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01.
arXiv (CS.CV) 2026-06-18

Do as I Do: Dexterous Manipulation Data from Everyday Human Videos

How can we scalably generate data for robotic manipulation, especially on human-like platforms such as dexterous multi-fingered hands? Learning from human videos has recently emerged as a likely answer to this question. However, difficulties in estimating hand-object interaction and crossing the human-to-robot embodiment gap have hindered the adoption of abundant monocular RGB-only human videos as the primary source of robot manipulation data. In this work, we present DO AS I DO, an algorithm to reconstruct and retarget monocular RGB human videos to multi-fingered dexterous robotic hands. DO AS I DO reconstructs hand-object interactions from various egocentric and exocentric in-the-wild video sources. The algorithm then retargets these hand-object interaction estimates into a sequence of actions executable in the real world, yielding robot-complete manipulation data from disparate human videos. Overall, DO AS I DO outperforms previous state of the art in estimating hand-object interactions and extracting dexterous manipulation trajectories from RGB videos, as we show in experiments on datasets with ground truths and on a dataset of video clips collected online. Our experiments enable us to propose an efficacy playbook for practitioners collecting human data for manipulation.

02.
arXiv (CS.CL) 2026-06-12

Structuring The Future: Diffusion LLM Speculative Decoding via Calibrated Draft Graphs

Diffusion LLMs (dLLMs) have recently emerged as a powerful alternative to autoregressive LLMs (AR-LLMs) with the potential to operate at significantly higher token-generation rates. To unlock this potential, we present Spiffy, a speculative decoding algorithm to accelerate dLLM inference while provably preserving the model's output distribution. This work addresses the unique challenges involved in applying ideas from speculative decoding of AR-LLMs to dLLMs. Spiffy performs auto-speculation to eliminate the overheads of an independent draft model, structuring draft states in the form of a novel directed draft graph to take advantage of the bidirectional, blockwise nature of dLLM generation. These draft graphs are calibrated offline to maximize acceptance rates and are dynamically pruned during inference for improved computational efficiency. We present a detailed formulation of Spiffy and demonstrate its ability to accelerate LLaDA, Dream, and SDAR models in combination with KV caching and threshold-based dynamic unmasking leading to up to $8.6\times$ reduction in model inferences and $6.3\times$ acceleration in token rate.

03.
arXiv (quant-ph) 2026-06-12

Testing the problem of time with cold atoms

arXiv:2509.07745v3 Announce Type: replace-cross Abstract: We realize a cold-atom system to quantitatively test relational constructions of time. A well-isolated atomic Bose-Einstein condensate evolves in a conservative trap that is partitioned by a thin optical barrier into an observed and unobserved sector, with negligible dissipation on the experimental timescale. Motivated by relational-time approaches discussed in the Wheeler-DeWitt framework, we ask whether the dynamics of the observed sector can be ordered using only internal degrees of freedom. To this end, we construct an entropic time from an experimentally defined coarse-grained entropy, and demonstrate that it can robustly order the events in the observed sector across repeated cycles of expansion and recollapse. We finally derive an effective Schroedinger equation parameterized by this internal time and show that it is able to reproduce the measured evolution. These results establish a controlled experimental setting in which relational-time constructions can be quantitatively tested.

04.
bioRxiv (Bioinfo) 2026-06-10

Is level-1 blob reconstruction under the network multispecies coalescent easy?

作者:

Hybridization is an important evolutionary process, commonly modeled by the network multispecies coalescent. Reconstructing evolutionary histories under this model is notoriously costly, even for level-1 networks where hybridization events are isolated from each other. The widely used methods that combine speed with statistical guarantees rely on quartet concordance factors computed for all subsets of four species, resulting in an o(n^4k) bottleneck that severely limits scalability to large numbers of species (n) and genes (k). Among quartet-based methods, NANUQ+ is notable because it decomposes the problem into two steps: first reconstructing a tree of blobs, which compresses each non-treelike part of the network, called a blob, into a single vertex, and second reconstructing the internal structure of each level-1 blob, specifically its circular order and hybrid vertex. Here, we investigate whether level-1 blob reconstruction is difficult once the tree of blobs is known. We present a fast and statistically consistent algorithm, called NetCS, based on two simple primitives: majority voting and merge sort, circumventing the bottleneck of computing all quartet concordance factors. In simulations, NetCS achieved comparable accuracy to NANUQ+ and was dramatically faster, enabling analyses of 200 taxa and 1000 genes in only a few minutes. Both methods attained near-perfect accuracy when given the true tree of blobs; however, their performance degraded in end-to-end pipelines due to errors in tree of blobs reconstruction. Strikingly, even methods that reconstruct level-1 networks directly struggled to accurately predict hybrid ancestry. Our results suggest that reconstructing level-1 blobs is unexpectedly easy once the tree of blobs is known, and that a major challenge for phylogenetic network inference lies in accurate tree of blobs reconstruction.

