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01.
arXiv (math.PR) 2026-06-15

Longest weakly increasing subsequences of discrete random walks on the integers with heavy tailed distribution of increments

arXiv:2603.29047v2 Announce Type: replace-cross Abstract: We investigate the behavior of the length of the longest weakly increasing subsequences (weak LIS) of $n$-step random walks with nonzero integer increments $k = \pm 1, \pm 2, \dots$ given by a symmetric heavy tailed mass distribution proportional to $|k|^{-1-\alpha}$ for several values of the real parameter $\alpha > 0$ together with that of the simple random walk ($k=\pm 1$), to which the $n$-step heavy tailed walks reduce when $\alpha$ grows large enough that step jumps beyond $\pm 1$ become essentially absent on the scale of $n$. By means of exploratory fits, weighted nonlinear least squares, and nested-model comparisons, we found that the sample average length $\langle{L_{n}}\rangle$ scales like $\langle{L_{n}}\rangle \sim \sqrt{n}\log{n}$ when the distribution of increments has finite variance ($\alpha > 2$) and $\langle{L_{n}}\rangle \sim n^{\theta}$ with a varying exponent $\theta > 0.5$ when the variance is infinite ($\alpha \leq 2$). Distributional diagnostics indicate that the bulk of the $L_{n}$ distribution is very well-approximated by a lognormal model, though systematic deviations are observed in the tails. Our results corroborate and expand upon previous results for the LIS of other types of heavy-tailed random walks and raise a conjecture as to whether the distribution of $L_{n}$ is given, or can be effectively described, by a lognormal distribution.

02.
bioRxiv (Bioinfo) 2026-06-11

Hyper3D-lite: count-preserving representation auditing for long-read multi-contact genome data

作者:

Long-read and single-molecule sequencing technologies are rapidly increasing molecule-level data, with platforms such as Oxford Nanopore, PacBio HiFi, and Roche sequencing-by-expansion advancing at different technology readiness levels. In the specific context of Pore-C and HiPore-C multi-contact chromatin-conformation assays, long-read multi-contact 3D genome assays preserve molecule-level contact context, but common downstream pairwise projections can expand one multi-contact molecule into many pair records. This creates a representation problem: apparent contact evidence can increase through the counting frame before biological interpretation begins. Hyper3D-lite addresses this problem as a representation-first audit tool for read-to-fragment-style long-read multi-contact inputs. It compares all-pair projection with CPB, a count-preserving statistical accounting reference point, and separates broad software outputs from conservative higher-order candidate calls.

03.
arXiv (CS.AI) 2026-06-16

TrustedARI: Towards Trust-Native Agentic Routing Infrastructure for Agentic AI

arXiv:2606.15822v1 Announce Type: new Abstract: AI agents increasingly access external models, tools, and services through Agentic Routing Infrastructure (ARI) to manage the overhead of heterogeneous interfaces and fragmented subscriptions. Yet, the architecture of ARI introduces fundamental trust risks: it obtains plaintext access to agent queries and service responses, while leaving agents unable to verify that their queries are routed to intended service providers or that requests and responses remain untampered. To address this problem, we present TrustedARI, the first trust-native agentic routing infrastructure for agentic AI. Architecturally, TrustedARI is built upon three core innovations: (i) an ARI-adapted three-party TLS handshake that enables the agent and ARI to jointly authenticate the service provider through role-specific distribution of TLS key materials; (ii) a privacy-preserving query-construction protocol that allows the agent and ARI to collaboratively construct well-formed queries without exposing their respective private inputs; and (iii) a verifiable billing protocol that supports fair usage-based settlement while preserving the integrity and confidentiality of service responses. We implemented and extensively evaluated a prototype of TrustedARI to validate its performance. Experiments confirm that TrustedARI is highly efficient: our ARI-adapted handshake protocol reduces communication overhead by 39.34% compared to the existing three-party TLS handshake. Furthermore, the privacy-preserving query-construction protocol imposes negligible overhead-averaging 0.19 seconds in computation time and 0.58 MB in communication costs-while the verifiable billing protocol speeds up proof generation by 28.20x. Crucially, TrustedARI is readily deployable without any modification to the service providers.

