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01.
arXiv (CS.AI) 2026-06-16

Adaptive and Explicit safe: Triggering Latent Safety Awareness in Large Reasoning Models

arXiv:2606.16808v1 Announce Type: new Abstract: While Large Reasoning Models (LRMs) excel at complex tasks, they remain highly vulnerable to sophisticated jailbreaks and direct harmful queries. To address this vulnerability, prior works depend heavily on external manual data annotation for safety alignment. However, we observe that LRMs can inherently identify safety risks when being re-presented with original queries alongside their own reasoning trajectories – a capability we term Latent Safety Awareness. To leverage this safety awareness, we first employ Supervised Fine-Tuning (SFT) to explicitly induce safe tags to trigger safety analysis and guidance following the initial reasoning content for unsafe queries, while preserving standard responses for general queries to ensure adaptive triggering. Subsequently, we apply Direct Preference Optimization (DPO) to further enhance the correctness and stability of the safety analysis and guidance. Notably, responses required for both training stages are entirely generated by models being optimized. With (Safe Trigger) SFT and DPO, experimental results demonstrate significant safety enhancement. For example, the Attack Success Rate (ASR) of DeepSeek-R1-Distill-Llama-8B, on average, drops 24.65% and 36.72% on harmful and jailbreak benchmarks, respectively. Finally, our Safe Trigger method exerts almost no negative impact on general performance or user experience.

02.
arXiv (CS.LG) 2026-06-15

SemPiper: Interactive Code Synthesis for Semantic Operators in Machine Learning Pipelines

arXiv:2606.14361v1 Announce Type: new Abstract: Machine learning (ML) pipelines require extensive data preparation, feature engineering, and integration across heterogeneous sources, making them tedious and error-prone to develop. While large language models (LLMs) have recently shown promise for assisting programming tasks, chat-based interfaces provide limited control over pipeline behavior and often produce code that is difficult to optimize or integrate into production systems. We demonstrate SemPipes, a novel programming model that extends ML pipelines with declarative, LLM-powered semantic data operators. SemPipes allows developers to specify high-level natural language instructions for data-centric operations, while seamlessly combining these operators with arbitrary Python code from standard data science libraries. For the semantic operators, it synthesizes specialized implementations at pipeline training time, conditioned on dataset characteristics and pipeline context, enabling the flexible yet controlled integration of LLM capabilities. We demonstrate SemPipes through SemPiper, an interactive interface that visualizes computational graphs of the pipelines, synthesized operator implementations, and optimization trajectories produced by an evolutionary search procedure. Attendees can explore three end-to-end scenarios, modify pipelines, inspect generated code, and observe how semantic operators are synthesized and iteratively optimized. The demonstration highlights how declarative semantic operators enable controllable, optimizable, and practical integration of LLMs into ML pipeline development.

03.
arXiv (CS.LG) 2026-06-12

Disentangling Dynamical Systems: Causal Representation Learning Meets Local Sparse Attention

arXiv:2603.14483v2 Announce Type: replace Abstract: Parametric system identification methods estimate the parameters of explicitly defined physical systems from data. Yet, they remain constrained by the need to provide an explicit function space, typically through a predefined library of candidate functions chosen via available domain knowledge. In contrast, deep learning can demonstrably model systems of broad complexity with high fidelity, but black-box function approximation typically fails to yield explicit descriptive or disentangled representations revealing the structure of a system. We develop a novel identifiability theorem, leveraging causal representation learning, to uncover disentangled representations of system parameters without structural assumptions. We derive a graphical criterion specifying when system parameters can be uniquely disentangled from raw trajectory data, up to permutation and diffeomorphism. Crucially, our analysis demonstrates that global causal structures provide a lower bound on the disentanglement guarantees achievable when considering local state-dependent causal structures. We instantiate system parameter identification as a variational inference problem, leveraging a sparsity-regularised transformer to uncover state-dependent causal structures. We empirically validate our approach across four synthetic domains, demonstrating its ability to recover highly disentangled representations that baselines fail to recover. Corroborating our theoretical analysis, our results confirm that enforcing local causal structure is often necessary for full identifiability.

