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01.
medRxiv (Medicine) 2026-06-13

Projected population level impact and cost-effectiveness of clinic and community-based tuberculosis screening approaches

The South Africa National Department of Health have set ambitious targets to scale up TB testing, focusing primarily on clinic attendees. In the context of declining funding for TB care and prevention, the most cost-effective approaches for targeting testing should be identified. We developed a mathematical model of TB in South Africa, explicitly incorporating clinic attendance by sex and HIV/ART status. We simulated six screening approaches over 2026-2035 (individually and in combination): three clinic-based (symptom screening, intensified targeted universal TB testing [TUTT, symptom-agnostic sputum testing of clinic attendees in key risk groups], and intensified TUTT allowing saliva samples) and three targeted community-based (community radiographic screening, symptom screening, and universal Xpert Ultra testing), each implemented at a range of coverage levels. Model outputs were combined with a mechanistic cost function to estimate potential impact and cost-effectiveness from a societal perspective. The most cost-effective standalone approach was community radiographic screening at 10% annual population coverage, with an incremental cost-effectiveness ratio (ICER) of $421 per disability-adjusted life year (DALY) averted. 10/11 scenarios along the expansion path included community radiographic screening at progressively higher coverage, combined with a clinic-based approach. Combining complementary approaches to reach both groups at increased risk of TB (e.g. clinic-based screening) and groups with lower screening coverage (e.g. community-based screening) may increase cost-effectiveness of TB screening, compared to standalone approaches. When designing TB screening strategies, both population risk and existing screening coverage should be considered.

02.
medRxiv (Medicine) 2026-06-15

Quantitative insights into the role of phages and plasmids in the persistence of nontuberculous mycobacteria in chloraminated drinking water

Nontuberculous mycobacteria (NTM) are opportunistic pathogens that persist in chloraminated drinking water systems, yet the roles of phages and plasmids in their persistence remain largely unexplored. Using genome-resolved and quantitative metagenomics, we characterized NTM, phages, prophages, and plasmids in a chloraminated building plumbing system. Bacterial metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) were quantified at mean concentrations of 8.41 * 10^7 and 8.00 * 10^8 copies/L, respectively, including seven NTM MAGs at a mean total concentration of 4.01 * 10^5 copies/L. NTM concentrations were highest at the site with the lowest bacterial and viral diversity. Predicted NTM-infecting virus concentrations were inversely related to NTM concentrations across sites, suggesting complex phage-host dynamics that warrant direct experimental investigation. NTM, putative phages, prophages, and plasmids encoded functions related to disinfectant tolerance, stress response, metal resistance, and secretion. These findings identify phage interactions, prophages, and plasmids as overlooked genomic and ecological dimensions of NTM persistence in engineered water systems.

03.
arXiv (CS.CV) 2026-06-18

ProductConsistency: Improving Product Identity Preservation in Instruction-Based Image Editing via SFT and RL

Recent advances in instruction-based image editing have enabled models to perform complex visual edits from natural language instructions. However, in product-centric scenarios where preserving product features, branding, and textual elements are critical, current open and closed source models often struggle to maintain this fine-grained object identity. This issue is further compounded by the lack of datasets for instruction-based product image editing with text fidelity constraints, leaving it largely treated as an implicit capability of instruction-based image editing models. In this work, we introduce the ProductConsistency dataset which is designed to improve product-centric image editing. Our approach includes a supervised fine-tuning (SFT) dataset of 87k samples for product editing, a reinforcement learning (RL) dataset with 869 unique product images, and a new benchmark dataset, the ProductConsistency Benchmark, to allow rigorous and standardized evaluation of editing models. To guide RL training, we propose a Cyclic Consistency reward that enforces semantic preservation of product identity by using caption similarity between the original product description and captions generated from the edited image. We fine-tune both Qwen-Image-Edit-2511 and Flux.1-Kontext-dev using our dataset and demonstrate consistent improvements over baseline models in OCR and Perceptual metrics, and MLLM-based evaluations as well, indicating stronger product consistency, text rendering, and overall visual quality; with the Qwen-Image-Edit-2511 model achieving a 5x reduction in the character error rate. The code and pipeline is available at https://anonymous.4open.science/r/ProductConsistency-6FCC/README.md