04.
arXiv (CS.LG) 2026-06-15

Neural ARFIMA model for forecasting BRIC exchange rates with long memory

arXiv:2509.06697v3 Announce Type: replace-cross Abstract: Exchange rate forecasting remains a challenging problem, particularly for emerging economies, where the observed time series exhibit pronounced long-memory dependence, nonlinear dynamics, and sensitivity to macro-financial drivers. Classical models such as ARFIMA capture long-range persistence but fail to adequately represent nonlinear relationships, while modern machine learning approaches often neglect the underlying long-memory structure in macroeconomic series. To address this gap, we propose a Neural AutoRegressive Fractionally Integrated Moving Average (NARFIMA) model that integrates ARFIMA-based long-memory modeling with neural networks for nonlinear function approximation, while incorporating exogenous macroeconomic and uncertainty indicators. The framework provides a unified approach for capturing persistence, nonlinear dynamics, and external shocks. We establish asymptotic stationarity of the NARFIMA process and develop conformal prediction intervals for distribution-free uncertainty quantification. Empirical results for BRIC exchange rates show that NARFIMA consistently outperforms a broad range of forecasting benchmarks across multiple horizons, underscoring the importance of explicitly modeling long-memory dependence in exchange rate dynamics. The `narfima' R package provides an implementation of our approach.

05.
arXiv (CS.CL) 2026-06-11

LatticeBridge: Rare-Event Sequential Inference for Faithful Structured Sequence Synthesis

Structured sequence generation often requires a model to satisfy several input-derived constraints in a single output. Standard decoding methods may assign high probability to fluent continuations while placing low mass on continuations that realize all required anchors jointly. We study this regime as a rare-event sequential inference problem. LatticeBridge combines a compact prefix language model, instance-compiled surface automata, and a twisted sequential Monte Carlo (SMC) decoder with resampling, multilevel splitting, and a source-support proposal term derived from instance-provided phrases. The constraint representation is compiled from each input instance and does not rely on manually curated lexical classes. On 2,610 attainable validation tasks spanning CommonGen, E2E NLG, and WikiBio, the particle decoder improves exact anchor satisfaction and mean anchor coverage over greedy, beam-filtered, and best-of-k ancestral baselines under a shared proposal model. Since exact anchor satisfaction alone does not rule out unsupported attribute substitutions, the evaluation reports required-anchor coverage, source coverage, source-intrusion diagnostics, overlap, runtime, and particle statistics jointly. The benchmark characterizes the faithfulness-overlap-latency frontier under a fixed proposal model.

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

OmniLoc: A Geometry-Aware Foundation Model for Anchor-Free UE Localization Across Diverse Indoor Environments

arXiv:2606.11490v1 Announce Type: new Abstract: Indoor localization from wireless measurements remains challenging in large-scale deployments due to substantial variation in building geometry, the set of detectable access points (APs), and the heterogeneity of received signals. Existing learning-based methods often perform well only in limited settings and degrade under environmental shifts, making robust anchor-free localization across diverse indoor environments notoriously difficult. In this paper, we present OmniLoc, an environment-interactive foundation model for anchor-free user equipment localization across diverse indoor environments. To the best of our knowledge, OmniLoc is the first foundation-model-based approach built directly on wireless measurements for this task. OmniLoc is built on three key designs. First, a unified input tokenization module converts heterogeneous wireless measurements into a common representation that is more amenable to learning. Second, a geometry-aware Transformer performs AP-aware feature extraction by emphasizing dominant APs while aggregating complementary evidence from supporting APs. Third, a geometry-aware location estimation module conditions regression on geometric embeddings to produce geometrically consistent location predictions. We evaluate OmniLoc on both a large-scale in-house dataset and a public benchmark dataset. Results show that OmniLoc significantly outperforms existing methods, consistently improves existing backbones when its design components are integrated, and demonstrates strong generalization in cross-environment evaluations.