04.
arXiv (CS.LG) 2026-06-17

Bounded Difference Concentration for Infinitely Exchangeable Sequences with Applications to AI Benchmark Uncertainty

arXiv:2606.17426v1 Announce Type: cross Abstract: We consider the concentration properties of functions of infinitely exchangeable random variables. By conditioning on the de Finetti directing measure, we show that the deviation of any function with bounded-difference constants $c_1, \dots, c_n$ decomposes into a conditional sampling fluctuation and a latent mixture fluctuation. When this latent mixture is $\sigma_{\mathrm{mix}}^2$-subgaussian, we establish a concentration inequality with an effective variance proxy of $\frac{1}{4}\sum_i c_i^2 + \sigma_{\mathrm{mix}}^2$. Crucially, we demonstrate that for zero-sum linear contrasts, such as the difference between a subsample mean and a full population mean, the latent mixture term cancels exactly. This cancellation yields a tight, mixture-free Hoeffding-type bound that provides a direct de Finetti mechanism for the infinite-extendibility limit of recent finite-exchangeable concentration results. We apply this framework to quantify uncertainty in composite AI benchmarks, such as MMLU, where question items naturally exhibit exchangeable dependence across domains. Our results provide both a domain-stratified hierarchical model for bounding the uncertainty of accuracy scores, and a distribution-free, cost-saving statistical guarantee for accurately estimating full benchmark scores from random subsets.

05.
arXiv (CS.LG) 2026-06-16

Robust Neural Tucker Factorization with Bias Correction and Adaptive Initialization

arXiv:2606.16388v1 Announce Type: new Abstract: High-dimensional incomplete (HDI) tensors are widely used in traffic and climate applications, but sparse observations make accurate completion difficult. The intrinsic non-linear dynamics and non-stationary variations across distinct multi-modal fields severely hinder the efficacy of conventional linear reconstruction frameworks. Neural Tucker factorization provides an effective framework for modeling high-order interactions among tensor modes. By parameterizing underlying structural characteristics into continuous latent spaces, neural representations circumvent the rigid low-rank constraints of classical algebra. However, its performance can still be affected by implementation-level choices, especially parameter initialization and the bias configuration of the final output mapping. Suboptimal initializations frequently lead to variance explosion across the cubically expanded interaction spaces, driving the subsequent non-linear activation boundaries into severe gradient saturation zones, while the omission of a dedicated translation parameter forces interaction weights to implicitly absorb global statistical deviations. This paper proposes a simple yet effective neural Tucker factorization model with Kaiming initialization and bias correction (KaBiN) for HDI tensor completion. The proposed model utilizes Kaiming uniform initialization for the embedding and Tucker linear parameters, and adopts a simple bias correction in output mapping. By elegantly decoupling global mean shifts from local structural representations, the framework provides a highly stable and well-conditioned optimization landscape. Experiments on three real-world HDI tensor datasets show that KaBiN achieves better performance than the original NeuTucF, while introducing minimal computational overhead.

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

SenFlow: Inter-Sentence Flow Modeling for AI-Generated Text Detection in Hybrid Documents

Sentence-level AI-generated text detection (S-AGTD) for hybrid documents, where humans and LLMs co-author one text, faces two gaps: existing methods classify each sentence in isolation, discarding inter-sentence dependencies, and existing benchmarks omit the newest generation of generators. We construct MOSAIC, a benchmark of 16,000 hybrid documents over PubMed and XSum, generated by DeepSeek-V3.2 and Kimi K2 under stringent quality controls including a perplexity-consistency filter absent from prior benchmarks. We recast S-AGTD as structured prediction over the document sentence sequence and instantiate it as SenFlow, integrating graph-based inter-sentence propagation with linear-chain CRF decoding in a single document-level pass over a sentence graph. SenFlow reaches state-of-the-art performance on MOSAIC, with a +4.15 pp average Macro-F1 margin on cross-domain transfer, the hardest of three protocols of increasing difficulty. We further find that even after the perplexity filter equalizes overt cues, AI insertions retain a generator-dependent sentence-length gap that sentence-level detectors still exploit. Code and data: https://github.com/luojingkun22/SenFlow