05.
arXiv (math.PR) 2026-06-17

Convergence Analysis of the Random Bisection Method

arXiv:2603.20483v2 Announce Type: replace-cross Abstract: We propose a generalized version of the bisection method where the cutting point between the two subintervals is chosen at random following an arbitrary distribution. We compute expected convergence rates with respect to any arbitrary a priori distribution for the position of the root in the initial interval and proved that it depends only on the the expectation $\mathbb{E}[c(1-c)]$ of the cut $c$. We also provide a generalization of the method for $K$ random cuts and study its convergence properties. Most probabilistic derivations are kept fairly simple for the ease of understanding of a larger audience. Our theoretical results are then validated numerically using statistical simulation.

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

Reinforcement Twinning for Hybrid Control of Flapping-Wing Drones

arXiv:2505.18201v2 Announce Type: replace-cross Abstract: Controlling flapping-wing drones requires controllers that handle time-varying, nonlinear, underactuated dynamics from incomplete, noisy sensor data. Recent advances in artificial intelligence (AI), particularly reinforcement learning (RL), have opened new perspectives for addressing such complex control problems through data-driven policy optimization from interaction with the environment. Yet purely data-driven methods are sample-inefficient, demanding extensive, sometimes unsafe exploration, especially without guiding physical models. This motivates hybrid AI-physics frameworks. This article proposes a hybrid model-free/model-based flight-control approach using the reinforcement twinning algorithm. The model-based (MB) component uses an adjoint formulation and an adaptive digital twin continuously identified from live trajectories; the model-free (MF) component uses RL. The two agents share knowledge via transfer learning, imitation learning, and shared experience between the real environment and the digital twin, coordinated by a policy referee that selects which agent acts in reality based on digital-twin performance and a real-to-virtual consistency ratio. The framework is evaluated for the longitudinal control of a flapping-wing drone, modelled as a nonlinear time-varying system driven by quasi-steady aerodynamic forces. The hybrid strategy is tested under three adaptive-model initializations: (1) offline identification from existing data, (2) random initialization with fully online identification, and (3) offline pre-training with biased parameters followed by online adaptation. In all cases, the hybrid framework improves performance, robustness, and sample efficiency over purely model-free and purely model-based approaches.

07.
arXiv (CS.LG) 2026-06-12

From Uncertain Judgments to Calibrated Rankings: Conformal Elo Estimation for LLM Evaluation

arXiv:2606.13221v1 Announce Type: new Abstract: Evaluating new large language models typically requires costly human annotation campaigns at scale. LLM-as-a-judge offers a cheaper alternative, but judge scores carry systematic errors - such as position bias, self-preference, or intransitivity - that can strongly miscalibrate the resulting rankings. We quantify the resulting judge-human disagreement at two complementary levels. At the local level, we estimate per-battle uncertainty from the judge's own score differences by propagating calibrated win probabilities rather than hard labels into the Bradley-Terry procedure. This alone provides a drastic improvement to Elo estimation accuracy, bringing LLM-derived ratings within 17.9 Elo MAE of human-derived ones when averaged over 55 held-out models on LMArena. At the global level, we apply split conformal prediction to the residual gap between LLM-derived and human-derived Elo ratings across held-out models, producing prediction intervals with distribution-free marginal coverage guarantees that account for irreducible LLM-human disagreement. Together, these two layers yield a low-cost evaluation tool that provides developers with calibrated Elo estimates and honest uncertainty bounds, without access to large-scale human annotations.To facilitate reproducibility, we release our code at https://github.com/kargibora/SoftElo .

08.
arXiv (CS.LG) 2026-06-19

Representing Piecewise-Linear Functions by Functions with Minimal Arity

arXiv:2406.02421v2 Announce Type: replace-cross Abstract: Any continuous piecewise-linear function $F\colon \mathbb{R}^{n}\to \mathbb{R}$ can be represented as a linear combination of $\max$ functions of at most $n+1$ affine-linear functions. In our previous paper [``Representing piecewise linear functions by functions with small arity'', AAECC, 2023], we showed that this upper bound of $n+1$ arguments is tight. In the present paper, we extend this result by establishing a correspondence between the function $F$ and the minimal number of arguments that are needed in any such decomposition. We show that the tessellation of the input space $\mathbb{R}^{n}$ induced by the function $F$ has a direct connection to the number of arguments in the $\max$ functions.

