Tootfinder

TIL: »Specific typographic rules have been developed for each language for centuries, but in recent decades, especially due to globalisation and the unification of software tools, they have been disregarded. The international project of a typographic proofreader for European languages will preserve these rules as an expression of European cultural diversity for future generations.«
Source:

Everyone must stop using the phrase "I did not have that on my bingo card" please.
It's tired and trite and that isn't even how Bingo works. You don't compile a card of all the numbers you expect to see. It's not weird when a number comes up that isn't on your card.
And the use of the phrase is growing. Soon it will be the only expression of surprise left!
Lets end this now before it's too late.

Test @…!
#RudolfRocker

A refinement of the Lorentz local field expression with impact on the Clausius-Mossotti and Lorentz-Lorenz models
Jeroen van Duivenbode, Anne-Jans Faber
https://arxiv.org/abs/2506.01993

A refinement of the Lorentz local field expression with impact on the Clausius-Mossotti and Lorentz-Lorenz models
In the 19th century Mossotti and Clausius formulated an expression that relates electrical permittivity of a dielectric to the product of molecular polarizability and number density. Lorenz and Lorentz extended the use of that expression to also cover the dielectric s refractive index. These expressions successfully predict the change of the dielectric s permittivity and refractive index as a function of a wide range of its number density, using the consideration that molecular polarizability s…

@… @… That expression doesn’t type-check, sorry.

#CFP: Meeting at the Crossroads: Understanding the Intersection of Rhetoric, Race, and Religion
https://ift.tt/BRQ0Ya6
Laurent Pernot wrote, “Religion is intimately linked with words. Everyone knows that the spoken…

#CFP: Meeting at the Crossroads: Understanding the Intersection of Rhetoric, Race, and Religion
Laurent Pernot wrote, “Religion is intimately linked with words. Everyone knows that the spoken and written word plays an essential role in religion, as language is necessarily used to address the gods or God, to speak about the divine or the sacred, and to express religious feeling or awareness”. Thus, Pernot called for an understanding of the role rhetoric plays in our expression and performance of religion.

"So let’s get one thing out of the way: I think “AI literacy” is a dangerous device of neoliberal education and it deserves to be dismissed out of hand."
"Using AI is not about communicating. It’s about avoiding communicating. It’s about not reading, not writing, not drawing, not seeing. It’s about ceding our powers of expression and comprehension to digital apps that will cushion us from fully participating in our own lives."

Against AI literacy: have we actually found a way to reverse learning?
So let’s get one thing out of the way: I think “AI literacy” is a dangerous device of neoliberal education and it deserves to be dismissed out of hand.

This https://arxiv.org/abs/2410.00399 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

The HOMFLY Polynomial of a Forest Quiver
We define the HOMFLY polynomial of a forest quiver $Q$ using a recursive definition on the underlying graph of the quiver. We then show that this polynomial is equal to the HOMFLY polynomial of any plabic link which comes from a connected plabic graph whose quiver is $Q$. We also prove a closed-form expression for the HOMFLY polynomial of a forest quiver $Q$ in terms of the independent sets of $Q$.

A robust approach to sigma point Kalman filtering
Shenglun Yi, Mattia Zorzi
https://arxiv.org/abs/2506.04815 https://arxiv.org/pdf/25…

A robust approach to sigma point Kalman filtering
In this paper, we address a robust nonlinear state estimation problem under model uncertainty by formulating a dynamic minimax game: one player designs the robust estimator, while the other selects the least favorable model from an ambiguity set of possible models centered around the nominal one. To characterize a closed-form expression for the conditional expectation characterizing the estimator, we approximate the center of this ambiguity set by means of a sigma point approximation. Furthermo…

As recently as last year I was recommending to my #Math students that if they were having trouble with an elementary algebra expression, they could try using the Google search bar to solve or simplify something. Maybe I should show them this instead.🤦

Closed-form survival probabilities for biased random walks at arbitrary step number
Debendro Mookerjee, Sarah Kostinski
https://arxiv.org/abs/2505.24814 ht…

Closed-form survival probabilities for biased random walks at arbitrary step number
We present a closed-form expression for the survival probability of a biased random walker to first reach a target site on a 1D lattice. The expression holds for any step number $N$ and is computationally faster than non-closed-form results in the literature. Because our result is exact even in the intermediate step number range, it serves as a tool to study convergence to the large $N$ limit. We also obtain a closed-form expression for the probability of last passage. In contrast to prediction…

This https://arxiv.org/abs/2411.13630 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

Competitive binding of Activator-Repressor in Stochastic Gene Expression
Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors) bind the promoter in a competitive way. We develop an analytical theory that offers detailed reaction kinetics of the competitive activator-repressor system which could be the powerful tools for extensive study and analysis of the genetic circuit in future resea…

