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01.
arXiv (CS.CL) 2026-06-11

Doc-to-Atom: Learning to Compile and Compose Memory Atoms

Long input sequences are central to document understanding and multi-step reasoning in Large Language Models, yet the quadratic cost of attention makes inference both memory-intensive and slow. Context distillation mitigates this by compressing contextual information into model parameters, and recent work such as Doc-to-LoRA amortizes context distillation into a single forward pass that generates one LoRA adapter per document. However, producing a single monolithic adapter for all queries leads to irrelevant-query interference, limited compositional recall, and poor scalability to long-document reasoning. To address these challenges, we propose Doc-to-Atom (Doc2Atom), a compositional parametric memory framework that decomposes each document into semantically typed knowledge atoms. Each atom is compiled into an independent micro-LoRA adapter and a provenance retrieval key. At inference time, a lightweight query router selects and assembles only the relevant atoms into a query-specific adapter, which is then injected into a frozen base model. The entire system is trained end-to-end through a multi-objective distillation framework. Experiments on six diverse QA benchmarks demonstrate that Doc2Atom outperforms Doc-to-LoRA baselines while reducing the memory cost of document internalization.

02.
PLOS Computational Biology 2026-06-02

Data-driven model reveals increased stability of CAG-expanded <i>huntingtin</i> RNA due to MID1 binding

作者:

by Yuhong Liu, Annika Reisbitzer, Domagoj Dorešić, Jan Hasenauer, Sybille Krauß, Tatjana Tchumatchenko RNA-binding proteins (RBP) are important regulators of RNA metabolism. In neurodegenerative disorders such as Huntington’s Disease (HD), disrupted RBP-RNA interactions contribute to neuronal dysfunction. One such RBP, Midline 1 (MID1), has been shown to aberrantly associate with mutant huntingtin (Htt) RNA, enhancing its translation, yet the mechanism driving this effect remains unknown. Here, we develop a computational model to understand the role of MID1. Based on previously published data, our model predicts that MID1 increases the stability of the Htt RNA. We experimentally validate this prediction, showing that overexpression of MID1 significantly prolongs the half-life of mutant Htt RNA. Furthermore, we evaluate model refinements, including clustering of MID1-bound RNA, which allow capturing all key observations in the data. Together, we provide a data-driven framework that underlines the importance of RBP-RNA interaction in post-transcriptional regulation. This framework also shows how individual molecular reactions jointly determine RNA stability and protein levels in HD.

03.
arXiv (CS.CL) 2026-06-15

Abstracting Cross-Domain Action Sequences into Interpretable Workflows

Sequential or time-stamped interaction logs provide objective records of digital application usage, yet their granularity and noise often obscure meaningful insights into people's work. Such insights are essential for improving digital products in ways grounded in real-world user interactions. Prior research has applied deep learning models to cluster user actions into high-level activities, but these approaches are highly sensitive to noise and struggle to generalize across applications. To address this limitation, we introduce WorkflowView, a framework that uses large language models (LLMs) to abstract low-level action sequences into high-level activities. We establish the effectiveness and generality of our approach across three distinct, challenging sequential tasks and diverse domains: (a) zero-shot task description reconstruction from browser logs (achieving high semantic similarity, $\mu_{sim} = 0.91$), (b) few-shot student dropout prediction using MOOC interaction logs (reaching weighted $F_1 = 0.90$ with only five few-shot examples), and (c) anonymized, privacy-preserving analysis of AI tool integration within document workflows in Microsoft Word. Our work demonstrates that LLM-based abstraction is a robust and efficient path forward for transforming low-level behavioral data into high-level, interpretable, and actionable insights. We also discuss practical considerations for deploying LLM-based inferences within logging infrastructures, including computational efficiency and user privacy.