04.
arXiv (CS.LG) 2026-06-18

Unsupervised Diffusion Solver for Combinatorial Optimization via Combinatorial Adjoint Matching

arXiv:2605.30920v2 Announce Type: replace Abstract: Diffusion-based neural solvers have shown strong promise for combinatorial optimization (CO), but existing methods typically rely on supervised training with large collections of near-optimal solutions. In this work, we extend adjoint-based trajectory optimization methods to discrete combinatorial domains. We formulate diffusion-based CO as a stochastic control problem over Continuous-Time Markov Chains and introduce discrete adjoint dynamics for propagating optimization signals through discrete generative trajectories. Building on this formulation, we propose Combinatorial Adjoint Matching (CAM), an unsupervised training framework for discrete diffusion solvers with structured and low-variance trajectory-level optimization signals. Empirically, CAM consistently outperforms existing unsupervised diffusion baselines and achieves performance competitive with strong supervised diffusion solvers and even traditional solvers across diverse combinatorial optimization problems. Our code is available at https://github.com/Shengyu-Feng/CAM.

05.
arXiv (CS.AI) 2026-06-17

Comprehensive pKa Data Augmentation from Limited Real Data through an Engineered Models-Quantum Framework

arXiv:2606.17077v1 Announce Type: cross Abstract: Proton dissociation constants (pKa) are critical for functional molecule discovery and molecular modeling. Building on iBonD, the largest experimental pKa database established, we and other researchers have developed several methods including machine-learning-based empirical prediction and high-accuracy energy calculations. Despite this foundation, the rapid augmentation of high-quality pKa data remains fundamentally constrained. As part of this work, we performed large-scale regression-based pKa prediction on unlabeled molecular datasets using a collection of extensively optimized machine-learning models. The results indicate that, since the feature distributions of unlabeled molecular datasets, the pKa data distribution approximates normality, with extreme scarcity of tail-region samples. Although such augmentation is highly valuable for improving overall data availability and predictive modeling, it remains insufficient for efficiently discovering molecules with broad-spectrum pKa properties. To address this, we explore the targeted generation of molecules with sparse pKa properties from the vast chemical space. Given that traditional continuous latent space VAE-RNN methods for molecular generation suffer from insufficient stability and fail to demonstrate clear advantages in complementing sparse data, we design and implement a quantum-assisted sparse-pKa molecular generation. Feasibility is validated on a simulated quantum annealer, and superior extreme-value sampling is further achieved on physical coherent Ising machines (CIMs). (to be continued)

06.
arXiv (math.PR) 2026-06-12

Scaling limit of additive functionals for reversible non-gradient exclusion process: critical cases

arXiv:2606.13442v1 Announce Type: new Abstract: For the reversible speed-change exclusion process $(\eta_t)_{t \geq 0}$ in $\mathbb{Z}^d$, we study the scaling limit of additive functionals ${\Gamma_t(f) = \int_0^t f(\eta_s)\, \mathrm{d} s}$. Concerning the local centered function $f$, the previous work [Commun. Math. Phys. 104, 1-19, 1986] by Kipnis and Varadhan and [Comm. Pure Appl. Math., 66: 649-677, 2013] by Gon{ç}alves and Jara respectively covered the cases $d \geq 3$ and $d=1$. The present paper completes the missing part $d=2$, and also develops the theory for functions with higher degree. The novelty is a quantitative homogenization of the resolvent, which allows to overcome the obstacle of correlation function in non-gradient models.