The free expression of the hopes and aspirations of a people is the greatest and only safety in a sane society.
---- - Emma Goldman - ----

This https://arxiv.org/abs/2506.01982 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_csHC_…

Music interpretation and emotion perception: A computational and neurophysiological investigation
This study investigates emotional expression and perception in music performance using computational and neurophysiological methods. The influence of different performance settings, such as repertoire, diatonic modal etudes, and improvisation, as well as levels of expressiveness, on performers' emotional communication and listeners' reactions is explored. Professional musicians performed various tasks, and emotional annotations were provided by both performers and the audience. Audio analysis r…

The non-Hermitian magnetic moment
Bar Alon, Moshe Goldstein, Roni Ilan
https://arxiv.org/abs/2506.05206 https://arxiv.org/pdf/2506.05…

The non-Hermitian magnetic moment
We construct a semiclassical theory for electrons in a non-Hermitian periodic system subject to perturbations varying slowly in space and time. We derive the energy of the wavepacket to first order in the gradients of the perturbations. Applying the theory to the specific case of a uniform external magnetic field, we obtain an expression for the orbital magnetization energy. Using the principles of non-Hermitian dynamics, we define a physically meaningful non-Hermitian generalization of the ang…

Read more at: #NSFIAA #IWA

Excited State Densities from Time-Dependent Density Functional Response Theory
Anna Baranova, Neepa T. Maitra
https://arxiv.org/abs/2506.05082 https://

Excited State Densities from Time-Dependent Density Functional Response Theory
While the variational principle for excited-state energies leads to a route to obtaining excited-state densities from time-dependent density functional theory, relatively little attention has been paid to the quality of the resulting densities in real space obtained with different exchange-correlation functional approximations, nor how non-adiabatic approximations developed for energies of states of double excitation character perform for their densities. Here we derive an expression directly i…

Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis
Chi-Jane Chen, Yuhang Chen, Sukwon Yun, Natalie Stanley, Tianlong Chen
https://arxiv.org/abs/2506.01918

Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis
Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry's analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information: they struggle to generalize spatial coordinates and effectively encode spatial context as …

This https://arxiv.org/abs/2505.20078 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_hept…

Notes on Rindler wave packets in Minkowski spacetime
We consider wave packets of a massless scalar field that have well-localized Rindler energy, and examine how their energy appears to a Minkowski observer to see how the classical gravitational blue-shift formula is modified quantum mechanically. We derive, by using the saddle point approximation, an analytic expression for the Minkowski momentum distribution of such Rindler wave packets. We find a universal lower bound on the uncertainty of Minkowski momentum; the momentum distribution can neve…

The 13yo was making instant mac & cheese (incorrectly), and my wife yelled "READ the instructions!"
The 13yo responded with, "I DID read the instructions,"and she replied "A day in the library saves a week in the lab." Which I guess is a real expression that scientists say?

Neural Face Skinning for Mesh-agnostic Facial Expression Cloning
Sihun Cha, Serin Yoon, Kwanggyoon Seo, Junyong Noh
https://arxiv.org/abs/2505.22416 https:…

Neural Face Skinning for Mesh-agnostic Facial Expression Cloning
Accurately retargeting facial expressions to a face mesh while enabling manipulation is a key challenge in facial animation retargeting. Recent deep-learning methods address this by encoding facial expressions into a global latent code, but they often fail to capture fine-grained details in local regions. While some methods improve local accuracy by transferring deformations locally, this often complicates overall control of the facial expression. To address this, we propose a method that combi…

On the heat kernel of a Cayley graph of $\operatorname{PSL}_2\mathbb{Z}$
Anders Karlsson, Kamila Kashaeva
https://arxiv.org/abs/2506.02340 https://

On the heat kernel of a Cayley graph of $\operatorname{PSL}_2\mathbb{Z}$
In this paper, we obtain an explicit formula for the heat kernel on the infinite Cayley graph of the modular group $\operatorname{PSL}_2\mathbb{Z}$, given by the presentation $\langle a,b\mid a^2=1, b^3=1\rangle$. Our approach extends the method of Chung--Yau in~\cite{MR1667452} by observing that the Cayley graph strongly and regularly covers a weighted infinite line. We solve the spectral problem on this line to obtain an integral expression for its heat kernel, and then lift this to the Cayle…

PBS station WNET removed at least three educational TV episodes that discuss transgender identity and drag expression, following a DOGE subcommittee hearing (Nikita Mazurov/The Intercept)
https://theintercept.com/2025/05/29/drag-trans-pbs-wnet-censorship-d…

PBS Station Wipes Drag and Trans Content After DOGE Outcry
PBS producer WNET quietly erased episodes containing a drag queen and a trans character from its platforms.