07.
arXiv (CS.CL) 2026-06-19

Group-Sparse Matrix Factorization for Transfer Learning of Word Embeddings

Unstructured text provides decision-makers with a rich data source in many domains, ranging from product reviews in retail to nursing notes in healthcare. To leverage this information, words are typically translated into word embeddings – vectors that encode the semantic relationships between words – through unsupervised learning algorithms such as matrix factorization. However, learning word embeddings from new domains with limited training data can be challenging, because the meaning/usage may be different in the new domain, e.g., the word ``positive'' typically has positive sentiment, but often has negative sentiment in medical notes since it may imply that a patient tested positive for a disease. In practice, we expect that only a small number of domain-specific words may have new meanings. We propose an intuitive two-stage estimator that exploits this structure via a group-sparse penalty to efficiently transfer learn domain-specific word embeddings by combining large-scale text corpora (such as Wikipedia) with limited domain-specific text data. We bound the generalization error of our transfer learning estimator, proving that it can achieve high accuracy with substantially less domain-specific data when only a small number of embeddings are altered between domains. Furthermore, we prove that all local minima identified by our nonconvex objective function are statistically indistinguishable from the global minimum under standard regularization conditions, implying that our estimator can be computed efficiently. Our results provide the first bounds on group-sparse matrix factorization, which may be of independent interest. We empirically evaluate our approach compared to state-of-the-art fine-tuning heuristics from natural language processing.

08.
arXiv (CS.LG) 2026-06-16

Mean-Field Parallel Decoding for Discrete Diffusion Language Models

arXiv:2606.15805v1 Announce Type: new Abstract: Discrete diffusion language models enable parallel token generation, offering a pathway to low-latency decoding. However, selecting tokens independently by marginal confidence limits effective parallelism: tokens that appear reliable in isolation can form incompatible configurations when several positions are updated at once. We introduce a training-free decoding framework that coordinates these parallel updates. At each forward pass, the method assigns a commit score to each masked position and refines these scores using pairwise interactions derived from the model's predictive distributions. A variational relaxation yields a simple fixed-point update that suppresses conflicting simultaneous commitments within a single forward pass. This mechanism allows the decoder to commit more tokens in parallel while maintaining competitive generation quality. The method is lightweight, requires no auxiliary model or retraining, and drops into existing diffusion decoding pipelines without modification. Experiments on reasoning and code-generation benchmarks show consistent improvements in the quality-latency trade-off.

09.
arXiv (CS.CV) 2026-06-11

Beyond Dark Knowledge: Mixup-Based Distillation for Reliable Predictions

Knowledge Distillation (KD) and mixup have proven effective at inducing smoothness in class boundaries; KD captures inherent class relationships in probability distributions, and mixup enforces them through convex combinations of inputs. Their interaction, however, remains poorly understood, particularly when mixup is applied only during student training. In this setting, the teacher is queried on inputs drawn from a vicinal distribution it never saw during training, a controlled mismatch whose effect on knowledge transfer has not been characterised. We show that this mismatch causes the teacher's supervisory signal to be dominated by distributional confusion rather than inter-class structure. Despite it, the student does not merely imitate the teacher: it independently acquires greater linearity in the vicinal region, a structural property that the teacher lacks, and goes beyond dark-knowledge transfer. KD with mixup consistently improves student accuracy and reduces overconfidence by an order of magnitude relative to the baseline, across CIFAR and ImageNet with varying-capacity teachers. Crucially, calibration propagates from teacher to student independently of accuracy transfer, and temperature scaling governs a measurable accuracy-calibration trade-off that becomes more pronounced under vicinal training. These results reframe mixup distillation not as a degraded version of standard KD, but as a richer transfer channel that simultaneously shapes discriminative performance, uncertainty estimation, and representational geometry.

10.
Nature (Science) 2026-06-10

A prognostic human brain network for diffuse midline glioma

作者:

Diffuse midline gliomas (DMGs) are near-universally lethal tumours of the childhood central nervous system1,2. In animal models, DMGs form brain-wide integrated networks through neuron-to-glioma synapses3–6 and glioma-to-glioma gap junctional coupling3. This extensive connectivity robustly promotes the growth and invasion of DMG3–9 and other glial malignancies10–12 through paracrine mechanisms and direct neuron-to-glioma synapses. However, the organization and clinical implications of these connections in the living human brain remain to be elucidated. Here, we develop tumour network mapping to compute the brain-wide connectivity profile of DMG, defining a conserved brain network across pontine and thalamic DMG associated with patient short-term survival (DMG network). Tumour functional connectivity with the DMG network was independently predictive of patient overall survival across two external validation cohorts. Tumour growth mapped to DMG network-specific trajectories and peak in-network neurometabolic changes across development spatiotemporally aligned with the peak age incidence of DMG. Analyses of single-nucleus RNA sequencing data confirmed diverse synaptic gene enrichment in high-connectivity DMG. Strikingly, incidental surgical resection of high-connectivity thalamic DMG tissue conferred a significant survival advantage. Collectively, these data define a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMGs exploit otherwise healthy brain circuits to promote tumour growth. Tumour network mapping of diffuse midline glioma (DMG) defines a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMGs exploit otherwise healthy brain circuits to promote tumour growth.