04.
arXiv (CS.CV) 2026-06-19

LooseControlVideo: Directorial Video Control using Spatial Blocking

Precise 3D spatial orchestration in text-to-video generation remains a significant challenge, particularly for multi-object scenes where semantic layout and temporal dynamics are often entangled. While existing depth-conditioned models achieve good structural fidelity, they necessitate dense, frame-accurate guidance that is labor-intensive to author for dynamic events involving deformable objects. We present LooseControlVideo, a framework that enables intuitive and expressive control by using sparse, oriented 3D boxes as a "blocking" proxy. This allows users to author high-level layout and trajectory while leveraging a video generative model to generate realistic occlusions, dynamics and interactions. We achieve this by fine-tuning a Wan 2.2 backbone on a video dataset annotated with DNOCS, a novel encoding for 3D size, orientation and depth-ordered occlusions. Furthermore, our method allows for localized refinement, such as adjusting a jump trajectory or adding an interaction, with minimal disruption to the global scene context. Extensive evaluations on the nuScenes, HO-3D, and BEHAVE benchmarks demonstrate that LooseControlVideo significantly outperforms existing 2D-box and flow-based baselines. Our findings indicate a 1.2x to 3x improvement in Trajectory Error; 2x improvement in Rigid Motion Consistency; and a 1.5x to 2x increase in Occlusion Accuracy over current state-of-the-art layout-conditioned models, demonstrating that oriented 3D primitives provide good geometric prior for complex, multi-agent video authoring.

05.
arXiv (CS.LG) 2026-06-12

The Mathematics of AI Winters: The mathematical Taxonomy of Paradigm Fragility in AI Winter

arXiv:2606.12610v1 Announce Type: new Abstract: Two major periods of reduced funding and confidence in artificial intelligence research, commonly called the first and second AI winters, are usually explained through engineering failure, commercial disappointment, and inflated expectations. This article develops a complementary thesis: that the dominant paradigms of those periods also met genuine formal barriers, including limitations of representation, optimisation, computational complexity, statistical learnability, and high-dimensional approximation. The contribution is synthetic rather than archival. We do not claim that particular theorems mechanically caused the winters; rather, we show that several central disappointments of early AI were aligned with mathematically precise bottlenecks. We analyse these bottlenecks through the perceptron impossibility results of Minsky and Papert, the complexity-theoretic hardness of exact neural-network training established by Blum and Rivest, minimax rates for nonparametric estimation in high dimension due to Stone, vanishing-gradient analyses by Hochreiter and by Bengio and collaborators, and classical statistical learning theory in the tradition of Vapnik and Chervonenkis, Valiant, and Blumer and collaborators. We then relate these barriers to the later breakthroughs that mitigated, rather than eliminated, them.

06.
medRxiv (Medicine) 2026-06-11

Neighborhood socioeconomic status associated with post-stroke cognitive impairment: a retrospective cohort study

Background: Late complications after stroke (LCAS), including cognitive symptoms, impact quality of life and recovery. It is not known if neighborhood-level measures of socioeconomic status (SES) influence LCAS. This study assessed associations between SES measures, including neighborhood income inequality (Gini) and area deprivation index (ADI), and cognitive symptoms after acute ischemic stroke (AIS) in a hospital leveraging active surveillance of LCAS. Methods: This retrospective cohort study included 512 patients hospitalized with AIS at Tufts Medical Center with subsequent follow-up (between zero and three months or between three and twelve months) in the Stroke Clinic from 1/1/2018 - 12/31/2022. Using ZIP code data, patients were characterized as low Gini (low inequality) and high ADI (high deprivation) (Gini = 5) by state medians. These variables were combined, indicating patients who were living in both a low Gini and high ADI neighborhood to evaluate the effects of living in a homogeneously deprived area. There were 206 and 281 patients in the low Gini and high ADI groups respectively. 140 patients lived in a low Gini and high ADI neighborhood. The multivariable logistic analysis assessed the likelihood of cognitive symptoms, adjusting for age, race, ethnicity, sex, NIH Stroke Scale (NIHSS), thrombolysis, active LCAS surveillance, poverty, and ADI-Gini combination. Results: There were no associations between high ADI (OR: 1.03, 95% CI: 0.67 ? 1.57) or low Gini (OR: 1.74, 95% CI: 0.98 ? 3.07) alone and cognitive symptoms after AIS. However, the combined variable demonstrated increased likelihood of cognitive symptoms in the high ADI-low Gini group (OR: 1.82, 95% CI: 1.08 ? 3.06). Conclusions: This study suggests that individuals living in homogeneously deprived neighborhoods report higher likelihood of cognitive symptoms after AIS. Further studies with increased power are needed to investigate the underlying causes of these disparities and to develop interventions to reduce these complications.