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

Least-Action-Guided Diffusion for Physical Extrapolation

arXiv:2606.11277v1 Announce Type: new Abstract: Reliable extrapolation remains a central challenge for generative models in computational physics, because models trained over finite ranges of time, parameters, or geometries may produce physically inconsistent predictions outside the training distribution. We introduce a least-action-principle-guided diffusion, LAPG, a framework that promotes physical consistency during inference rather than relying solely on constraints imposed during training. The method combines a conditional score-based diffusion model with an action-derived physical guidance score. In the first stage, the learned score model generates an in-distribution proposal; in the second, an action-based variational prior refines this proposal toward the target out-of-distribution condition. This formulation turns the principle of least action into a differentiable inference-time correction mechanism and provides an alternative to pointwise residual penalties that often require empirical loss balancing. We evaluate LAPG on representative ordinary- and partial-differential-equation systems, including free fall, conservative and dissipative spring-mass dynamics, interacting point vortices, and potential flow over parameterized airfoils. In temporal, parameter, and geometric extrapolation tests, LAPG reduces phase drift, preserves dissipative decay, captures vortex motion, and improves the lift response of airfoil flows compared with training-time physics-informed baselines.

08.
arXiv (CS.LG) 2026-06-11

Efficient Multinomial Logistic Bandit via Frequent Directions

arXiv:2606.11968v1 Announce Type: new Abstract: This paper studies efficient online algorithms for multinomial logistic bandits (MLogB), where the feedback distribution over $K+1$ outcomes follows a multinomial logistic model of $d$-dimensional action vectors. A representative UCB-type algorithm, OFUL-MLogB, achieves a regret bound of $\tilde{\mathcal{O}}(Kd\sqrt{T})$, but still requires $\mathcal{O}(K^3d^3)$ time and $\mathcal{O}(K^2d^2)$ space per round due to parameter estimation and optimistic reward construction, which is prohibitive in high-dimensional settings. To address this limitation, we propose EOFD-MLogB, which integrates frequent directions matrix sketching into OFUL-MLogB. By maintaining a low-rank SVD sketch of the accumulated Hessian, constrained online Newton updates in parameter estimation and $Kd \times K$ spectral-norm computations in the reward bonus are reduced to one-dimensional root-finding tasks and $K \times K$ eigenvalue computations, respectively. This yields dominant per-round time complexity $\mathcal{O}(Kd(m+K)^2)$ and space complexity $\mathcal{O}(Kd(m+K))$, where $m \ll d$ is the sketch size. We further prove a regret bound of $\tilde{\mathcal{O}}(\Delta_T(Kd\ln\Delta_T+m)\sqrt{T})$, where the sketching error factor $\Delta_T$ is controlled by the $m$-truncated spectral tail of the Hessian. Thus, when the Hessian is approximately low-rank, the regret is close to that of OFUL-MLogB. Experiments validate the computational efficiency and competitive performance.

09.
arXiv (CS.AI) 2026-06-17

Quantum Cinema: An Interactive Cinematic Exploration of Quantum Computing Hardware via Generative World Models

arXiv:2606.17102v1 Announce Type: cross Abstract: Quantum computing promises transformative advances across science and industry, yet the physical hardware that enables these computations remains invisible to the public: quantum processors operate inside sealed dilution refrigerators at temperatures near absolute zero, making direct observation impossible. This "imagination gap" between quantum computing's growing societal impact and the public's ability to visualize it represents a significant barrier to quantum literacy and workforce development. We present Quantum Cinema, an open-source, browser-based interactive application that closes this gap by transforming invisible quantum hardware into explorable, cinematic experiences using generative world models. Quantum Cinema guides users through a four-act narrative – from the foundational Nobel Prize-winning science of quantum entanglement, through curated video introductions to three major quantum computing architectures (trapped-ion, neutral-atom, and superconducting systems), into immersive three-dimensional generative worlds that make invisible quantum phenomena observable, and finally to interactive radar-chart comparisons grounded in real quantum device specifications. All three-dimensional environments are generated using WorldLabs' generative world model platform and are scientifically grounded in curated metrics from Amazon Web Services (AWS) Braket quantum hardware. Quantum Cinema requires no installation, no specialized hardware, and no quantum computing background. It is designed to serve two distinct communities: scholars and developers seeking to replicate or extend the platform, and educators, researchers, and science communicators seeking an intuitive tool for explaining quantum hardware to diverse audiences. This paper describes the system architecture, the generative world model pipeline, use cases for both communities, and directions for future work.