11.
arXiv (CS.AI) 2026-06-12

An Explainable AI Assistant for Introductory Programming Education: Improving Feedback Reliability with Instructor-AI Collaboration

arXiv:2606.12425v1 Announce Type: cross Abstract: Active learning is widely recognized as an effective approach for improving learning outcomes in introductory programming courses. However, insufficient instructional support often limits students' access to timely, personalized feedback, which is crucial for mastering foundational programming concepts. Although recent advances in AI, particularly large language models, offer scalable opportunities for feedback, concerns about explainability and reliability remain. In this paper, we present an AI-driven classroom assistant that leverages an explainable AI model to analyze student code, map logical errors to instructor-identified misconceptions, and deliver instructor-authored feedback, thereby grounding reliability in instructor-defined pedagogical knowledge. To evaluate the effectiveness of our framework, we conducted an expert evaluation to examine its alignment with instructor-verified feedback and deployed the system in a classroom setting to assess students' perceptions of its usability. Results indicate that the assistant can provide accurate, instructor-verified feedback to students while fostering a positive experience.

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

Adaptive Weighted Averaging

arXiv:2606.12763v1 Announce Type: new Abstract: We study the problem of selecting the largest among $n$ unknown values $x_1,\dots,x_n$ given only a single unbiased estimate $y_i$ for each $x_i$. We design strategies that are simultaneously admissible (not uniformly dominated by any other strategy) and also never worse than a given baseline such as uniform random selection. We provide an application to stochastic optimization, where we obtain online-to-batch conversion bounds with a desirable "no-compromise" guarantee: they are never worse than standard random iterate selection, and yet can be significantly better in benign settings.

13.
arXiv (quant-ph) 2026-06-19

Fidelity bounds for adiabatic gates and other quantum operations with time-dependent dissipation

arXiv:2606.20501v1 Announce Type: new Abstract: As quantum-computing platforms are susceptible to noise, the fidelity of quantum operations is limited by decoherence. Understanding this limitation is crucial for building utility-scale quantum processors. In previous works [Phys. Rev. Lett. 129, 150504 (2022); Quantum 9, 1684 (2025)], we presented analytical formulae for the average gate fidelity of multi-qubit operations under static Markovian noise processes, including operations that temporarily leave the computational subspace. However, some quantum-computing architectures dynamically modulate qubit or coupler frequencies to implement two-qubit gates, e.g., baseband flux gates; such modulation can lead to dissipation rates varying in time. In this Letter, we therefore generalize the fidelity-reduction formulae to encompass time-dependent dissipation. Applying our generalized formula, we obtain a fidelity bound for adiabatic operations and demonstrate that flux-dependent noise sensitivity, combined with qubit-coupler hybridization, significantly reduces the fidelity of adiabatic controlled-Z (CZ) gates in superconducting quantum computers. Our work thus provides essential theoretical tools for evaluating error budgets and optimizing the design of quantum operations in tunable quantum-computing architectures, and may also find applications in quantum-sensing and quantum-communication protocols that are affected by time-dependent dissipation.

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

Towards Mitigating Hallucinations in Large Vision-Language Models by Refining Textual Embeddings

Hallucinations in Large Vision-Language Models (LVLMs) remain a persistent challenge, often stemming from inadequate integration of visual information during multimodal reasoning. A key cause is the model's over-reliance on textual priors and underutilization of visual cues, leading to outputs that are linguistically fluent but visually inaccurate. For example, given an image of an empty kitchen countertop, an LVLM might hallucinate a "bowl of fruit" or "cup of coffee", relying on language associations rather than visual evidence. Most LVLMs incorporate visual features by appending them to the input stream of a pre-trained LLM and training on large-scale vision-language datasets. Our systematic analysis reveals that this strategy often leads to over-dependence on textual information due to the inherent bias of LLMs towards language-dominant representations. This imbalance skews attention towards the text over visual content, weakening the model's ability to ground outputs in visual inputs. To address this, we propose a simple yet effective visual feature incorporation method that encourages the model to learn visually-informed textual embeddings distinct from those of the base LLM and promotes a more balanced attention distribution. Experimental results across multiple hallucination benchmarks demonstrate that our method significantly reduces hallucinations and fosters more balanced multimodal reasoning. Notably, our approach achieves substantial gains, including +9.33% on MMVP-MLLM, +2.99% on POPE-AOKVQA, up to +3.4% on Merlin, and +3% on the hard-data split of HallusionBench.