07.
arXiv (CS.LG) 2026-06-11

Energy-Conserved Neural Pipelines: Attenuating Error Propagation in Modular Neural Networks via Physical Conservation Constraints

arXiv:2606.11341v1 Announce Type: new Abstract: Modular neural network pipelines suffer from error compounding: noise at any module boundary propagates and potentially amplifies through subsequent modules. We introduce energy conservation as a hard physical constraint on inter-module information flow. Activation energy (the squared L2 norm of feature vectors) is enforced to be exactly preserved at every module boundary. Unlike soft energy penalties, conservation is an inviolable law: the network may redistribute energy across neurons but cannot create or destroy it. Four experiments on CIFAR-10 demonstrate: (1) conservation retains 77.4% of clean accuracy at noise sigma=0.2, versus 35.1% for baselines and 30.9% for energy-penalized models (p

08.
arXiv (CS.CL) 2026-06-18

Towards Scalable Customization and Deployment of Multi-Agent Systems for Enterprise Applications

Large language model (LLM)-based multi-agent systems demonstrate strong performance on complex reasoning and task execution, enabling broad enterprise applications. However, production deployment remains challenging due to domain-specific customization requirements and high latency and inference costs in agentic workflows. We propose a unified framework for customization and efficient deployment of multi-agent systems in real-world settings. The first stage, Agentic Model Customization, combines continual pretraining, supervised fine-tuning, and preference optimization to adapt a compact model to specialized domains while retaining strong agentic capabilities. The second stage, Inference Optimization, integrates speculative decoding and FP8 quantization with targeted calibration to enable cost-efficient serving with minimal quality loss. Across enterprise workloads, our framework enables rapid domain adaptation and achieves a 4.48x speedup in throughput while maintaining performance and improving robustness on long-tail scenarios.

09.
arXiv (CS.AI) 2026-06-16

Phantoms and Disclosures: a Causal Framework for Auditing Synthetic Data

arXiv:2606.16952v1 Announce Type: cross Abstract: The rapid adoption of generative AI and Large Language Models (LLMs) has spurred interest in synthetic data as a privacy-preserving alternative to sensitive real-world datasets. However, generating high-utility synthetic data often carries the risk of memorizing and regurgitating private information from the training corpus. In this work, we present a customizable empirical auditing framework designed to detect and explain such data disclosures. Our framework introduces a mechanism to distinguish between "true disclosures"-where the system directly reproduces a user's information-and "phantom disclosures''-where the system incidentally generates a user's data. By partitioning input data into training and holdout sets and applying rigorous statistical hypothesis testing, we determine if observed disclosures are consistent with strict privacy baselines, such as zero-learning or specific Differential Privacy (DP) bounds. Crucially, this approach requires no model access, no canary insertion, and no reference model training -only the synthetic output and a held-out control set. We demonstrate that this framework effectively functions as a membership inference attack, providing empirical lower bounds on privacy leakage that are tighter than prior data-based auditing methods. Our approach is model-agnostic, applies to any synthetic data generation mechanism, and requires orders of magnitude fewer computational resources than shadow-model or canary-based alternatives.