07.
arXiv (CS.CL) 2026-06-16

Control-Plane Placement Shapes Forgetting: An Architectural Study of Agent Memory Across Thirteen System Configurations

作者:

Where an LLM sits in an agent memory pipeline – between the recall plane that retrieves stored facts (extensively benchmarked) and the control plane that mutates them via supersede, release, purge (largely untested) – shapes which forgetting failure modes the system recovers. Comparing thirteen system configurations on a 385-case adversarial surface, we observe three placement regimes with partly complementary coverage: deterministic primitives suffice for lexical/temporal categories but fail canonicalization (5% on identifier-obfuscation, 0% on cross-lingual); inscribe-time LLM recovers canonicalization (100%) but cannot help intent-aware deletion (0% on prefix-collision and compound-fact); a mutation-time hook recovers intent-aware deletion (78-85%) and brightens nearly all categories simultaneously (91.7-93.2% overall, $0.17 per 385-case run, 2.3s/case mutation latency vs. 64-191ms/case deterministic, recall path unchanged). We expose the trade-off via ForgetEval, a 1000-case templated suite plus a 385-case adversarial layer (132 hand-crafted + 253 LLM-drafted oracle-validated) scored by deterministic substring match, paired with a six-method Adapter Protocol with honest N/A scoring that lets heterogeneous memory stores enter in 130 lines. Admission is corroborated by 10-annotator IAA (Fleiss' kappa = 0.958) and a 77-case external-authored subset (four blind contributors) that replicates the canonicalization asymmetry and amplifies the joint-placement lift (+27.8 pt). Production failures are predominantly forgetting failures rather than recall failures, yet existing benchmarks measure only recall. ForgetEval and all adapters are released under MIT.

08.
bioRxiv (Bioinfo) 2026-06-20

Seed variation impacts clustering stability in Single-Cell RNA-Seq and can be mitigated by StAbility-BasEd-Reassignment (SABER)

Single-cell RNA-seq clustering is commonly treated as reproducible once a random seed is fixed, yet the choice of seed itself may alter cell assignments and downstream interpretation. We systematically quantified seed-induced clustering variability by running Louvain and Leiden clustering across 100 seeds in Seurat and Scanpy on 28 single-cell RNA-seq datasets from the Human Cell Atlas and IMMUcan. Using Element-Centric Consistency, we found that seed choice affected a substantial fraction of cells, with Scanpy showing more unstable assignments than Seurat on average, 40.46% versus 26.78% unstable cells, respectively. This increased stability came at a marked computational cost: Seurat required approximately 19-fold higher median memory than Scanpy. Seed-dependent clustering variability also propagated to cell-type annotation, particularly among transcriptionally related populations including macrophage/monocyte, endothelial/epithelial and T/NK cell states. To mitigate this instability, we developed StAbility-BasEd Reassignment (SABER), a Scanpy-based framework that identifies seed-sensitive cells across repeated clusterings and reassigns them to stable cluster cores using cosine similarity. SABER improved clustering quality while preserving annotation concordance and reduced median memory usage 3.5-fold compared with Seurat-Louvain. Our results identify seed choice as an underappreciated source of variability in single-cell analysis and provide a scalable strategy to improve clustering robustness.

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

Benchmarking LLM Agents on Meta-Analysis Articles from Nature Portfolio

Meta-analysis is a demanding form of evidence synthesis that combines literature retrieval, PI/ECO-guided study selection, and statistical aggregation. Its structured, verifiable workflow makes it an ideal substrate for evaluating systematic scientific reasoning, yet existing benchmarks lack ground truth across the full retrieval-screening-synthesis pipeline. We introduce MetaSyn, a dataset of 442 expert-curated meta-analyses from Nature Portfolio journals. Each entry pairs a research question with PI/ECO criteria, a retrieval corpus of 140k PubMed articles, verified positive studies, hard negatives that are topically similar but PI/ECO-ineligible, and complete search strategies and date bounds. Benchmarking twelve pipeline configurations (nine RAG variants and a protocol-driven agent) reveals a critical screening bottleneck: despite a retrieval ceiling of 90.9% recall at K=200, no system recovers more than 52.7% of ground-truth included literature. Current LLMs fail to reliably separate eligible studies from PI/ECO-failing distractors in pools of comparable topical relevance. Stage-attributed metrics capture where systems succeed and fail; a single end-to-end score does not.