15.
arXiv (CS.CV) 2026-06-11

Motion Reinforces Appearance: RGB-Skeleton Gated Residual Fusion for Micro-Gesture Online Recognition

Micro-gesture analysis attracts increasing attention for inferring spontaneous emotion from subtle body movements. Micro-gesture online recognition, which localizes and classifies each gesture instance in untrimmed videos, is a core task in the 4th EI-MiGA-IJCAI Challenge. Compared with typical temporal action detection, MGR emphasizes the localization and classification of actions, requiring the model to output the start time, end time, and category of each micro-gesture. Moreover, since micro-gestures are highly spontaneous, relying solely on a single modality makes it difficult to capture the complete and accurate multi-modal cues. In this work, we propose DyFADet+, which extends DyFADet into a dual-stream RGB-skeleton framework. In our model, both modalities are projected into shared multi-scale temporal embeddings and fused through a gated residual module, which adaptively injects skeleton motion into the RGB representation rather than using naive concatenation. Finally, these fused features are decoded by a Dynamic TAD head for online classification and boundary regression. On the SMG dataset, our method achieves an F1 score of 40.88, ranking 2nd in the Micro-gesture Online Recognition track.

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

Provable quantum speedups for computing persistence in topological data analysis

arXiv:2410.21258v2 Announce Type: replace-cross Abstract: Topological data analysis (TDA) aims to extract noise-robust features from a data set by examining the number and persistence of holes in its topology. We provide an efficient quantum algorithm for a computational problem closely related to a core task in TDA – determining whether a given hole persists across different length scales. Further, we prove the problem itself is $\mathsf{BQP}_1$-hard, implying that a classical solution is extremely unlikely; this stands in contrast to all previous quantum approaches to TDA, where the problems were also intractable for quantum computers, or where a rigorous proof of classical hardness still remains open. This result implies an {exponential} quantum speedup for this problem under standard complexity-theoretic assumptions. Our approach relies on encoding the persistence of a hole in a variant of the guided sparse Hamiltonian problem, where the guiding state is constructed from a harmonic representative of the hole.

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

CHORUS: Decentralized Multi-Embodiment Collaboration with One VLA Policy

arXiv:2606.12352v1 Announce Type: cross Abstract: Multi-robot collaboration allows robots to efficiently take on a wide range of tasks, from moving a couch through a doorway to assembling structures on a construction site. However, achieving such coordination in mobile multi-robot settings remains challenging: centralized methods conditioned on the combined observations of a team scale poorly with team size, and decentralized methods that train one policy per robot often require explicit alignment procedures or information sharing at inference time to overcome partial observability. Our key insight is that the visuomotor priors of pretrained vision-language-action (VLA) models should enable reactive, decentralized collaboration from each robot's local observations alone, without these inference-time assumptions. We propose CHORUS, a framework that adapts a single VLA backbone to control diverse, multi-robot teams. At inference time, each robot runs an independent copy of CHORUS, conditioned only on its own observations and a robot-identifying prompt. In real-world experiments including mobile tape measurement, library book handovers, and laundry basket lifting, CHORUS achieves a 64% point improvement over decentralized, from-scratch models, improves reactivity to teammate behavior by 40% points, and outperforms centralized baselines. Together, these results show that a shared VLA backbone is capable of achieving decentralized multi-robot collaboration, without per-robot policies or inter-robot communication at inference.

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

RepWAM: World Action Modeling with Representation Visual-Action Tokenizers

This work presents RepWAM, a representation-centric world action model (WAM) built on representation visual-action tokenizers. Existing WAMs typically inherit reconstruction-oriented video tokenizers from pretrained video generation models. Although these tokenizers preserve visual fidelity, pixel reconstruction alone provides limited guidance for learning instruction-following dynamics that connect future prediction with robot control. To address this, we explore a semantic visual-action latent space for representation-centric world action modeling. Specifically, we train a representation visual-action tokenizer that maps visual inputs into aligned visual and latent action tokens. We then pretrain our WAM to jointly model future visual states and the latent actions that connect them under language instructions, followed by adaptation to real robot trajectories for closed-loop manipulation. Experiments on real-world manipulation tasks and simulation benchmarks show that RepWAM delivers strong performance across diverse manipulation settings, while ablations highlight the value of semantic visual-action tokenization over reconstruction-oriented alternatives. These results establish representation visual-action tokenization as a promising foundation for world action models and a step toward generalist robot policies. Code and weights will be available at https://github.com/wdrink/RepWAM.