This https://arxiv.org/abs/2505.23638 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qu…

Visualizing Three-Qubit Entanglement
We present a graphical framework to represent entanglement in three-qubit states. The geometry associated with each entanglement class and type is analyzed, revealing distinct structural features. We explore the connection between this geometric perspective and the tangle, deriving bounds that depend on the entanglement class. Based on these insights, we conjecture a purely geometric expression for both the tangle and Cayley's hyperdeterminant for non-generic states. As an application, we analy…

This https://arxiv.org/abs/2504.18292 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Large time cumulants of the KPZ equation on an interval
We consider the Kardar-Parisi-Zhang equation on the interval $[0,L]$ with Neumann type boundary conditions and boundary parameters $u,v$. We show that the $k$-th order cumulant of the height behaves as $c_k(L,u,v)\, t$ in the large time limit $t \to +\infty$, and we compute the coefficients $c_k(L,u,v)$. We obtain an expression for the upper tail large deviation function of the height. We also consider the limit of large $L$, with $u=\tilde u/\sqrt{L}$, $u=\tilde v/\sqrt{L}$, which should give …

Weaponized Storytelling: How AI Is Helping Researchers Sniff Out Disinformation Campaigns (The Conversation, 28 May 2025)
https://theconversation.com/weaponized-storytelling-how-ai-is-helping-researchers-sniff-out-disinf…

Weaponized storytelling: How AI is helping researchers sniff out disinformation campaigns
Disinformation campaigns are using AI to tell false but compelling stories. AI tools are also helping counter the campaigns by detecting incongruities in usernames, cultural references and timelines.

Phenotypic Profile-Informed Generation of Drug-Like Molecules via Dual-Channel Variational Autoencoders
Hui Liu, Shiye Tian, Xuejun Liu
https://arxiv.org/abs/2506.02051

Phenotypic Profile-Informed Generation of Drug-Like Molecules via Dual-Channel Variational Autoencoders
The de novo generation of drug-like molecules capable of inducing desirable phenotypic changes is receiving increasing attention. However, previous methods predominantly rely on expression profiles to guide molecule generation, but overlook the perturbative effect of the molecules on cellular contexts. To overcome this limitation, we propose SmilesGEN, a novel generative model based on variational autoencoder (VAE) architecture to generate molecules with potential therapeutic effects. SmilesGEN…

STARS-assisted Near-field ISAC: Sensor Deployment and Beamforming Design
Na Xue, Xidong Mu, Yue Chen, Yuanwei Liu
https://arxiv.org/abs/2506.00192 https://…

STARS-assisted Near-field ISAC: Sensor Deployment and Beamforming Design
A simultaneously transmitting and reflecting surface (STARS) assisted near-field (NF) integrated sensing and communication (ISAC) framework is proposed, where the radio sensors are installed on the STARS to directly conduct the distance-domain sensing by exploiting the characteristic spherical wavefront. A new squared position error bound (SPEB) expression is derived to reveal the dependence on beamforming (BF) design and sensor deployment. To balance the trade-off between the SPEB and the sens…

This https://arxiv.org/abs/2412.12405 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_sta…

Generalized entropy calibration for analyzing voluntary survey data
Statistical analysis of voluntary survey data is an important area of research in survey sampling. We consider a unified approach to voluntary survey data analysis under the assumption that the sampling mechanism is ignorable. Generalized entropy calibration is introduced as a unified tool for calibration weighting to control the selection bias. We first establish the relationship between the generalized calibration weighting and its dual expression for regression estimation. The dual relations…

Improving statistical learning methods via features selection without replacement sampling and random projection
Sulaiman khan, Muhammad Ahmad, Fida Ullah, Carlos Aguilar Iba\~nez, Jos\'e Eduardo Valdez Rodriguez
https://arxiv.org/abs/2506.00053

Improving statistical learning methods via features selection without replacement sampling and random projection
Cancer is fundamentally a genetic disease characterized by genetic and epigenetic alterations that disrupt normal gene expression, leading to uncontrolled cell growth and metastasis. High-dimensional microarray datasets pose challenges for classification models due to the "small n, large p" problem, resulting in overfitting. This study makes three different key contributions: 1) we propose a machine learning-based approach integrating the Feature Selection Without Re-placement (FSWOR) technique…

This https://arxiv.org/abs/2411.16699 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_nli…

Bistability and chaos in the discrete two-gene Andrecut-Kauffman model
We conduct numerical analysis of the 2-dimensional discrete-time gene expression model originally introduced by Andrecut and Kauffman (Phys. Lett. A 367: 281-287, 2007). In contrast to the previous studies, we analyze the dynamics with different reaction rates $α_1$ and $α_2$ for each of the two genes under consideration. We explore bifurcation diagrams for the model with $α_1$ varying in a wide range and $α_2$ fixed. We detect chaotic dynamics by means of the positive maximum Lyapunov expo…