10.
bioRxiv (Bioinfo) 2026-06-21

DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads

Accurate coding sequence prediction in short prokaryotic metagenomic reads remains challenging due to sequence fragmentation, unknown sequence origins, and sequencing errors. Here we introduce DeepCDS, a deep learning-based ab initio coding sequence predictor trained on short prokaryotic sequences with and without simulated Illumina-like sequencing errors. DeepCDS integrates ESM-2 protein language model embeddings with nucleotide-level information to predict complete and fragmented coding sequence regions. Benchmarking on 215 phylogenetically diverse prokaryotic organisms demonstrates that DeepCDS consistently outperforms current state-of-the-art methods in coding sequence detection, start and stop codon localization, and robustness to different sequencing error profiles, while remaining operational at shorter sequence lengths than existing tools support. These findings demonstrate that protein language models capture distinct signals relevant for nucleotide-level coding sequence detection, especially at very short lengths. Ultimately, DeepCDS may help uncover the functional potential of the vast microbial diversity that remains genomically uncharacterized.

11.
arXiv (CS.CV) 2026-06-16

Bridging Geographic Bias in Urban Streetscape Inference via Lifelong Learning with Visual-Semantic Pivoting

Authors:

Visual perception of urban streetscapes underpins evidence-based decisions in landscape planning, public health, and place-making. Yet models trained on a few well-photographed metropolises systematically misjudge underrepresented districts, propagating geographic bias into downstream policy. We address this gap with HVSP-LL, a lifelong learning framework that couples a stratified visual-semantic pivoting module with an equity-aware rehearsal mechanism. The pivoting module organises landscape concepts along a three-tier ontology (macro structure, meso composition, micro element) and aligns image features to learnable semantic anchors at each tier, providing transferable representations that resist distributional drift. The lifelong adaptation component sequentially absorbs new urban regions while constraining inter-region perception gaps through a worst-region sample-reweighting objective and a structurally-aware exemplar buffer. We evaluate HVSP-LL on a panoramic streetscape benchmark assembled from twelve cities across four continents and seven perceptual dimensions. The framework attains 0.834 Spearman correlation on the held-out city sequence, an absolute 6.1 point improvement over the strongest continual baseline, and shrinks the inter-city perception gap to 0.094 – a 38% reduction relative to the strongest continual baseline (0.151) and a 57% reduction relative to a representative regularisation baseline (0.218). Ablations confirm that each tier of the pivoting hierarchy contributes monotonically, and the equity-aware rehearsal converts mean backward transfer from -0.038 (without retention) to +0.013, eliminating catastrophic forgetting on the held-out sequence. Our results indicate that hierarchical anchoring is a practical pathway toward geographically equitable streetscape inference at city scale.

12.
arXiv (CS.LG) 2026-06-17

Conditional Attribution for Root Cause Analysis in Time-Series Anomaly Detection

arXiv:2604.17616v3 Announce Type: replace Abstract: Root cause analysis (RCA) for time-series anomaly detection is critical for the reliable operation of complex real-world systems. Existing explanation methods often rely on unrealistic feature perturbations and ignore temporal and cross-feature dependencies, leading to unreliable attributions. We propose a conditional attribution framework that explains anomalies relative to contextually similar normal system states. Instead of using marginal or randomly sampled baselines, our method retrieves representative normal instances conditioned on the anomalous observation, enabling dependency-preserving and operationally meaningful explanations. To support high-dimensional time-series data, contextual retrieval is performed in learned low-dimensional representations using both variational autoencoder latent spaces and UMAP manifold embeddings. By grounding the retrieval process in the system's learned manifold, this strategy avoids out-of-distribution artifacts and ensures attribution fidelity while maintaining computational efficiency. We further introduce confidence-aware and temporal evaluation metrics for assessing explanation reliability and responsiveness. Experiments on the SWaT and MSDS benchmarks demonstrate that the proposed approach consistently improves root-cause identification accuracy, temporal localization, and robustness across multiple anomaly detection models. These results highlight the practical utility of conditional attribution for explainable anomaly diagnosis in complex time-series systems. Code and models are available at: https://github.com/dfki-av/Conditional-Attribution-for-Root-Cause-Analysis-in-Time-Series-Anomaly-Detection.