10.
arXiv (CS.CV) 2026-06-18

Rethinking the Pointer Loss in Table Structure Recognition: Geometry-Aware Pointer Loss for Spatial Locality

Table Structure Recognition (TSR) using a pointer network achieves impressive results by predicting HTML sequences while aligning tags to detected text (or cell) regions. However, our analysis reveals that when pointer networks fail, 79.6% of errors occur between spatially adjacent cells (Manhattan distance

11.
arXiv (quant-ph) 2026-06-11

Tight Bounds for Quantum Phase Estimation and Related Problems

arXiv:2305.04908v3 Announce Type: replace Abstract: Phase estimation, due to Kitaev [arXiv'95], is one of the most fundamental subroutines in quantum computing. In the basic scenario, one is given black-box access to a unitary $U$, and an eigenstate $\lvert \psi \rangle$ of $U$ with unknown eigenvalue $e^{i\theta}$, and the task is to estimate the eigenphase $\theta$ within $\pm\delta$, with high probability. The cost of an algorithm for us is the number of applications of $U$ and $U^{-1}$. We tightly characterize the cost of several variants of phase estimation where we are no longer given an eigenstate, but are required to estimate the maximum eigenphase of $U$, aided by advice in the form of states (or a unitary preparing those states) which are promised to have at least a certain overlap $\gamma$ with the top eigenspace. We give algorithms and nearly matching lower bounds for all ranges of parameters. We show that a small number of copies of the advice state (or of an advice-preparing unitary) are not significantly better than having no advice at all. We also show that having lots of advice (applications of the advice-preparing unitary) does not significantly reduce cost, and neither does knowledge of the eigenbasis of $U$. We immediately obtain a lower bound on the complexity of the Unitary recurrence time problem, resolving an open question of She and Yuen~[ITCS'23]. Lastly, we study how efficiently one can reduce the error probability in the basic phase-estimation scenario. We show that a phase-estimation algorithm with precision $\delta$ and error probability $\epsilon$ has cost $\Omega\left(\frac{1}{\delta}\log\frac{1}{\epsilon}\right)$, matching an easy upper bound. This contrasts with some other scenarios in quantum computing (e.g., search) where error-probability reduction costs only a factor $O(\sqrt{\log(1/\epsilon)})$. Our lower bound uses a variant of the polynomial method with trigonometric polynomials.

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

TetherCache: Stabilizing Autoregressive Long-Form Video Generation with Gated Recall and Trusted Alignment

Autoregressive video diffusion models provide a natural formulation for streaming and variable-length video generation by conditioning newly generated frames on previously generated content. However, extending these models to minute-level generation remains challenging: the limited KV-cache budget prevents the model from retaining the full history, while repeatedly conditioning on self-generated frames induces a context distribution shift that accumulates over time, leading to visual artifacts, quality degradation, and temporal drift. In this paper, we propose TetherCache, a training-free and plug-and-play cache management strategy for drift-resistant long video generation. TetherCache organizes the cache into sink, memory, and recent regions, and introduces two complementary mechanisms. First, GRAB (Gated Recall with Attention-Diversity Balancing) selects long-range memory frames using a gated score that combines attention-based relevance with temporal diversity, preserving informative yet diverse historical context under a fixed cache budget. Second, TAME (Trusted Alignment via Memory Editing) lightly edits newly recalled memory tokens by aligning their statistics to a trusted context distribution, reducing the pollution caused by drifted historical features. Built on Self-Forcing, TetherCache consistently improves long-video generation quality on VBench-Long across 30s, 60s, and 240s settings. In particular, for 240s generation, it substantially improves overall and semantic scores while reducing quality drift from 7.84 to 1.33, demonstrating its effectiveness for stable long-horizon autoregressive video diffusion.