Small Stickers, Big Meanings: A Multilingual Sticker Semantic Understanding Dataset with a Gamified Approach
Heng Er Metilda Chee, Jiayin Wang, Zhiqiang Guo, Weizhi Ma, Min Zhang
https://arxiv.org/abs/2506.01668

Small Stickers, Big Meanings: A Multilingual Sticker Semantic Understanding Dataset with a Gamified Approach
Stickers, though small, are a highly condensed form of visual expression, ubiquitous across messaging platforms and embraced by diverse cultures, genders, and age groups. Despite their popularity, sticker retrieval remains an underexplored task due to the significant human effort and subjectivity involved in constructing high-quality sticker query datasets. Although large language models (LLMs) excel at general NLP tasks, they falter when confronted with the nuanced, intangible, and highly spec…

Series D, Episode 13 - Blake
DEVA: Hm. You've been given a temporary appointment as a law enforcement officer.
BLAKE: That central computer doesn't care who it makes respectable, does it?
DEVA: It's an inferior model, I'm afraid.
https://blake.torpidity.net/m/413/260

Blakes7Bot | Search
Companion site to the Blakes7Bot Twitter, Mastodon, and Bluesky accounts. Automated lines of Blakes 7 dialog. Includes a script search facility.

Music interpretation and emotion perception: A computational and neurophysiological investigation
Vassilis Lyberatos, Spyridon Kantarelis, Ioanna Zioga, Christina Anagnostopoulou, Giorgos Stamou, Anastasia Georgaki
https://arxiv.org/abs/2506.01982

Music interpretation and emotion perception: A computational and neurophysiological investigation
This study investigates emotional expression and perception in music performance using computational and neurophysiological methods. The influence of different performance settings, such as repertoire, diatonic modal etudes, and improvisation, as well as levels of expressiveness, on performers' emotional communication and listeners' reactions is explored. Professional musicians performed various tasks, and emotional annotations were provided by both performers and the audience. Audio analysis r…

Hilbert polynomials of configuration spaces over graphs of circumference at most 1
Byung Hee An, Jang Soo Kim
https://arxiv.org/abs/2505.24416 https://

Hilbert polynomials of configuration spaces over graphs of circumference at most 1
The $ k $-configuration space $ B_kΓ$ of a topological space $ Γ$ is the space of sets of $ k $ distinct points in $ Γ$. In this paper, we consider the case where $ Γ$ is a graph of circumference at most $1$. We show that for all $ k\ge0 $, the $ i $-th Betti number of $ B_kΓ$ is given by a polynomial $P_Γ^i(k)$ in $ k $, called the Hilbert polynomial of $ Γ$. We find an expression for the Hilbert polynomial $P_Γ^i(k)$ in terms of those coming from the canonical $1$-bridge decomposition…

On cluster structures of bosonic extensions
Yingjin Bi
https://arxiv.org/abs/2506.00882 https://arxiv.org/pdf/2506.00882

On cluster structures of bosonic extensions
In this paper, we analyze the transition maps for Lusztig's parameterization of the global basis for the bosonic extension $\widehat{\mathcal{A}}(b)$ of the quantum coordinate ring of a unipotent group, where $b$ belongs to the positive braid group $\operatorname{Br}^+$. By examining different reduced expressions of $b$, we establish that the cluster structure on $\widehat{\mathcal{A}}(b)$ remains invariant regardless of the chosen reduced expression. For the simply-laced case, we construct a c…

Singer-songwriter Nemahsis on the importance of being uncompromising
https://thecreativeindependent.com/people/singer…

Singer-songwriter Nemahsis on the importance of being uncompromising – The Creative Independent
Singer-songwriter Nemahsis discusses breaking through despite hardships, freedom of expression, and the power of building a genuine community online

This https://arxiv.org/abs/2505.00878 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_csSC_…

SynPAT: A System for Generating Synthetic Physical Theories with Data
Machine-assisted methods for discovering new physical laws of nature, starting from a given background theory and data, have recently emerged, and seem to hold the promise of someday advancing our understanding of the physical world. To address these needs, we have developed SynPAT, a system for generating synthetic physical theories comprising (i) a set of consistent axioms, (ii) a symbolic expression that is a consequence of the axioms and the challenge to be discovered, and (iii) noisy data …

Learning a foreign language in older adults shapes the functional connectivity of distinct cerebellar sub-regions with cortical areas rich in CB1 receptor expression https://onlinelibrary.wiley.com/doi/10.1002/brb3.70565

Why Academics Are Leaving Twitter for Bluesky
Dorian Quelle, Frederic Denker, Prashant Garg, Alexandre Bovet
https://arxiv.org/abs/2505.24801 https://

Why Academics Are Leaving Twitter for Bluesky
We analyse the migration of 300,000 academic users from Twitter/X to Bluesky between 2023 and early 2025, combining rich bibliometric data, longitudinal social-media activity, and a novel cross-platform identity-matching pipeline. We show that 18% of scholars in our sample transitioned, with transition rates varying sharply by discipline, political expression, and Twitter engagement but not by traditional academic metrics. Using time-varying Cox models and a matched-pairs design, we isolate gen…