13.
arXiv (CS.CV) 2026-06-18

Optimizing Incomplete, Large-Scale and Sparse Multi-Graph Matching in Bioimaging

Multi-graph matching is a fundamental problem in computer vision. Our work is motivated by a challenging application in bioimaging, where dozens or even hundreds of 3D microscopy images of worms must be brought into correspondence. Existing datasets do not cover this large-scale regime, and virtually all existing methods are inapplicable because they assume a complete or dense problem setting. To support further research, our first contribution is a new large-scale dataset based on problem instances from bioimaging. Our second contribution is a comprehensive analysis of the two main multi-graph matching paradigms: direct and permutation synchronization-based formulations. We argue, in part by proof, that practical large-scale methods must explicitly address problem sparsity and incompleteness. Since standard permutation synchronization approaches fail in this setting, we further introduce a sparse permutation synchronization paradigm. Our final contribution is GREEDA, a general method for sparse and incomplete problems that can be instantiated across cost orders and paradigms. While our paper focuses on objective functions up to quadratic order, GREEDA is inherently generalizable to arbitrary orders. On larger, sparse instances, GREEDA outperforms competing methods in both objective value and runtime. For example, for moderately-sized problems based on 30 worm images GREEDA produces a high-quality solution within 2 minutes, whereas competitors require at least half an hour and yield far worse results. On smaller dense problems, GREEDA remains on par with leading methods while being an order of magnitude faster.

14.
arXiv (CS.LG) 2026-06-18

Spatiotemporal downscaling and nowcasting of urban land surface temperatures with deep neural networks

arXiv:2605.13566v2 Announce Type: replace Abstract: Land Surface Temperature (LST) is a key variable for various applications, such as urban climate and ecology studies. Yet, existing satellite-derived LST products provide either high spatial or high temporal resolution, resulting in a fundamental trade-off between the two. To address this trade-off, we combine observations from a geostationary and a polar orbiting satellite and provide LST fields at high spatial and high temporal resolution (1 km at 15-min intervals). We demonstrate their application for intraday forecasting of LSTs. To estimate LST fields at high spatiotemporal resolution, a U-Net model is trained to map LST fields from SEVIRI/MSG (3 km and 15 min resolution) to LST fields from Terra/Aqua MODIS (1 km, 4 overpasses per day) that are collocated in space and time. The presented model has been trained on LSTs across large European cities with a population exceeding 1 million inhabitants, and achieves an RMSE = $1.92${\deg}C and near-zero bias MBE = $0.01${\deg}C on the hold-out test set. As a second step, we present an LST nowcasting model based on ConvLSTM architecture, trained across downscaled LST fields with forecast lead times of 15 to 75 minutes. The nowcasting model outperforms a persistence and a Climatological Rolling Median benchmarks, with RMSEs of $0.57$ to $1.15${\deg}C for the considered lead times and biases ranging from $-0.1$ to $0.14${\deg}C. An additional validation conducted against independent MODIS overpasses confirms robust performance. Our LST forecast model at high spatiotemporal resolution is directly applicable to operational satellite-based LST monitoring.

15.
Nature (Science) 2026-06-10

The Amazon can be saved — with concerted action inside and outside Brazil

Authors: Unknown Author

As deforestation in the Amazon falls, fresh evidence shows that the rainforest can withstand global warming, but only if there is a worldwide effort to stop cutting it down. As deforestation in the Amazon falls, fresh evidence shows that the rainforest can withstand global warming, but only if there is a worldwide effort to stop cutting it down.

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

LEAP: Layer-skipping Efficiency via Adaptive Progression for Vision Transformer Distillation

Vision Foundation Models (VFMs) with Vision Transformer (ViT) backbones, such as DINOv2, have become essential for downstream tasks like object recognition and semantic segmentation. The immense computational requirements of backbones often necessitate distillation into smaller architectures for edge deployment. Feature-based knowledge distillation (KD) often suffers from the teacher-student gap; the student struggles to imitate teacher's complex feature map due to its limited capacity. To mitigate this bottleneck, we propose LEAP: Layer-skipping Efficiency via Adaptive Progression, a training curriculum for ViT feature-based knowledge distillation. By utilizing the teacher's intermediate feature maps as a sequence of progressively more difficult targets, our curriculum allows the student to build a foundational representation before tackling higher-level abstractions. Our results demonstrate that this paradigm significantly accelerates convergence through adaptive difficulty selection across various student model sizes and dataset scales. With our curriculum, the LEAP-distilled ViT-S achieves 90.1% accuracy on ImageNet-100, a +12.24% improvement compared with baseline. On ImageNet-1K, LEAP achieves +3.84% and +7.75% improvement for the instance retrieval task on the Oxford and Paris datasets, respectively. Furthermore, the curriculum enables 25.1% savings in training FLOPs and 21% savings in training time on ImageNet-100 by implementing early-stopping for teacher inference during the initial stages of training. Code is available at https://github.com/KevinZ0217/LEAP