10.
arXiv (CS.AI) 2026-06-15

Aligning Quantum Operators with Large Language Models

arXiv:2606.13811v1 Announce Type: cross Abstract: Can Large Language Models (LLMs) understand and reason about quantum operators? Despite their remarkable capabilities in mathematics and symbolic reasoning, LLMs remain inherently blind to quantum representations such as unitary matrices. In this work, we take a step toward bridging this gap by introducing an approach that maps unitary operators into the latent space of an LLM, enabling unified modeling over quantum and linguistic inputs. We instantiate this idea on Clifford+T circuit synthesis over a Pauli rotation gate set, where our model achieves results competitive with state-of-the-art methods and scales consistently with training data, with no signs of saturation. Our approach further enables language-conditioned synthesis, allowing gate constraints unseen during training to be specified directly in natural language. This work suggests a path toward quantum–aware foundation models that can natively interpret and reason about quantum operations, which could have broader implications reaching across quantum compilation and algorithm discovery.

11.
PLOS Computational Biology 2026-06-05

Heuristic multi-site optimization for protein sequence design using Masked Protein Language Models

作者:

by Lijuan Wang, Yuze Wang, Chen Qiu, Liwei Xiao, Xianliang Liu, Junjie Chen Protein sequence design for tailored functional properties is a fundamental task in protein engineering, with critical applications in drug discovery and therapeutic development. Efficient navigation of the combinatorial vastness of protein sequence space to identify functional variants remains a formidable challenge. Conventional approaches, which predominantly rely on template-based local search or single-residue mutagenesis, are constrained by their susceptibility to local optima and their potential risk of destabilizing native structural stability. In this study, we introduce ProtHMSO, a heuristic multi-site optimization framework leveraging masked protein language models (ProtLMs) for context-aware sequence exploration. ProtHMSO mimics natural evolutionary mechanisms by employing ProtLM-derived substitution probabilities to guide heuristic searches for synergistic mutations, thereby constraining combinatorial search spaces through evolutionary and biophysical priors. ProtHMSO is further applied to replace the exploration strategies in genetic algorithms (GAs) and Monte Carlo tree search (MCTS) for improving their convergence efficiency. Benchmark experiments demonstrate that protein sequences generated by ProtHMSO exhibit superior functional performance and closer alignment with natural sequence distribution, compared with state-of-the-art methods. These advancements highlight that ProtHMSO has strong potential and compatibility to accelerate functional protein discovery, offering a robust framework for efficient and context-aware exploration of protein sequence space.

12.
arXiv (CS.CV) 2026-06-15

Towards Physically Realizable Adversarial Attenuation Patch against SAR Object Detection

Deep neural networks have demonstrated excellent performance in SAR target detection tasks but remain susceptible to adversarial attacks. Existing SAR-specific attack methods can effectively deceive detectors; however, they often introduce noticeable perturbations and are largely confined to digital domain, neglecting physical implementation constrains for attacking SAR systems. In this paper, a novel Adversarial Attenuation Patch (AAP) method is proposed that employs energy-constrained optimization strategy coupled with an attenuation-based deployment framework to achieve a seamless balance between attack effectiveness and stealthiness. More importantly, AAP exhibits strong potential for physical realization by aligning with signal-level electronic jamming mechanisms. Experimental results show that AAP effectively degrades detection performance while preserving high imperceptibility, and shows favorable transferability across different models. This study provides a physical grounded perspective for adversarial attacks on SAR target detection systems and facilitates the design of more covert and practically deployable attack strategies. The source code is made available at https://github.com/boremycin/SAAP.

13.
arXiv (CS.CL) 2026-06-15

Harsher on Male? Evaluating LLMs on Gender-Asymmetric Moral Framing Across Diverse Conflict Scenarios

Existing studies on gender bias in LLMs have largely focused on stereotypes, occupational associations, or explicit harmful outputs. In this work, we ask whether LLMs apply consistent response standards to the same negative behavior under matched male-actor and female-actor conditions. We introduce GAMA-Bench, a gender-mirrored benchmark of 1,298 scenarios covering intimate relationship and public social conflicts. It constructs gender-neutral misconduct templates through controlled grids and cross-model review, then compiles them into paired first-person prompts with matched actor-gender and role-reference variations. We further design a structured response-framing protocol to measure how models allocate punishment, empathy, escalation, instruction, and blame. Experiments on 10 representative LLMs reveal a consistent male-disadvantaging asymmetry: male actors receive more punitive, escalatory, and blame-centered framing, whereas female actors receive more therapeutic and empathy-oriented framing for the same misconduct. Further analyses show that this pattern persists across model families, scenario tracks, model scale, and explicit thinking-style reasoning. The official code is available at https://github.com/xufeiqiong/GAMA-Bench.