On the rejection of Argentina and Poland (among others) proposals for a moon treaty by the USA and the USSR.
#SpacePolicy

Synergistic motifs in linear Gaussian systems
Enrico Caprioglio, Luc Berthouze
https://arxiv.org/abs/2505.24686 https://arxiv.org/pdf…

Synergistic motifs in linear Gaussian systems
Higher-order interdependencies are central features of complex systems, yet a mechanistic explanation for their emergence remains elusive. For linear Gaussian systems of arbitrary dimension, we derive an expression for synergy-dominance in terms of signed network motifs in the system's correlation matrix. We prove that antibalanced correlational structures ensure synergy-dominance and further show that antibalanced triads in the dyadic interaction matrix of Ornstein-Uhlenbeck processes are nece…

Thinking in Character: Advancing Role-Playing Agents with Role-Aware Reasoning
Yihong Tang, Kehai Chen, Muyun Yang, Zhengyu Niu, Jing Li, Tiejun Zhao, Min Zhang
https://arxiv.org/abs/2506.01748

Thinking in Character: Advancing Role-Playing Agents with Role-Aware Reasoning
The advancement of Large Language Models (LLMs) has spurred significant interest in Role-Playing Agents (RPAs) for applications such as emotional companionship and virtual interaction. However, recent RPAs are often built on explicit dialogue data, lacking deep, human-like internal thought processes, resulting in superficial knowledge and style expression. While Large Reasoning Models (LRMs) can be employed to simulate character thought, their direct application is hindered by attention diversi…

This https://arxiv.org/abs/2301.07476 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Negative Moment Bounds for Sample Autocovariance Matrices of Stationary Processes Driven by Conditional Heteroscedastic Errors and Their Applications
We establish a negative moment bound for the sample autocovariance matrix of a stationary process driven by conditional heteroscedastic errors. This moment bound enables us to asymptotically express the mean squared prediction error (MSPE) of the least squares predictor as the sum of three terms related to model complexity, model misspecification, and conditional heteroscedasticity. A direct application of this expression is the development of a model selection criterion that can asymptotically…

Now starting: the #SecurityNarratives workshop, a very interesting expression of the #DigitalHumanities and a collaboration between the Department of Interdisciplinary Studies of Culture and Department of Information Security and Communication Technology at

Hey everyone!
What do you think about Greta Tintin Eleonora Ernman Thunberg heading to Gaza with the Freedom Flotilla to deliver humanitarian aid and challenge the blockade?
I’m honestly mixed on it, and I would love to hear your thoughts.
#GretaThunberg #GretaTintinEleonoraErnmanThunberg

This https://arxiv.org/abs/2404.19158 has been replaced.
initial toot: https://mastoxiv.page/@arX…

Protein-DNA Co-condensation is Prewetting to a Collapsed Polymer
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations many of these nuclear proteins can phase-separate in the absence of DNA, and it has been hypothesized that, in vivo, the thermodynamic forces driving these phases help determine chromosomal organizati…

Un pognon de dingue: le soutien public global aux entreprises privées lucratives en Belgique a atteint 51,9 milliards d’euros en 2022, soit 9,2% du PIB et 17,6% des dépenses publiques.
https://www.econospheres.be/Un-pognon-de-dingue

Distributed Neural Policy Gradient Algorithm for Global Convergence of Networked Multi-Agent Reinforcement Learning
Pengcheng Dai, Yuanqiu Mo, Wenwu Yu, Wei Ren
https://arxiv.org/abs/2505.24113

Distributed Neural Policy Gradient Algorithm for Global Convergence of Networked Multi-Agent Reinforcement Learning
This paper studies the networked multi-agent reinforcement learning (NMARL) problem, where the objective of agents is to collaboratively maximize the discounted average cumulative rewards. Different from the existing methods that suffer from poor expression due to linear function approximation, we propose a distributed neural policy gradient algorithm that features two innovatively designed neural networks, specifically for the approximate Q-functions and policy functions of agents. This distri…

As I was zipping by Blackwall, I saw Benicio’s expression, the title, and I immediately realized I was looking at the poster of Wes’ last movie.
Can’t wait
https://www.themoviedb.org/movie/1137350-the-phoenician-scheme

The Phoenician Scheme
The story of a family and a family business.