19.
arXiv (CS.AI) 2026-06-16

TS-Memory: Plug-and-Play Memory for Time Series Foundation Models

arXiv:2602.11550v2 Announce Type: replace-cross Abstract: Time Series Foundation Models (TSFMs) achieve strong zero-shot forecasting through large-scale pre-training, but adapting them to downstream domains under distribution shift remains challenging. Existing solutions face a trade-off: Parametric Adaptation can cause catastrophic forgetting and requires costly multi-domain maintenance, while Non-Parametric Retrieval improves forecasts but incurs high inference latency due to datastore search. We propose Parametric Memory Distillation and implement it as TS-Memory, a lightweight memory adapter that augments frozen TSFMs. TS-Memory is trained in two stages. First, we construct an offline, retrieval-leakage-safe kNN teacher that synthesizes confidence-aware quantile targets from retrieved futures. Second, we distill this retrieval-induced distributional correction into a lightweight memory adapter via confidence-gated supervision. During inference, TS-Memory fuses memory and backbone predictions with constant-time overhead, enabling retrieval-free deployment. Experiments across diverse TSFMs and benchmarks demonstrate consistent improvements in both point and probabilistic forecasting over representative adaptation methods, with efficiency comparable to the frozen backbone. Code: https://github.com/sisuolv/TS-Memory.

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

Conservation Laws for Modern Neural Architectures

arXiv:2606.17816v1 Announce Type: cross Abstract: Understanding gradient descent dynamics is key to explaining the success of over-parameterized models, where implicit bias manifests through conservation laws in gradient flow. While such laws are well understood for linear and ReLU networks, they remain largely unexplored for modern architectures. This work develops a unified framework to characterize conservation laws for contemporary models, including feedforward networks with GELU, SiLU, and SwiGLU activations, multihead attention with sinusoidal and rotary positional encodings, and Mixture-of-Experts architectures under diverse gating designs. Our theoretical findings are supported by experiments that validate the predicted invariants.

21.
Nature Biotechnology 2026-06-05

Structural motif search across the protein universe with Folddisco

作者:

Detecting similar protein structural motifs in large structure collections is computationally expensive. We developed Folddisco, a fast structural motif search tool that uses an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco is 20-fold faster in querying and fourfold more storage-efficient than existing methods while improving accuracy. Folddisco is freely available online ( https://folddisco.foldseek.com ), along with a webserver ( https://search.foldseek.com/folddisco ). Folddisco enables protein structural motif search in million scale databases.

22.
arXiv (CS.LG) 2026-06-17

Decision-Driven Geosteering Under Uncertainty: A Unified Framework for Sequential Decision Optimization

arXiv:2606.17331v1 Announce Type: new Abstract: Geosteering requires navigating a well trajectory through an unknown geological configuration, while sequentially updating decisions based on indirect measurements acquired during drilling. This work presents an uncertainty-aware geosteering framework that tightly integrates particle filtering for probabilistic subsurface interpretation with value-based reinforcement learning for sequential decision-making. Geological uncertainty ahead of the drill bit is represented explicitly through a particle filter (PF), enabling belief-informed control rather than deterministic trajectory correction. The framework couples PF belief updates with belief-informed decision policies and evaluates three decision-making options that operate under identical uncertainty representations: an interpretable Approximate Dynamic Programming (ADP) scheme, a Deep Q-learning baseline, and a Dual Deep Reinforcement Learning (Dual DRL) architecture trained with a target Q-network scheme for stability, using a dueling (value/advantage) decomposition for Q-value parameterization. Beyond final placement performance, we assess policy behavior using stability-oriented metrics that quantify steering smoothness over time, providing additional operational insight into how decision policies respond as uncertainty evolves. The framework is integrated with an API for validation within an industrial geosteering simulator under realistic measurement noise and drilling constraints. Using identical geological realizations, operational limits, and reward definitions across methods, the experiments provide a controlled and high-fidelity evaluation of how alternative decision policies behave throughout the drilling process, rather than evaluating performance solely from the final well trajectory.