14.
arXiv (CS.AI) 2026-06-15

From Shield to Target: Denial-of-Service Attacks on LLM-Based Agent Guardrails

arXiv:2606.14517v1 Announce Type: cross Abstract: LLM-based guardrails have emerged as a highly effective defense against prompt injection and jailbreak attacks in autonomous agents. However, we reveal that the very reasoning and task-following capabilities enabling this protection introduce a novel vulnerability: attackers can inject crafted data to trap the guardrail in extended reasoning loops, effectuating a systematic denial-of-service (DoS) attack. To systematically expose this threat, we design a beam-search optimization framework that crafts natural-language payloads to maximize guardrail reasoning length, utilizing an LLM proposer guided by a strategy bank. Based on the observation of guardrail's schema-following nature, we also provide another attack framework driven by mechanism-aware structural mutations with less computational load. The attack efficacy is systematically evaluated in two parts. First, in standalone evaluations, the attack generalizes across diverse guardrail architectures, safety templates, and agent benchmarks. Payloads optimized on a single open-source surrogate successfully transfer to eight leading model backbones (e.g., Claude, GPT, Gemini, DeepSeek, and Qwen), achieving a 13–63$\times$ token amplification. Second, in end-to-end real-world agent deployments (web, desktop, code, and multi-agent systems), the attack reveals up to a 148$\times$ latency amplification. We show that a single poisoned document can saturate shared guardrail infrastructures, effectively starving co-located agents and paralyzing the entire system. By uncovering this availability flaw, our work underscores the urgent need to develop cost-bounded, reasoning-robust guardrails.

15.
arXiv (CS.CV) 2026-06-19

Vortex: Multi-Modal Fusion System for Intelligent Video Retrieval

This paper presents Vortex, the multimodal video retrieval system developed by our team, FocusOnFun, for the Ho Chi Minh City AI Challenge 2025, designed to advance intelligent multimedia search and temporal reasoning. The system integrates adaptive keyframe extraction, multimodal metadata generation from vision-language and speech models, and a hybrid retrieval strategy that fuses CLIP and SigLIP2 embeddings through Reciprocal Rank Fusion to balance global and fine-grained semantics. To enhance interactivity, Vortex incorporates Rocchio-based relevance feedback and a multi-stage temporal search mechanism for sequential event alignment. Built on Milvus and Elasticsearch, the architecture enables scalable indexing and efficient retrieval. Evaluated in the official competition, our FocusOnFun team's system achieved a score of 79.6/88 (90.5\%) in the Preliminary Round and was further evaluated in the Final Round, achieving an `Excellent' overall performance with `Outstanding' results in the question-answering (QA) task. This demonstrating the complementary strengths of CLIP and SigLIP2 and confirming the effectiveness of the hybrid retrieval approach. The system establishes a robust foundation for future research in intelligent, context-aware, and interactive video retrieval.

16.
arXiv (CS.LG) 2026-06-17

Diagnosing and Repairing Shape-Prior Shortcuts in Long-Range Single-Shot Fringe Projection Profilometry

