variadic expressions (common in abstract syntax trees and programming languages), the approach addresses key challenges such as overemphasis on bound variable names and difficulty handling insertions or deletions in code fragments. The algorit…

🌠 Ryugu asteroid research reveals mineral history predating any on Earth
#astronomy

Ryugu asteroid research reveals mineral history predating any on Earth
In 2020, the Hayabusa2 uncrewed spacecraft successfully returned small fragments from the near-Earth asteroid Ryugu, providing the first pristine samples from a carbonaceous asteroid. Grains from those samples were studied at the National Synchrotron Light Source II (NSLS-II), revealing new details into the asteroid's composition and origin. This insight could ultimately help answer big questions about how water and organic matter came to exist on early Earth, forming the building blocks of lif…

QCell: Comprehensive Quantum-Mechanical Dataset Spanning Diverse Biomolecular Fragments
Adil Kabylda, Sergio Su\'arez-Dou, Nils Davoine, Florian N. Br\"unig, Alexandre Tkatchenko
https://arxiv.org/abs/2510.09939

QCell: Comprehensive Quantum-Mechanical Dataset Spanning Diverse Biomolecular Fragments
Recent advances in machine learning force fields (MLFFs) are revolutionizing molecular simulations by bridging the gap between quantum-mechanical (QM) accuracy and the computational efficiency of mechanistic potentials. However, the development of reliable MLFFs for biomolecular systems remains constrained by the scarcity of high-quality, chemically diverse QM datasets that span all of the major classes of biomolecules expressed in living cells. Crucially, such a comprehensive dataset must be c…

AuthenTree: A Scalable MPC-Based Distributed Trust Architecture for Chiplet-based Heterogeneous Systems
Ishraq Tashdid, Tasnuva Farheen, Sazadur Rahman
https://arxiv.org/abs/2508.13033

AuthenTree: A Scalable MPC-Based Distributed Trust Architecture for Chiplet-based Heterogeneous Systems
The rapid adoption of chiplet-based heterogeneous integration is reshaping semiconductor design by enabling modular, scalable, and faster time-to-market solutions for AI and high-performance computing. However, multi-vendor assembly in post-fabrication environments fragments the supply chain and exposes SiP systems to serious security threats, including cloning, overproduction, and chiplet substitution. Existing authentication solutions depend on trusted integrators or centralized security anch…

Molecular Tools for Non-Planar Surface Chemistry
Taleana Huff, Brandon Blue, Terry McCallum, Mathieu Morin, Damian G. Allis, Rafik Addou, Jeremy Barton, Adam Bottomley, Doreen Cheng, Nina M. \'Culum, Michael Drew, Tyler Enright, Alan T. K. Godfrey, Ryan Groome, Aru J. Hill, Alex Inayeh, Matthew R. Kennedy, Robert J. Kirby, Mykhaylo Krykunov, Sam Lilak, Hadiya Ma, Cameron J. Mackie, Oliver MacLean, Jonathan Myall, Ryan Plumadore, Adam Powell, Henry Rodriguez, Luis Sandoval, Marc Sav…

Molecular Tools for Non-Planar Surface Chemistry
Scanning probe microscopy (SPM) investigations of on-surface chemistry on passivated silicon have only shown in-plane chemical reactions, and studies on bare silicon are limited in facilitating additional reactions post-molecular-attachment. Here, we enable subsequent reactions on Si(100) through selectively adsorbing 3D, silicon-specific "molecular tools". Following an activation step, the molecules present an out-of-plane radical that can function both to donate or accept molecular fragments,…

🇺🇦 #NowPlaying on KEXP's #EasternEchoes
KIRARA:
🎵 Swervy
#KIRARA
https://stqpkiraradongjae.bandcamp.com/track/fragments-with-swervy-with

Replaced article(s) found for cs.AI. https://arxiv.org/list/cs.AI/new
[4/6]:
- Date Fragments: A Hidden Bottleneck of Tokenization for Temporal Reasoning
Gagan Bhatia, Maxime Peyrard, Wei Zhao

Evalet: Evaluating Large Language Models by Fragmenting Outputs into Functions
Tae Soo Kim, Heechan Lee, Yoonjoo Lee, Joseph Seering, Juho Kim
https://arxiv.org/abs/2509.11206 h…

Evalet: Evaluating Large Language Models by Fragmenting Outputs into Functions
Practitioners increasingly rely on Large Language Models (LLMs) to evaluate generative AI outputs through "LLM-as-a-Judge" approaches. However, these methods produce holistic scores that obscure which specific elements influenced the assessments. We propose functional fragmentation, a method that dissects each output into key fragments and interprets the rhetoric functions that each fragment serves relative to evaluation criteria -- surfacing the elements of interest and revealing how they fulf…

Uniformization of ladder system colorings and stationary precaliber forcings
Yushiro Aoki
https://arxiv.org/abs/2508.18900 https://arxiv.org/pdf/2508.18900…