13.
arXiv (CS.AI) 2026-06-16

Intelligence Is Not the Bottleneck: Validating an LLM First-Pass Manuscript Score Against Peer-Review Outcomes

arXiv:2606.15887v1 Announce Type: cross Abstract: Large language model (LLM) systems are increasingly proposed to assist peer review, yet most evaluations judge the prose of machine-generated review text, not the validity of the numeric score a system assigns. We validate AIPR, which reads a submitted manuscript and emits five 0-100 quality dimensions and a weighted overall score, against the public decision outcomes of a major machine learning venue. AIPR grades by prompting alone, with no fine-tuning on reviews or decisions. Across 300 ICLR submissions with public decision tiers and reviewer ratings, graded under a frozen pipeline with hypotheses pre-registered before any score met any outcome, the overall score separates rejected from accepted submissions (AUROC 0.82, 95% CI 0.78-0.87), rises monotonically across tiers, and tracks the mean reviewer rating. The signal is strongest where we claim it: the lowest-scoring fifth is rejected far above the base rate, with oral papers absent. The validity comes mostly from the model: a one-paragraph prompt on the same model discriminates almost as well as the full pipeline (the small gap favours the pipeline but does not meet the pre-declared criterion, p = 0.09). What the engineering adds is reliability and a grounded review: AIPR's score barely moves across repeated runs (0.7 vs. 2.8 points within-paper SD) where the bare prompt swings, and the same pass returns a rubric-structured, evidence-grounded review rather than a bare number, with the human keeping the decision.

14.
arXiv (CS.LG) 2026-06-16

Design and Scheduling of an AI-based Queueing System

arXiv:2406.06855v3 Announce Type: replace-cross Abstract: To leverage prediction models to make optimal scheduling decisions in service systems, we must understand how predictive errors impact congestion due to externalities on the delay of other jobs. Motivated by applications where prediction models interact with human servers (e.g., content moderation), we consider a large queueing system comprising of many single server queues where the class of a job is estimated using a prediction model. By characterizing the impact of mispredictions on congestion cost in heavy traffic, we design an index-based policy that incorporates the predicted class information in a near-optimal manner. Our theoretical results guide the design of predictive models by providing a simple model selection procedure with downstream queueing performance as a central concern, and offer novel insights on how to design queueing systems with AI-based triage. We illustrate our framework on a content moderation task based on real online comments, where we construct toxicity classifiers by finetuning large language models.

15.
arXiv (CS.AI) 2026-06-18

HAARES Half-Split Residual Basis Routing for Deep Transformers

作者:

arXiv:2606.06564v2 Announce Type: replace-cross Abstract: Block-level residual routing makes learned residual aggregation practical by routing over block summaries, but each summary compresses an ordered sequence of attention and MLP updates into one cumulative vector. We propose \method{}, a lightweight residual basis router that keeps the cumulative block source and adds one half-split detail basis, computed as the difference between first-half and second-half residual updates. The detail basis is RMS-matched and updated online, exposing coarse intra-block trajectory information without dense sublayer-level routing. Across OpenWebText, cross-domain character-level benchmarks, and BPE-tokenized OpenWebText, the empirical pattern is depth-dependent: gains are small or mixed at shallow depth and most reliable in 48-layer models. In the 201M 48-layer setting, \method{} improves over Block AttnRes across all three seeds, while a 453M two-seed probe shows the same direction. Ablations rule out source duplication, random signed details, fixed detail-source biases, or block-count changes alone. Cost analysis shows that the method is FLOP-light but not wall-clock-free: it adds memory and routing overhead, yet its relative arithmetic cost is amortized as width grows and earlier convergence can reduce time-to-target.

16.
arXiv (CS.LG) 2026-06-12

Robustness Verification of Recurrent Neural Networks with Abstraction Refinement

arXiv:2606.12490v1 Announce Type: new Abstract: Certified local robustness verification for recurrent neural networks (RNNs) is challenging because approximation errors introduced by nonlinear relaxations can propagate through recurrent connections and accumulate over time. As a result, scalable linear bound propagation methods often become overly conservative and fail to certify inputs that are in fact robust, especially when many pre-activation intervals cross zero. We propose an abstraction-refinement framework for RNN verification that partitions such intervals to remove the dominant relaxation error: on each refined branch, ReLU becomes exact, and smooth activations such as tanh and sigmoid admit substantially tighter linear envelopes. To control the combinatorial cost of splitting in long sequences, we introduce a SHAP-guided timestep selection strategy that ranks hidden states by their contribution to the verification objective and refines only the most critical timesteps in temporal order. Experiments on CIFAR10 and MNIST stroke benchmarks demonstrate consistent improvements in verification success and robustness-margin tightness over abstraction-only baselines, while exposing clear runtime trade-offs between ReLU and tanh models.