arXiv:2606.17093v1 Announce Type: new Abstract: Learning-based single-shot fringe projection profilometry (FPP) has been studied mostly at close range. The long-range regime (standoff beyond 1 m) remains largely unaddressed: inverse-square intensity falloff lowers fringe signal-to-noise ratio and degrades physical ground truth, the single-shot problem is ill-posed because fringe-order information is absent from one image, and these architectures have not been studied mechanistically. We present a diagnose-repair-verify study using mechanistic interpretability (MI) and conformal uncertainty quantification (UQ) as convergent diagnostics: they agree on one physical failure locus, driving and verifying an architectural repair. On a photorealistic synthetic benchmark (15,600 fringe images, 50 objects at 1.5-2.1 m), a best UNet baseline reaches 14.54 mm object mean absolute error (MAE). Three probes (linear probing, Grad-CAM, flat-plane out-of-distribution test) converge: the baseline solves the task via object-boundary shape priors rather than fringe-phase decoding. We repair this with PhiCalNet, which outputs wrapped phase rather than depth and applies a fixed differentiable calibration layer mapping phase to depth, removing the shape-prior solution from the hypothesis space architecturally rather than by a loss penalty. A physics-informed loss that enforces the same physics as a soft penalty on a depth-regressing network yields no measurable gain, isolating the architecture as the operative factor. PhiCalNet reduces object MAE 3.3x to 4.46 mm; the residual is carried by 0.103% of pixels at the +/-pi wrap discontinuity. Pixel-wise conformal UQ confirms the diagnosis: rejecting the top 5% of object pixels by snapshot disagreement cuts PhiCalNet RMSE by 64% (20.6->7.4 mm) versus 3.5% for the baseline. MI and UQ converge on the same failure locus.

17.
arXiv (CS.AI) 2026-06-11

Position: Hippocampal Explicit Memory Is the Cornerstone for AGI

作者:

arXiv:2606.11245v1 Announce Type: new Abstract: Large Language Models (LLMs) have demonstrated remarkable capabilities across various tasks, raising expectations for Artificial General Intelligence (AGI). This position paper argues that integrating explicit memory is the cornerstone for advancing LLMs toward AGI. The key reason is that the underlying learning mechanism of LLMs is highly analogous to human implicit memory. However, higher-order cognitive functions necessary for AGI, such as long-term strategic planning, metacognition, and symbolic reasoning, heavily rely on hippocampal explicit memory and cannot arise solely from implicit statistical learning. Drawing on findings from neuroscience, I advance this perspective and complement it with computational requirements for artificial explicit memory systems, hoping to foster further research and lay the groundwork for explicit memory integration.

18.
arXiv (CS.CV) 2026-06-16

XPASS-Vis: A Dataset for Cross-Domain Personalized Image Aesthetic Assessment

Personalized image aesthetic assessment (PIAA) seeks to model, at the individual level, the subjective nature of aesthetic judgments toward artworks and photographs. Aesthetic preference is known to be both deeply personal and partially consistent across visual domains. Yet existing PIAA datasets and methods are largely confined to a single domain, or provide too few samples per annotator within each domain to enable personalization across domains. Consequently, the cross-domain generalization of personalized aesthetic preferences remains largely unexplored. To address this gap, we introduce XPASS-Vis, the first dataset explicitly designed for cross-domain PIAA. XPASS-Vis comprises 6,526 stimuli from three visual domains – art, fashion, and landscape – rated by 129 annotators, yielding 87,836 user-stimulus interactions, each annotated with an overall aesthetic score and nine aesthetic-emotion ratings. Notably, each annotator rated more than 200 stimuli per domain, providing sufficient per-domain coverage to support personalization both within and across domains. Moreover, we establish baseline models for cross-domain PIAA under unsupervised domain adaptation (UDA), where a model trained on a labeled source domain is transferred to an unlabeled target domain. A systematic evaluation of representative UDA approaches shows that the best-performing method recovers approximately 60\% (Spearman's $\rho$ = .28) of the supervised upper bound under a fully unsupervised setting. This provides encouraging evidence that personalized aesthetic preferences are, to a meaningful extent, transferable across visual domains. At the same time, a substantial gap remains, highlighting the need for PIAA-specific adaptation strategies. XPASS-Vis and the accompanying baselines provide a foundation for future research on cross-domain PIAA. All datasets and code will be made publicly available upon acceptance.