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

ISE: An Execution-Grounded Recipe for Multi-Turn OS-Agent Trajectories

Training capable OS agents requires data that simultaneously captures structured user intents, multi-turn task delegation, and grounded tool execution–properties absent from existing datasets. We propose ISE (Intent -> Simulate -> Execute), a three-stage synthesis paradigm that addresses these gaps jointly. Stage 1 constructs roughly 50000 structured intents via a 4D framework (Persona x Domain x Task x Complexity); after deduplication the pool contains 43956 unique intents and attains a Vendi Score of 61.57 over the entire pool on mpnet-base-v2 embeddings (cosine kernel, q=1). Stage 2 drives multi-turn user-agent interaction through a role-locked user simulator that grounds each user turn in actual execution outcomes, producing 23132 complete trajectories averaging 8.12 user turns and 68.24 total dialogue turns. Stage 3 runs every tool call inside a live, isolated OS workspace, generating authentic failure-recovery dynamics instead of simulated responses. Fine-tuning on ISETrace improves ClawEval pass@1 from 19.3 to 37.7 using Qwen3-8B on agent tool-use tasks with a standard protocol. This result outperforms zero-shot GPT-4o and the larger Qwen3-32B base model which is four times bigger. An ablation on Stage 2 proves multi-turn simulation brings a large portion of the performance gain. We release all source code and dataset at https://github.com/Valiere01/ISE-Trace.

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

Flood and Harvest: The Provable Necessity of Trivia for Generating Valuable Mathematics via the Lens of Language Generation in the Limit

AI systems coupled to proof assistants now generate formal mathematics at scale, and the gap between what a checker can verify and what a mathematician would value has become the binding constraint. We model the generation of valuable mathematics as nested language generation in the limit: a verifiable formal language $F$, accessed through a membership oracle (the proof checker), contains an unknown valuable language $H \in \mathcal{H}$ revealed only through an adversarial enumeration of a core $C \subseteq H$ of exact density $\alpha$ (the literature). Every output is valuable ($\in H$), trivial ($\in F \setminus H$), or a hallucination ($\notin F$). We settle four questions. First, the verifier is not taste: the collections admitting generation with breadth are exactly those of the oracle-free model, characterized fiber-wise by Angluin's condition. Second, the verifier does buy sound coverage, covering all unseen valuable statements while asserting only valid ones: possible with it, impossible without it; it relocates unavoidable errors from false to trivial. Third, and centrally, a sharp dichotomy on the tight family: generators emitting finitely many trivia achieve optimal coverage $\alpha/2$, while any infinite trivia allowance, even at vanishing rate, jumps the optimum to $1-\alpha/2$ (both tight, for cores presented as the candidate intersection), and one generator attains both ends. The transition is in trivia count, not rate; the gap $1-\alpha$ is the unrecorded mass. Fourth, both regimes instantiate in a compression model of mathematics. A perfect verifier cannot substitute for taste: the unbounded stream of correct-but-worthless statements is not an engineering accident but a provable necessity, since covering unrecorded valuable mathematics requires an infinite, but asymptotically negligible, stream of certified trivia.

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

Quantile of Means: A Bonus-Free Ensemble Method for Minimax Optimal Reinforcement Learning

arXiv:2606.20107v1 Announce Type: new Abstract: Optimal Reinforcement Learning (RL) algorithms typically rely on carefully constructed count-based uncertainty estimates to drive exploration. Although theoretically sound, such estimates are hard to compute in practical settings and therefore offer limited insight for designing exploration heuristics. Meanwhile, ensembling has emerged as a practical approach, but remains without theoretical justification. Building on a recent ensemble-based method for Multi-Armed Bandits, we propose a quantile-based ensemble method for finite-horizon Markov Decision Processes (MDPs). Our simple count-free approach achieves optimal variance-dependent regret bounds, providing theoretical grounding for ensemble-based exploration in RL.

20.
bioRxiv (Bioinfo) 2026-06-11

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele- and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

21.
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.