17.
arXiv (CS.AI) 2026-06-15

TwinBI: An Agentic Digital Twin for Efficient Augmented Interactions with Business Intelligence Dashboards

arXiv:2606.13731v1 Announce Type: new Abstract: Business intelligence (BI) increasingly combines dashboard interaction with LLM-based assistance, but these two modes often fall out of sync during multi-step analysis. As users switch between direct dashboard manipulation and natural-language queries, it becomes difficult to preserve a consistent analytical state across filters, hierarchies, metrics, and chart context. We present TwinBI, an agentic digital-twin framework that couples an LLM-based agent system with an executable BI dashboard state. TwinBI unifies conversational interaction, dashboard manipulation, semantic grounding, and provenance tracking through a shared analytical state reconstructed from a unified interaction log. It also exposes artifacts such as schema views, SQL, logs, and an /insights command for state-grounded analytical summaries. We evaluate TwinBI in two complementary ways. In a controlled A/B benchmark with the same backbone agent, TwinBI improves exact-match accuracy from 43.3% to 63.3%, partial-credit accuracy from 48.3% to 70.8%, and substantially reduces timeout rate from 40.0% to 10.0% relative to Dashboard alone. In a usability study, participants benefited from the integrated dashboard-and-chat workflow, with high task accuracy, moderate workload, and favorable ratings for state-aware interaction mechanisms. These results suggest that TwinBI improves both agent-level analytical reliability and user-facing analytical support by turning visible dashboard state into richer actionable context. Our dataset and source code are available at: https://github.com/simonjisu/TwinBI

18.
arXiv (CS.AI) 2026-06-12

Competition and Diversity in Generative AI

arXiv:2412.08610v3 Announce Type: replace-cross Abstract: Recent evidence, both in the lab and in the wild, suggests that the use of generative artificial intelligence reduces the diversity of content produced. The use of the same or similar AI models appears to lead to more homogeneous behavior. Our work begins with the observation that there is a force pushing in the opposite direction: competition. When producers compete with one another (e.g., for customers or attention), they are incentivized to create novel or unique content. We explore the impact competition has on both content diversity and overall social welfare. Through a formal game-theoretic model, we show that competitive markets select for diverse AI models, mitigating monoculture. We further show that a generative AI model that performs well in isolation (i.e., according to a benchmark) may fail to provide value in a competitive market. Our results highlight the importance of evaluating generative AI models across the breadth of their output distributions, particularly when they will be deployed in competitive environments. We validate our results empirically by using language models to play Scattergories, a word game in which players are rewarded for answers that are both correct and unique. Overall, our results suggest that homogenization due to generative AI is unlikely to persist in competitive markets, and instead, competition in downstream markets may drive diversification in AI model development.

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

Quantum ring all-reduce: communication and privacy advantages for distributed learning

arXiv:2606.20344v1 Announce Type: cross Abstract: Machine learning models have scaled to unprecedented sizes, making training across distributed devices the de facto standard in the field. In this work, we explore how quantum communications can make distributed training both more communication-efficient and information-theoretically private, for both classical and quantum learning models. Ring all-reduce is the foundational communication primitive for large-scale distributed training. We present a quantum version that reduces per-link online communication by a provably optimal factor of two using pre-shared entanglement and superdense coding, without requiring the learning model or gradient computation to change. Beyond bandwidth, the primitive enables privacy guarantees that are information-theoretically impossible for any classical protocol, achieving composable {\epsilon}-secure aggregation, via verified entanglement, at a 2x overhead in GHZ copies. Our hybrid quantum-classical communication architecture yields simultaneous communication and security advantages for large scale distributed training, regardless of whether the learning itself is quantum or classical. Finally, we characterise quantum advantages in gradient conflict detection for server-to-client communication under bandwidth constraints, a setting that arises after ring all-reduce is completed, when full gradient broadcast to external clients is infeasible. Two variants of the problem admit different separations. For margin-based alignment testing (\textsc{GapIP}_{\tau}), the quantum advantage is quadratic in the margin parameter: \widetilde{O}({\tau}^{-1}\log P) qubits versus \widetilde{O}(\min(\{\tau}^{-2},P)) bits. For sign-consistency auditing against a private parameter matching (\textsc{TieAudit}_{\epsilon}), the advantage represents an exponential separation in communication complexity: \Omega(\sqrt{P}) bits whereas O({\epsilon}^{-2}\log P) qubits suffice.