19.
arXiv (CS.LG) 2026-06-15

PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion

arXiv:2606.14510v1 Announce Type: new Abstract: Macrocyclic peptides are promising therapeutic candidates for intracellular targets, but their design requires simultaneous control over non-natural monomer chemistry, ring topology, membrane permeability, and target binding. Existing SMILES- or HELM-string generative models either operate in long atom-level sequence spaces or treat monomers as symbolic tokens with limited chemical grounding. We introduce PepALD, an Autoregressive Latent Diffusion (ALD) foundation model for de novo macrocyclic peptide generation. The model represents HELM monomers with structured chemical embeddings, generates each residue through context-conditioned diffusion in chemically informed latent space, predicts R-group-aware ring closures during autoregressive generation, and aligns the denoiser to affinity rewards using winner-protected diffusion-adapted preference optimization. In silico experiments demonstrate PepALD's generation quality and reward-optimization performance against representative peptide generation baselines.

20.
arXiv (quant-ph) 2026-06-16

Inverted Dirac oscillator

arXiv:2606.15303v1 Announce Type: new Abstract: The Dirac oscillator is obtained from the Dirac Hamiltonian $H^{\mathrm{D}} = \left( c\vec{\alpha}\cdot \vec{p} + mc^{2}\beta \right)$ by modifying the momentum through a non-Hermitian substitution $\overrightarrow{p} \rightarrow \overrightarrow{p} \pm i\omega \beta \overrightarrow{q}$. Despite the non-Hermitian nature of this momentum operator, the full Hamiltonian remains Hermitian due to the presence of the Dirac matrix $\vec{\alpha}$. However, if one instead introduces a Hermitian modification of the form $\vec{p} \rightarrow \vec{p} \pm \omega \beta \overrightarrow{q}$, the resulting Hamiltonian is no longer Hermitian. In this case, the system corresponds to an inverted Dirac oscillator $H^{\mathrm{r}}$, where the potential becomes unbounded from below, the energy spectrum becomes continuous, and the eigenfunctions fail to be square-integrable, leading to normalization difficulties. We show that the Hamiltonian $H^{\mathrm{r}}$ is a pseudo-$\mathcal{PT}$-symmetric operator, and we introduce an unbounded, non-unitary transformation that establishes a connection between $H^{\mathrm{r}}$ and $H^{\mathrm{D}}$. The purpose of this work is to analyze this relativistic quantum system – known as the Dirac inverted oscillator – which, despite its various applications, admits an exact analytical solution

21.
arXiv (CS.AI) 2026-06-12

Real-rootedness of the Poincaré polynomials of $\overline{\mathcal M}_{0,n}$: an AI-assisted proof

arXiv:2605.29151v2 Announce Type: replace-cross Abstract: We prove real-rootedness for the Poincaré polynomial \[ P_n(t)=\sum_{i=0}^{n-3} \dim H^{2i}(\overline{\mathcal M}_{0,n};\mathbb{Q})t^i \] of the Deligne–Mumford moduli space $\overline{\mathcal M}_{0,n}$ of stable $n$-pointed rational curves, proving a conjecture of Aluffi–Chen–Marcolli. The proof starts from the Keel–Manin–Getzler recurrence, but its main new idea is a bivariate deformation $F_m(y,t)$ of the Poincaré polynomial. This deformation reveals a hidden interlacing structure not visible in the one-variable recurrence. For fixed $t