Uniformization of ladder system colorings and stationary precaliber forcings
We investigate the relationship between variants of the uniformization property for ladder system colorings and fragments of Martin's Axiom. The well-known forcing properties of having precaliber $\aleph_1$ and being $σ$-centered correspond to uncountable refinement and countable decomposition into centered subsets, respectively, and the associated forcing axioms have been widely studied. In this paper, we focus on a forcing axiom for the property corresponding to stationary refinement, namely…

CLARA: A Developer's Companion for Code Comprehension and Analysis
Ahmed Adnan, Mushfiqur Rahman, Saad Sakib Noor, Kazi Sakib
https://arxiv.org/abs/2509.09072 https://

CLARA: A Developer's Companion for Code Comprehension and Analysis
Code comprehension and analysis of open-source project codebases is a task frequently performed by developers and researchers. However, existing tools that practitioners use for assistance with such tasks often require prior project setup, lack context-awareness, and involve significant manual effort. To address this, we present CLARA, a browser extension that utilizes a state-of-the-art inference model to assist developers and researchers in: (i) comprehending code files and code fragments, (i…

Guarded Fragments Meet Dynamic Logic: The Story of Regular Guards (Extended Version)
Bartosz Bednarczyk, Emanuel Kiero\'nski
https://arxiv.org/abs/2509.09218 https://…

Guarded Fragments Meet Dynamic Logic: The Story of Regular Guards (Extended Version)
We study the Guarded Fragment with Regular Guards (RGF), which combines the expressive power of the Guarded Fragment (GF) with Propositional Dynamic Logic with Intersection and Converse (ICPDL). Our logic generalizes, in a uniform way, many previously-studied extensions of GF, including (conjunctions of) transitive or equivalence guards, transitive or equivalence closure and more. We prove 2EXPTIME-completeness of the satisfiability problem for RGF, showing that RGF is not harder than ICPDL or …

Putting Tutte's counterexample to Tait's conjecture in perspective to hamiltonicity and non-hamiltonicity in certain planar cubic graphs
Herbert Fleischner, Enrico Iurlano, G\"unther R. Raidl
https://arxiv.org/abs/2510.08310

Putting Tutte's counterexample to Tait's conjecture in perspective to hamiltonicity and non-hamiltonicity in certain planar cubic graphs
Using the graphs of prisms and Tutte Fragments, we construct an infinite family of hamiltonian and non-hamiltonian graphs in which Tutte's counterexample to Tait's conjecture appears in a certain sense as a minimal element. We observe that generalizations of the minimum-cardinality counterexamples of Holton and McKay to Tait's conjecture are as well contained in this family.

Jet quenching without energy loss
Liliana Apolin\'ario, Chiara Le Roux, Korinna Zapp
https://arxiv.org/abs/2510.11914 https://arxiv.org/pdf/2510.11914

Jet quenching without energy loss
The onset of jet quenching, i.e. the suppression of high transverse momentum particles and jets, is an important question in the context of understanding the onset of collective behaviour and small collision systems. We investigate a minimal scenario where a hard parton experiences a single soft re-scattering that leaves the kinematics unmodified, but the colour exchange leads to a loss of colour coherence that is observable in the final distribution of fragments. In particular, the formation t…

Flow-Based Fragment Identification via Binding Site-Specific Latent Representations
Rebecca Manuela Neeser, Ilia Igashov, Arne Schneuing, Michael Bronstein, Philippe Schwaller, Bruno Correia
https://arxiv.org/abs/2509.13216

Flow-Based Fragment Identification via Binding Site-Specific Latent Representations
Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly and non-specifically. We developed a protein-fragment encoder that relies on a contrastive learning approach to map both molecular fragments and protein surfaces in a shared latent space. The encoder captures interaction-relevant features and allows to perfor…

On the Expressiveness of Languages for Querying Property Graphs in Relational Databases
Hadar Rotschield, Liat Peterfreund
https://arxiv.org/abs/2510.07062 https://

On the Expressiveness of Languages for Querying Property Graphs in Relational Databases
SQL/PGQ is the emerging ISO standard for querying property graphs defined as views over relational data. We formalize its expressive power across three fragments: the read-only core, the read-write extension, and an extended variant with richer view definitions. Our results show that graph creation plays a central role in determining the expressiveness. The read-only fragment is strictly weaker than the read-write fragment, and the latter is still below the complexity class NL. Extending view d…

Excitation energy of fission fragments within nuclear time-dependent density functional theory
Antonio Bjel\v{c}i\'c, Nicolas Schunck, Marc Verriere
https://arxiv.org/abs/2510.06701

Excitation energy of fission fragments within nuclear time-dependent density functional theory
The number and properties of the neutrons and photons emitted in nuclear fission are directly related to the excitation energy of the fission fragments when they are formed at scission. Though not observable experimentally because of the extremely short time scales, the excitation energy of fission fragments can be predicted by microscopic theory based on time-dependent density functional theory (TDDFT). Initial results on the value of the total kinetic energy of fission reactions were very pro…

Separating Maximality Principles
Takehiko Gappo, Andreas Lietz
https://arxiv.org/abs/2508.16506 https://arxiv.org/pdf/2508.16506