20.
arXiv (CS.LG) 2026-06-17

On Randomized Algorithms in Online Strategic Classification

arXiv:2602.06257v2 Announce Type: replace Abstract: Online strategic classification studies settings in which agents strategically modify their features to obtain favorable predictions. For example, given a classifier that determines loan approval based on credit scores, applicants may open or close credit cards and bank accounts to obtain a positive prediction. The learning goal is to achieve low mistake or regret bounds despite such behavior. While randomized algorithms have the potential to offer advantages to the learner in strategic settings, they have been largely underexplored. In the realizable setting, no lower bound is known for randomized algorithms, and existing lower bound constructions for deterministic learners can be circumvented by randomization. In the agnostic setting, the best known regret upper bound is $O(T^{3/4}\log^{1/4}T|\mathcal H|)$, which is far from the standard online learning rate of $O(\sqrt{T\log|\mathcal H|})$. In this work, we provide refined bounds for online strategic classification in both settings; our bounds depend on the Littlestone dimension $\mathrm{Ldim}(\mathcal H)$ of the hypothesis class $\mathcal H$ and the maximum degree $\Delta$ of the manipulation graph. In the realizable setting, we extend, for $T > \mathrm{Ldim}(\mathcal H) \Delta^2$, the existing lower bound $\Omega(\mathrm{Ldim}(\mathcal H) \Delta)$ for deterministic learners to all learners. This yields the first lower bound that applies to randomized learners. We then provide the first randomized learner that improves the known (deterministic) upper bound of $O(\mathrm{Ldim}(\mathcal H) \cdot \Delta \log \Delta)$. In the agnostic setting, we give an improper randomized learner that improves the regret upper bound to $O(\sqrt{T\log|\mathcal H|})$, matching the standard online learning rate. We also show a larger lower bound for all proper learning rules, demonstrating that improperness is necessary to achieve the optimal rate.

21.
arXiv (CS.AI) 2026-06-19

Computational Identifiability

arXiv:2606.19361v1 Announce Type: cross Abstract: Identification conditions describe the computability of a target query or parameter of interest as a function of the type and amount of information available. In causal identification, this information is often expressed in the form of a causal graph, and data are observed or collected for some subset of variables in the graph. Target queries may be for a single effect alone or for a class of effects in a given model. The derivation of an identification algorithm then defines mathematically the process by which the desired causal effect(s) can be uniquely determined, theoretically, in expectation. Identifiability in expectation, or 'theoretical identifiability,' generally assumes asymptotic properties, infinite data, or other mathematically idealized conditions. In this paper, we explore a fundamental distinction between this theoretical, idealized notion of identifiability and a proposed alternative that is computation-bound. The framework we propose - 'computational identifiability' - is to instead define a finite computational search procedure for an empirical estimator. If this process finds an estimator empirically, within a desired error tolerance, then identifiability is satisfied, conditional on the specified assumptions of the search (i.e., a prior distribution over the parameters) and conditional on the search procedure itself. Through several experiments, we demonstrate how this framework allows us to answer fine-grained, practical identification questions, such as identification with small finite samples, with ambiguous graphical criteria, with mixed observational-interventional data, and across counterfactual data and estimands. Code is available at https://github.com/lbynum/metadentify.