This https://arxiv.org/abs/2501.18569 has been replaced.
initial toot: https://mastoxiv.page/@…

Derivation of the free energy, entropy and specific heat for planar Ising models: Application to Archimedean lattices and their duals
The 2d ferromagnetic Ising model was solved by Onsager on the square lattice in 1944, and an explicit expression of the free energy density $f$ is presently available for some other planar lattices. But an exact derivation of the critical temperature $T_c$ only requires a partial derivation of $f$. It has been performed on many lattices, including the 11 Archimedean lattices. In this article, we give general expressions of the free energy, energy, entropy and specific heat for planar lattices w…

Multi-omic Causal Discovery using Genotypes and Gene Expression
Stephen Asiedu, David Watson
https://arxiv.org/abs/2505.15866 https://

Multi-omic Causal Discovery using Genotypes and Gene Expression
Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden confounders. We introduce GENESIS (GEne Network inference from Expression SIgnals and SNPs), a constraint-based algorithm that leverages the natural causal precedence of genotypes to infer ancestral relationships in transcriptomic data. Unlike traditional causal…

This https://arxiv.org/abs/2505.15004 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_ees…

EASY: Emotion-aware Speaker Anonymization via Factorized Distillation
Emotion plays a significant role in speech interaction, conveyed through tone, pitch, and rhythm, enabling the expression of feelings and intentions beyond words to create a more personalized experience. However, most existing speaker anonymization systems employ parallel disentanglement methods, which only separate speech into linguistic content and speaker identity, often neglecting the preservation of the original emotional state. In this study, we introduce EASY, an emotion-aware speaker an…

Time For 9 o'clock #HashTagGames hosted by @… Let's play!
#UninvitedGuestASongOrPoem

This https://arxiv.org/abs/2505.20262 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_hept…

On world-sheet S-matrix of NSR string in static gauge
As was shown in arXiv:1203.1054, expanding the Nambu action near the "long string" vacuum in the static gauge one finds that the one-loop 2 to 2 scattering amplitude of the $D-2=24$ transverse 2d fluctuations $X^i$ is given by a pure phase expression consistent with underlying integrability. Similar computation in the Green-Schwarz superstring was carried out in arXiv:2404.09658. Here we consider the case of the NSR string starting with its manifestly 2d covariant action given by $D$ scalar mul…

Discrete and Continuous Muttalib--Borodin process: Large deviations and Riemann--Hilbert analysis
Jonathan Husson, Guido Mazzuca, Alessandra Occelli
https://arxiv.org/abs/2505.23164

Discrete and Continuous Muttalib--Borodin process: Large deviations and Riemann--Hilbert analysis
In this paper, we study the asymptotic behaviour of plane partitions distributed according to a weighted $q^{Volume}$ Muttalib--Borodin ensemble. Specifically, we establish a Large Deviation principle for the discrete Muttalib--Borodin process, characterising the rate function. Furthermore, through Riemann--Hilbert analysis, we give an explicit expression for the asymptotic shape of the partition.

Series D, Episode 13 - Blake
DEVA: Hm. You've been given a temporary appointment as a law enforcement officer.
BLAKE: That central computer doesn't care who it makes respectable, does it?
DEVA: It's an inferior model, I'm afraid.
https://blake.torpidity.net/m/413/260

Blakes7Bot | Search
Companion site to the Blakes7Bot Twitter, Mastodon, and Bluesky accounts. Automated lines of Blakes 7 dialog. Includes a script search facility.

A New Deep-learning-Based Approach For mRNA Optimization: High Fidelity, Computation Efficiency, and Multiple Optimization Factors
Zheng Gong, Ziyi Jiang, Weihao Gao, Deng Zhuo, Lan Ma
https://arxiv.org/abs/2505.23862

A New Deep-learning-Based Approach For mRNA Optimization: High Fidelity, Computation Efficiency, and Multiple Optimization Factors
The mRNA optimization is critical for therapeutic and biotechnological applications, since sequence features directly govern protein expression levels and efficacy. However, current methods face significant challenges in simultaneously achieving three key objectives: (1) fidelity (preventing unintended amino acid changes), (2) computational efficiency (speed and scalability), and (3) the scope of optimization variables considered (multi-objective capability). Furthermore, existing methods often…

This https://arxiv.org/abs/2504.07873 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

On the Spectrality of the Differential Operators with Periodic Coefficients
In this paper, we establish a condition on the coefficients of differential operators generated in the space of square-integrable functions on the entire real line by an ordinary differential expression with periodic, complex-valued coefficients, under which the operator is a spectral operator in the sense of Dunford [1].

#CFP: Meeting at the Crossroads: Understanding the Intersection of Rhetoric, Race, and Religion #acrel #Religidons #AARSBL

#CFP: Meeting at the Crossroads: Understanding the Intersection of Rhetoric, Race, and Religion
Laurent Pernot wrote, “Religion is intimately linked with words. Everyone knows that the spoken and written word plays an essential role in religion, as language is necessarily used to address the gods or God, to speak about the divine or the sacred, and to express religious feeling or awareness”. Thus, Pernot called for an understanding of the role rhetoric plays in our expression and performance of religion.