Separating Maximality Principles
We investigate fragments of generic absoluteness principles known as Maximality Principles. We determine the consistency strength of $Σ_n$-$\mathsf{MP}(\mathbb R)$ and $Π_n$-$\mathsf{MP}(\mathbb R)$, the boldface Maximality Principle restricted respectively to $Σ_n$- and $Π_n$-formulas. Further, we show that no implication between $Σ_n$-$\mathsf{MP}(\mathbb R)$ and $Π_n$-$\mathsf{MP}(\mathbb R)$ is provable in $\mathsf{ZFC}$. We also establish the consistency, relative to a Woodin cardina…

Decidability in First-Order Modal Logic with Non-Rigid Constants and Definite Descriptions
Alessandro Artale, Christopher Hampson, Roman Kontchakov, Andrea Mazzullo, Frank Wolter
https://arxiv.org/abs/2509.08165

Decidability in First-Order Modal Logic with Non-Rigid Constants and Definite Descriptions
While modal extensions of decidable fragments of first-order logic are usually undecidable, their monodic counterparts, in which formulas in the scope of modal operators have at most one free variable, are typically decidable. This only holds, however, under the provision that non-rigid constants, definite descriptions and non-trivial counting are not admitted. Indeed, several monodic fragments having at least one of these features are known to be undecidable. We investigate these features syst…

Le Chatelier principle and field-induced change in magnetic entropy leading to spin lattice partitioning and magnetization plateau
Myung-Hwan Whangbo, Hyun-Joo Koo, Olga S. Volkova
https://arxiv.org/abs/2509.05525

Le Chatelier principle and field-induced change in magnetic entropy leading to spin lattice partitioning and magnetization plateau
For a certain antiferromagnet, the magnetization does not increase gradually with increasing magnetic field but exhibits field region(s) typically at an integer fraction of its saturation magnetization. This phenomenon is understood by the supposition that such an antiferromagnet undergoes field-induced partitioning of its spin lattice into ferrimagnetic fragments. We searched for a theoretical basis for this supposition by investigating how external magnetic fields affect the magnetic entropy …

Transport properties of nuclear matter from anomalous fission yields
Karl-Heinz Schmidt, Christelle Schmitt, Andreas Heinz
https://arxiv.org/abs/2509.24590 https://

Transport properties of nuclear matter from anomalous fission yields
In nuclear fission, a heavy nucleus splits into two fragments, driven by the Coulomb repulsion between the positively charged protons. The fission process is governed by the potential energy and basic transport properties of nuclear matter like inertial mass and viscosity. While inertia induces features of memory, viscosity attenuates these features by damping. Exploring signatures of memory in fission is crucial for overcoming the current severe lack of experimental information on the transpor…

HemePLM-Diffuse: A Scalable Generative Framework for Protein-Ligand Dynamics in Large Biomolecular System
Rakesh Thakur, Riya Gupta
https://arxiv.org/abs/2508.16587 https://

HemePLM-Diffuse: A Scalable Generative Framework for Protein-Ligand Dynamics in Large Biomolecular System
Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce HemePLM-Diffuse, an innovative generative transformer model that is designed for accurate simulation of protein-ligand trajectories, inpaints the missing ligand fragments, and sample transition paths in systems with more than 10,000 atoms. HemePLM-Diffuse has features of …

Path through the ferns in Shindagin Hollow State Forest
#photo #photography #forest #shindaginhollow

Arithmetics within the Linear Time Hierarchy
Chris Pollett
https://arxiv.org/abs/2508.13195 https://arxiv.org/pdf/2508.13195…

Arithmetics within the Linear Time Hierarchy
We identify fragments of the arithmetic $S_1$ that enjoy nice closure properties and have exact characterization of their definable multifunctions. To do this, in the language of $S_1$, $L_1$, starting from the formula classes, $Σ^{\mathsf b}_{i}$, which ignore sharply bounded quantifiers when determining quantifier alternations, we define new syntactic classes by counting bounded existential sharply bounded universal quantifiers blocks. Using these, we define arithmetics: $\breve{S}^{i}_{1}$,…

Weighted First Order Model Counting for Two-variable Logic with Axioms on Two Relations
Qipeng Kuang, V\'aclav K\r{u}la, Ond\v{r}ej Ku\v{z}elka, Yuanhong Wang, Yuyi Wang
https://arxiv.org/abs/2508.11515

Weighted First Order Model Counting for Two-variable Logic with Axioms on Two Relations
The Weighted First-Order Model Counting Problem (WFOMC) asks to compute the weighted sum of models of a given first-order logic sentence over a given domain. The boundary between fragments for which WFOMC can be computed in polynomial time relative to the domain size lies between the two-variable fragment ($\text{FO}^2$) and the three-variable fragment ($\text{FO}^3$). It is known that WFOMC for \FOthree{} is $\mathsf{\#P_1}$-hard while polynomial-time algorithms exist for computing WFOMC for $…

Replaced article(s) found for cs.LO. https://arxiv.org/list/cs.LO/new
[1/1]:
- Separation and Definability in Fragments of Two-Variable First-Order Logic with Counting
Louwe Kuijer, Tony Tan, Frank Wolter, Michael Zakharyaschev