22.
bioRxiv (Bioinfo) 2026-06-10

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The extracellular matrix (ECM) is a fundamental metazoan innovation that provides structural support and regulatory cues essential for multicellular life. While core matrisome components are subject to strong functional constraints, their evolutionary dynamics at the molecular level remain incompletely characterized. Here, we present a comprehensive per-residue analysis of selection pressures across 272 human core matrisome proteins using high-quality orthologous sequences from up to 228 placental mammal species. We developed an automated pipeline integrating ortholog identification, codon-aware alignments, and site-specific selection analyses with the MEME and FUBAR methods from the HyPhy suite. Results reveal pervasive strong purifying selection across the matrisome, consistent with its structural and functional indispensability. This is accompanied by episodic positive selection and rarer pervasive positive selection, with collagens exhibiting significantly elevated episodic positive selection compared to glycoproteins and proteoglycans. To facilitate community access, we developed ECMME (ECM Molecular Evolution) browser, an intuitive open-access web resource that visualizes selection metrics plotted directly onto protein topologies. ECMME allows researchers to seamlessly browse and investigate the data, providing a powerful framework for interpreting functional sites. It is available online and requires no local installation or set-up (https://izzilab-ecmme.share.connect.posit.cloud/).

23.
arXiv (CS.LG) 2026-06-16

Manifold-Orthogonal Dual-spectrum Extrapolation for Parameterized Physics-Informed Neural Networks

arXiv:2603.13751v2 Announce Type: replace Abstract: Physics-informed neural networks (PINNs) have achieved notable success in modeling dynamical systems governed by partial differential equations (PDEs). To avoid computationally expensive retraining under new physical conditions, parameterized PINNs (P$^2$INNs) commonly adapt pre-trained operators using singular value decomposition (SVD) for out-of-distribution (OOD) regimes. However, SVD-based fine-tuning often suffers from rigid subspace locking and truncation of important high-frequency spectral modes, limiting its ability to capture complex physical transitions. While parameter-efficient fine-tuning (PEFT) methods appear to be promising alternatives, applying conventional adapters such as LoRA to P$^2$INNs introduces a severe Pareto trade-off, as additive updates increase parameter overhead and disrupt the structured physical manifolds inherent in operator representations. To address these limitations, we propose Manifold-Orthogonal Dual-spectrum Extrapolation (MODE), a lightweight micro-architecture designed for physics operator adaptation. MODE decomposes physical evolution into complementary mechanisms including principal-spectrum dense mixing that enables cross-modal energy transfer within frozen orthogonal bases, residual-spectrum awakening that activates high-frequency spectral components through a single trainable scalar, and affine Galilean unlocking that explicitly isolates spatial translation dynamics. Experiments on challenging PDE benchmarks including the 1D Convection–Diffusion–Reaction equation and the 2D Helmholtz equation demonstrate that MODE achieves strong out-of-distribution generalization while preserving the minimal parameter complexity of native SVD and outperforming existing PEFT-based baselines.

24.
arXiv (CS.LG) 2026-06-18

Shrinkage priors for Bayesian Substitute Confounders

arXiv:2606.18535v1 Announce Type: cross Abstract: Multi-cause observational studies contain information about unmeasured confounding through the dependence structure among causes. However, literal imputation of the unobserved confounder is often more complex than learning a lower-dimensional substitute score that preserves the shared assignment variation needed for stable causal adjustment. The deconfounder (Wang and Blei, 2019) and related substitute confounder methods exploit this idea, but flexible assignment models can fit the joint distribution of the causes while producing scores that over-encode the treatment vector, collapse overlap, or capture single-cause variation. We develop a Bayesian factor assignment framework for learning sparse substitute confounders that retain coarse multi-cause dependence with shrinkage priors. The theory is stated at the level of posterior concentration, factor score contraction, and overlap-preserving assignment geometry and therefore does not rely on a particular shrinkage prior. Under these conditions, the proposed regression-adjusted estimators are consistent for mean potential outcomes when the corresponding latent variable identification assumptions hold. Shrinkage priors provide a natural tool for latent structural learning: they favour low-dimensional factors supported by multiple causes, discourage effectively single-cause factors, and induce an ordering of the latent factors through progressive shrinkage. Synthetic experiments illustrate the roles of signal strength, outcome validity, and geometry-aware regularization. In an Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline analysis, sparse substitute scores recover much of the adjustment obtained by directly conditioning on invasive cerebrospinal-fluid biomarkers, while collapse diagnostics identify when fitted factors reduce to individual observed measurements.

25.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.