23.
bioRxiv (Bioinfo) 2026-06-16

Phylogenetic tree inference using generative models

Accurate inference of phylogenetic trees is fundamental to evolutionary biology, yet existing methods rely on complex pipelines involving multiple sequence alignment, explicit evolutionary models, and computationally intensive tree search procedures. Here, we present BetaInfer, a generative framework that reformulates phylogenetic tree inference as a sequence transduction problem. BetaInfer leverages hybrid transformer-based architectures to directly map sets of unaligned sequences to phylogenetic trees represented in Newick format. Trained on large-scale simulated evolutionary data with known ground truth, BetaInfer learns to capture complex evolutionary signals directly from sequence data. Ensemble-based generation of multiple candidate trees further improves robustness, reducing reconstruction error by over 30% relative to single predictions. Across extensive evaluations on both simulated and empirical datasets, BetaInfer achieves competitive performance relative to state-of-the-art phylogenetic pipelines, matching, and in some cases exceeding, the accuracy of established likelihood-based and distance-based methods under a wide range of conditions. Interpretability analyses reveal that BetaInfer leverages internal pairwise-distance computations to synthesize evolutionary relationships into an integrated, global representation that supports direct tree generation. Together, these results demonstrate that generative models can serve as a viable and scalable alternative to standard phylogenetic pipelines.

24.
arXiv (CS.CV) 2026-06-16

HadBalance: A Plug-and-Play Unified Global Geometric Prior Framework for Generalizable Biomedical Segmentation

Precise biomedical image segmentation is crucial for clinical diagnosis. Geometric cues (e.g., boundary, shape, and topology) can improve structural consistency, yet most are task-specific and lack a unified geometric foundation that generalizes across organs and modalities. We are motivated by the observation that several medical segmentation targets can be approximated as globally near-convex shapes. A convex region is one in which any two interior points can be connected by a line segment entirely contained within the region. In practice, medical targets may exhibit small local concavities or boundary irregularities; we refer to such globally convex-like shapes as near-convex. Motivated by this, we derive Hadwiger Shape Priors from Hadwiger's theorem as an interpretable global regularizer using three 2D measures: area A, perimeter P, and Euler characteristic chi, enabling transfer across organs and modalities. However, because medical datasets are shape-heterogeneous, enforcing near-convex priors uniformly can over-regularize non-convex anatomy with significant concavities, washing out concavities and fine details and degrading segmentation accuracy. To address this challenge, we propose Conflict-Aware Objective Balancing (CAOB), which integrates shape priors with segmentation in a gradient-aware manner. For each prior, CAOB removes only the gradient component that conflicts with segmentation while preserving the remaining aligned component, and adaptively regulates objective influences to prevent prior dominance. This enables stable use of shape priors on shape-heterogeneous data without erasing genuine concavities or fine structural details. We call this plug-and-play framework HadBalance.

25.
arXiv (CS.AI) 2026-06-11

Search Discipline for Long-Horizon Research Agents

arXiv:2606.11522v1 Announce Type: new Abstract: Autoresearch agents now propose, evaluate, and select scientific candidates against a metric, and that metric is usually an aggregate reduced over a heterogeneous space of regions, slices, or cohorts. We show that when scientific validity lives in that disaggregated structure, the aggregate can rank the wrong candidate first. The headline number improves while the structure underneath inverts, so a decision made on the number accepts a candidate that quietly breaks the model. The failure is not domain-specific. It appears wherever a candidate's validity is multi-dimensional but its verifier is a single reduction. We demonstrate the inversion on a fire-model task in the Ecosystem Demography model. The highest-scoring candidate and a slightly lower one are within noise of each other on global score, yet the top-scoring one collapses the protected boreal regions while the other preserves them. What separates them is the per-region behavior, not the headline number. This decision should not be left to the agent that produced the candidates. The agent optimizing the score is the last party likely to catch the score being wrong, and a prompt has no remaining turn once the agent has stopped. We move the decision to an external control loop that audits each candidate on its disaggregated behavior and acts after the agent has decided. It can demote a candidate the agent would have accepted, and it can reopen a run the agent had declared finished. Our contribution is the inversion finding itself, and a search-discipline protocol that decides on reviewable candidate-effect evidence instead of the score.