Oh Wikipedia, never change... Four tabs back I was poking around at the topic of #ASD. "Eight hours of fascinated clicking later", as the #xkcd strip says, I'm here. (I know nothing about biology, and less than that about molecular biology and genetics and such. Will any of this stuff I'…

This https://arxiv.org/abs/2410.09346 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

Transcriptome and Redox Proteome Reveal Temporal Scales of Carbon Metabolism Regulation in Model Cyanobacteria Under Light Disturbance
We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory networks under light disturbance. Our approach is a data-driven modeling workflow using a physics-informed machine learning algorithm to train a non-linear mathematical model for interpreting gene expression dynamics and to lead discovery for protein regulators usi…

Me? An Anarcho-syndicalist? Yes!
#Anarchism #Syndicalism #AnarchoSyndicalism

This scouting leader came out almost like a movie poster
#photo #photography #portrait #ithaca

Series C, Episode 01 - Aftermath
LAUREN: I wonder what's made them so determined suddenly.
AVON: Survivors, like me, probably.
https://blake.torpidity.net/m/301/272 B7B4

Blakes7Bot | Search
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From PEN America:
A Five-Alarm Fire for Free Speech
The Trump Administration’s 100 Day Assault on Free Expression
#Press #Journalism #FreePress #PENAmerica

DeepPlantCRE: A Transformer-CNN Hybrid Framework for Plant Gene Expression Modeling and Cross-Species Generalization
Yingjun Wu, Jingyun Huang, Liang Ming, Pengcheng Deng, Maojun Wang, Zeyu Zhang
https://arxiv.org/abs/2505.09883

DeepPlantCRE: A Transformer-CNN Hybrid Framework for Plant Gene Expression Modeling and Cross-Species Generalization
The investigation of plant transcriptional regulation constitutes a fundamental basis for crop breeding, where cis-regulatory elements (CREs), as the key factor determining gene expression, have become the focus of crop genetic improvement research. Deep learning techniques, leveraging their exceptional capacity for high-dimensional feature extraction and nonlinear regulatory relationship modeling, have been extensively employed in this field. However, current methodologies present notable limi…

Series C, Episode 01 - Aftermath
LAUREN: I wonder what's made them so determined suddenly.
AVON: Survivors, like me, probably.
https://blake.torpidity.net/m/301/272 B7B4

Blakes7Bot | Search
Companion site to the Blakes7Bot Twitter, Mastodon, and Bluesky accounts. Automated lines of Blakes 7 dialog. Includes a script search facility.

Series C, Episode 10 - Ultraworld
DAYNA: And if we agree?
ULTRA 1: We shall reconsider the fate of your friends. And, of course, yourselves.
TARRANT: Is that the best you can do? No deal.
https://blake.torpidity.net/m/310/506 B7B5

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Relatable AF! I actually witnessed this happen back in my school days. 😂📚
#IT #Linux #School #Meme

Plasma Frequency of Wire Medium Revisited
Denis Sakhno, Pavel A. Belov
https://arxiv.org/abs/2505.17900 https://arxiv.org/pdf/2505.17…

Plasma Frequency of Wire Medium Revisited
This paper revisits a model for the plasma frequency of a simple wire medium formed by a square lattice of parallel metallic wires. We provide a comparative analysis of existing formulas for estimating the plasma frequency and derive a new expression taking into account the second-order correction by the period to wavelength ratio. The proposed formula demonstrates superior accuracy for thin wires, with a relative error of less than $0.16\%$ for ratio of wires radii to period smaller than $0.13…

HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity
Xuejun Sun, Yiran Song, Xiaochen Zhou, Ruilie Cai, Yu Zhang, Xinyi Li, Rui Peng, Jialiu Xie, Yuanyuan Yan, Muyao Tang, Prem Lakshmanane, Baiming Zou, James S. Hagood, Raymond J. Pickles, Didong Li, Fei Zou, Xiaojing Zheng
https://

HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity
Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To addre…

Series C, Episode 10 - Ultraworld
DAYNA: And if we agree?
ULTRA 1: We shall reconsider the fate of your friends. And, of course, yourselves.
TARRANT: Is that the best you can do? No deal.
https://blake.torpidity.net/m/310/506 B7B5

Blakes7Bot | Search
Companion site to the Blakes7Bot Twitter, Mastodon, and Bluesky accounts. Automated lines of Blakes 7 dialog. Includes a script search facility.