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

Revisiting LLM Adaptation for 3D CT Report Generation: A Study of Scaling and Diagnostic Priors

Recent advances in multimodal learning, including large language models (LLMs) and vision-language models (VLMs), have demonstrated strong adaptability to natural images. However, extending their use to the medical domain, particularly for volumetric (3D) images, is challenging due to high computational complexity, volumetric dependencies and the semantic gap between visual features and clinical terminology. Naively fine-tuning LLMs on limited medical data often leads to overfitting and clinical hallucination, where linguistic fluency is prioritized over clinical factuality. In this study, we investigate parameter-efficient adaptation strategies for volumetric CT report generation and introduce RAD3D-Prefix, a lightweight diagnostic-prior conditioning framework that minimizes the need for extensive parameter training. This module integrates image embeddings with multi-label diagnostic classification logits, preserving critical clinical details while bridging the semantic gap. By keeping the LLM frozen, our method requires minimal trainable parameters and mitigates the risk of overfitting on small, domain-specific datasets. Through a systematic study spanning LLMs from 96.1M to 1.6B parameters, we find that fine-tuning is most beneficial for smaller LLMs, whereas freezing larger (~1B+ LLMs and training only lightweight projection layers provides a superior trade-off between performance, generalization, and computational efficiency. Across multiple automatic metrics and a clinical reader study, RAD3D-Prefix outperforms comparable parameter-efficient baselines and demonstrates strong out-of-domain generalization while using substantially fewer trainable parameters than fully fine-tuned alternatives.

23.
arXiv (CS.CL) 2026-06-18

Trade-offs in Medical LLM Adaptation: An Empirical Study in French QA

The development of large language models (LLMs) has led to an increased focus on their adaptation to specialized domains and languages, yet the effectiveness of domain adaptation strategies remains unclear. We present a study of medical domain adaptation using French medical question-answering (QA) as a case study. We compare continual pretraining (CPT), supervised fine-tuning (SFT), and their combination across three model families, multiple sizes, and three initialization types, explicitly disentangling adaptation effects from base model choice. We evaluate both multiple-choice (MCQA) and open-ended QA (OEQA) under greedy and constrained decoding using automatic metrics and LLM-as-a-Judge evaluation. For MCQA, CPT+SFT most often achieves the best scores, but gains over SFT are small and frequently not statistically significant, making SFT a strong and cost-effective default. For OEQA, CPT consistently improves overlap-based metrics, while SFT often degrades generation quality; instruction tuning and CPT+SFT are preferred by LLM-based evaluation. Cross-lingual experiments further show effective transfer from French adaptation to English benchmarks. Overall, we provide practical guidelines for selecting adaptation strategies under computational constraints.

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

Prediction of Runtime Parameters of Parallel Chemistry Applications via Active and Generative Learning

arXiv:2606.16226v1 Announce Type: new Abstract: In this work, we develop two main Machine Learning based approaches to predict the runtime parameters of highly scalable parallel chemistry computations.These approaches employ active and generative learning together with the empirically determined gradient boosted regression tree models chosen among a rich suite of machine learning models. When evaluated on Coupled-Cluster with Singles and Doubles computations, our models achieve a mean absolute error percentage (MAPE) as low as 0.023 and a coefficient of determination as high as 99.9%. Furthermore, when combined with active learning to mitigate the lack of large amounts of training data, our models score a MAPE about 0.2 with 20-25% of the original dataset.

25.
arXiv (CS.CL) 2026-06-16

Dealing with Annotator Disagreement in Hate Speech Classification

Hate speech detection is a crucial task, especially on social media where harmful content can spread quickly. Collecting social media content (tweets etc.) to train machine learning models is easy, but detecting and categorizing hate speech can be difficult due to the inherently subjective nature. This subjectivity leads to frequent disagreement among annotators, particularly for subtle or borderline content. Traditional approaches either discard non-consensus samples or force a ''gold standard'' through expert adjudication, ignoring valuable information about uncertainty and diverse human perspectives. We examine the largely overlooked problem of annotator disagreement in hate speech classification and evaluate a range of aggregation methods, including majority voting, ordinal strategies (minimum, maximum, and mean), and analyze their impact across binary, 4-class, and 6-class classification tasks. In addition, we leverage annotators' perceived hate speech strength scores to explore regression-based and hybrid modeling approaches. Among others, we show that filtering non-consensus samples results in over-optimistic results and that the perceived strength provides a complementary signal that enhance classification performance. Finally, we establish new state-of-the-art results for hate speech detection in Turkish tweets, and demonstrate that annotator disagreement, when properly modeled, is a valuable resource for building more robust and reliable systems.