22.
arXiv (CS.AI) 2026-06-15

Hierarchical ODE: Learning Continuous-Time Physical Prototypes for Early Link Failure Detection

arXiv:2606.14284v1 Announce Type: cross Abstract: Time series prototype learning is fundamentally challenged by observational ambiguity. Discrete architectures fail to resolve this, as they lack the capacity to decouple stochastic noise from continuous dynamics. Furthermore, rigid closed-set assumptions fail to capture unseen diversity. To address these limitations, we propose a hierarchical ordinary differential equation clustering network, which utilizes neural ordinary differential equation to model latent state evolution as a continuous integral curve. This formulation enforces temporal continuity to effectively disentangle smooth feature trends from stochastic noise, while our adaptive hierarchical mechanism autonomously determines the appropriate number of prototypes without rigid prior constraints. Validated on the early link failure detection task with irregularly sampled time series, the proposed method effectively extracts underlying physical prototypes, thereby enabling robust failure detection. Our code is available at https://github.com/NJ-LNN/Hierarchical-ODE.

23.
bioRxiv (Bioinfo) 2026-06-14

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

24.
arXiv (CS.AI) 2026-06-15

Learning Coordinated Preference for Multi-Objective Multi-Agent Reinforcement Learning

arXiv:2606.14693v1 Announce Type: cross Abstract: Cooperative multi-objective multi-agent reinforcement learning (MOMARL) models team decision making under multiple, potentially conflicting objectives. In this setting, conflicts arise not only across objectives but also across agents with different observations, roles, and contributions. We propose Preference Coordinated Multi-agent Policy Optimization (PCMA), which learns coordinated agent-specific preferences to enable complementary trade-offs among agents. Theoretically, we formulate cooperative MOMARL as a team-optimal game and show that, under suitable conditions, preference diversity can induce team improvement through a first-order improvement decomposition. Experiments on multiple cooperative MOMA environments and a practical traffic-control scenario show that PCMA improves both performance and trade-off coordination.

25.
bioRxiv (Bioinfo) 2026-06-17

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

Temperature is a fundamental constraint on biological systems, yet how it is reflected in genome sequence organization remains unclear. Here, we show that genome-wide distributions of short DNA sequences contain a robust signal of thermal adaptation that is largely independent of phylogeny. Using Structural Topic Modelling (STM), a machine-learning approach for identifying groups of co-occurring sequence motifs, we analyze canonical 6-mer and 9-mer frequency profiles of bacterial and archaeal genome proxies (randomly sampled genomic regions) and identify motif families systematically associated with thermophiles and psychrophiles. In bacterial thermophiles, the identified motif families are dominated by highly specific, overrepresented and co-occurring C- and G-stacked hexamers, and a distinct family of CG-periodic hexamers recurring across multiple temperature comparisons. In contrast, bacterial psychrophile-associated motifs are dominated by low-complexity A-, T-, and AT-run hexamers. Thermophilic archaea generally exhibit a distinct CTAG-centred hexamer family, suggesting that different domains may adapt to similar environmental constraints through different sequence-level solutions. However, this domain-level contrast is not absolute: in a targeted analysis of two thermophilic bacterium–archaeon pairs, we find unusually similar frequencies of all the STM-identified thermophile-associated hexamer families, suggesting that shared high-temperature environments can, in specific cases, partially override phylogenetic divergence. Notably, the identified motif families constitute only a small and highly selective subset of the vast space of possible G+C-rich or A+T-rich sequences. This indicates that thermal adaptation is associated with specific sequence architectures rather than broad shifts in nucleotide composition. Accordingly, the observed signal cannot be explained by overall base composition alone, but instead arises from structured combinations and positional arrangements of nucleotides within short sequence contexts. Related motif families are recovered at both k=6 and k=9, indicating that the signal reflects systematic shifts in genome-wide sequence organization rather than isolated sequence motifs. These patterns are consistent with known sequence-dependent DNA physical properties documented in biochemical and biophysical studies, including differences in base-stacking interactions and conformational flexibility. Together, our results suggest that genome-wide sequence organization reflects sequence-dependent DNA physical properties associated with thermal adaptation, revealing a previously underappreciated physical layer of genomic information beyond phylogenetic history.