Using random perturbations to infer the structure of feedback control in gene expression
Seshu Iyengar, Andreas Hilfinger
https://arxiv.org/abs/2505.04912 …

Using random perturbations to infer the structure of feedback control in gene expression
Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities between cellular modules. However, in large-scale drug perturbation studies the effect of any given drug may not be known and may not only affect one module at a time. Here, we analyze the response of gene expression models to random perturbations that affect mu…

This https://arxiv.org/abs/2505.10246 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_csSC_…

An Algorithm for the Leading Monomials of a Minimal Groebner Basis of Generic Sequences
We present an efficient algorithm for computing the leading monomials of a minimal Groebner basis of a generic sequence of homogeneous polynomials. Our approach bypasses costly polynomial reductions by exploiting structural properties conjectured to hold for generic sequences-specifically, that their leading monomial ideals are weakly reverse lexicographic and that their Hilbert series follow a known closed-form expression. The algorithm incrementally constructs the set of leading monomials deg…

#Blakes7 Series A, Episode 02 - Space Fall
BLAKE: [To Avon] Could it be altered?
AVON: What?
BLAKE: The running log. Could the readings be faked?
AVON: Only by a top-line technician. Nobody on this ship could do it.
BLAKE: Except you.

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#Blakes7 Series A, Episode 02 - Space Fall
BLAKE: [To Avon] Could it be altered?
AVON: What?
BLAKE: The running log. Could the readings be faked?
AVON: Only by a top-line technician. Nobody on this ship could do it.
BLAKE: Except you.

Blakes7Bot | Search
Companion site to the Blakes7Bot Twitter, Mastodon, and Bluesky accounts. Automated lines of Blakes 7 dialog. Includes a script search facility.

This https://arxiv.org/abs/2410.21295 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

TRENDY: Gene Regulatory Network Inference Enhanced by Transformer
Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and more recent deep learning techniques, the last of which often overlook the underlying gene expression mechanisms. In this work, we introduce TRENDY, a novel GRN inference method that integrates transformer models to enhance the mechanism-based WENDY approach.…

This https://arxiv.org/abs/2405.12897 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

From Single Genes to Populations: Quantifying Broken Detailed Balance in Transcription
Are there thermodynamic or information theoretic constraints governing mRNA expression? Here we use the framework of stochastic thermodynamics to assess detailed balance breaking in transcription. For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, expressions that can be evaluated from knowledge of the kinetic parameters of the two-state model. This allows us to easily evaluate the entropy pr…

This https://arxiv.org/abs/2503.09605 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

QWENDY: Gene Regulatory Network Inference Enhanced by Large Language Model and Transformer
Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based on a linear gene expression model, it solves the transformation for the covariance matrices. Unlike its predecessor WENDY, QWENDY avoids solving a non-convex optimization problem and produces a unique solution. Then we enhance QWENDY by the transformer neural …

In silico tool for identification of colorectal cancer from cell-free DNA biomarkers
Kartavya Mathur (Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, School of Biotechnology, Gautam Buddha University, Uttar Pradesh), Shipra Jain (Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi), Nisha Bajiya (Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi), Nishant Ku…

In silico tool for identification of colorectal cancer from cell-free DNA biomarkers
Colorectal cancer remains a major global health concern, with early detection being pivotal for improving patient outcomes. In this study, we leveraged high throughput methylation profiling of cellfree DNA to identify and validate diagnostic biomarkers for CRC. The GSE124600 study data were downloaded from the Gene Expression Omnibus, as the discovery cohort, comprising 142 CRC and 132 normal cfDNA methylation profiles obtained via MCTA seq. After preprocessing and filtering, 97,863 CpG sites w…

Mathematical models for the EP2 and EP4 signaling pathways and their crosstalk
Alessandra Cambi, Diane S Lidke, Mariya Ptashnyk, Willemijn Smit, Stefanie Sonner
https://arxiv.org/abs/2505.11712

Mathematical models for the EP2 and EP4 signaling pathways and their crosstalk
The G-protein coupled receptors EP2 and EP4 both transduce the signal of the lipid messenger Prostaglandin E2 (PGE2). Changes in the cell response to PGE2 can have important effects on immunity and development of diseases, however, a thorough understanding of the EP2-EP4 receptors' signaling pathways is lacking. Experimental data show that receptor activity (indicated by cAMP expression) has a different kinetics depending on which receptor is triggered by PGE2 and that crosstalk exists between …

KINDLE: Knowledge-Guided Distillation for Prior-Free Gene Regulatory Network Inference
Rui Peng, Yuchen Lu, Qichen Sun, Yuxing Lu, Chi Zhang, Ziru Liu, Jinzhuo Wang
https://arxiv.org/abs/2505.09664

KINDLE: Knowledge-Guided Distillation for Prior-Free Gene Regulatory Network Inference
Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of thes…

The Dynamics of Inducible Genetic Circuits
Zitao Yang, Rebecca J. Rousseau, Sara D. Mahdavi, Hernan G. Garcia, Rob Phillips
https://arxiv.org/abs/2505.07053

The Dynamics of Inducible Genetic Circuits
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches and oscillators of various kinds. And yet, there is more to the story than which transcription factors control these various circuits. These transcription factors are often themselves under the control of effector molecules that bind them and alter their level …