09.
arXiv (CS.LG) 2026-06-18

Hierarchical Attention via Domain Decomposition

arXiv:2606.18525v1 Announce Type: new Abstract: We propose a hierarchical attention mechanism based on two-level overlapping Schwarz domain decomposition. The method is motivated by the observation that two-level Schwarz domain decomposition methods combine local subdomain corrections with a coarse level that communicates global, long-range information. We test its usefulness in the context of finite-dimensional operator learning using a simple, one-dimensional diffusion problem with homogeneous Dirichlet boundary conditions. Although elementary, this problem provides a controlled sequence-to-sequence setting in which the exact nonlocal solution operator is known. After discretization, learning the solution operator amounts to approximating the inverse of a symmetric positive definite matrix. As a baseline, we use a global softmax-free low-rank attention operator of the form $QK^T$. The proposed construction replaces this dense global factorization by a two-level additive structure: local low-rank attention blocks on overlapping subdomains are combined with a coarse attention block. The resulting operator has the form $$M_{\theta}^{-1} = \Phi Q_0 K_0^T \Phi^T + \sum_{i=1}^{N} R_i^T D_i^{1/2} Q_i K_i^T D_i^{1/2} R_i.$$ Here $R_i$ restricts to an overlapping subdomain, $D_i$ is a partition-of-unity weight, and $\Phi$ is a coarse interpolation (or prolongation) matrix. Numerical experiments for synthetic Fourier right-hand sides indicate that the domain-decomposition attention operator is able to train faster and can give more accurate approximations than a global low-rank attention baseline while using significantly fewer parameters.

10.
arXiv (CS.LG) 2026-06-16

Context-Aware Markov VAE for CSI Compression in Wireless Systems

arXiv:2606.16607v1 Announce Type: cross Abstract: This paper considers neural channel state information (CSI) compression for time-varying massive multiple-input multiple-output (MIMO) channels in frequency division duplex (FDD) systems with limited feedback resources. The main challenge lies in obtaining a compact and efficient representation of the CSI given that it exhibits strong temporal correlation across successive snapshots. Existing memoryless compression models do not exploit this property, while simple temporal extensions often incorporate multiple observations without explicitly modeling the latent dynamics. We propose a context-aware compression framework based on a k-memory Markov variational autoencoder (k-MMVAE), which uses a finite temporal window to capture the evolution of CSI in the latent space. The model introduces Markov-structured latent dynamics with finite memory, enabling efficient use of temporal dependencies for compression. Simulation results show that the proposed approach improves target CSI reconstruction performance compared to memoryless and weakly sequential baselines, particularly at low and moderate compression rates. These results suggest that explicit latent temporal modeling can provide an effective mechanism for CSI compression under limited feedback constraints.

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

Beyond Predefined Schemas: TRACE-KG for Context-Enriched Knowledge Graph Generation

arXiv:2604.03496v2 Announce Type: replace Abstract: Knowledge graph generation typically relies either on predefined ontologies or on schema-free extraction. Ontology-driven pipelines enforce consistent typing but require costly schema design and maintenance, whereas schema-free methods often produce fragmented graphs with weak global organization, especially in long technical documents with dense, context-dependent information. We propose TRACE-KG (Text-dRiven schemA for Context-Enriched Knowledge Graphs), a framework that jointly constructs a context-enriched knowledge graph and an induced schema without assuming a predefined ontology. TRACE-KG captures conditional relations through structured qualifiers and organizes entities and relations using a data-driven schema that serves as a reusable semantic scaffold while preserving full traceability to the source evidence. Experiments show that TRACE-KG produces structurally coherent, traceable knowledge graphs and offers a practical alternative to both ontology-driven and schema-free construction pipelines.

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

RetailBench: Benchmarking long horizon reasoning and coherent decision making of LLM agents in realistic retail environments

arXiv:2606.15862v1 Announce Type: new Abstract: Large language model (LLM) agents have made rapid progress on short-horizon, well-scoped tasks, yet their ability to sustain coherent decisions in dynamic long-horizon environments remains uncertain. We introduce RetailBench, a data-grounded simulation benchmark for evaluating tool-using LLM agents in single-store supermarket operation. RetailBench models retail management as a partially observable decision process and is designed to support thousand-day-scale simulations. In this environment, agents must manage pricing, replenishment, supplier selection, shelf assortment, inventory aging, customer feedback, external events, and cash-flow constraints. We evaluate seven contemporary LLMs under representative agent frameworks over a 180-day evaluation horizon and compare them with a privileged oracle policy. Results show substantial variation across models: only a small subset survives the full evaluation horizon, and even the strongest LLM runs remain substantially behind the oracle policy in final net worth and sales outcomes. Behavioral analysis attributes these gaps to incomplete evidence acquisition, surface-level decision making, and the lack of a consistent long-horizon policy. RetailBench provides a controlled testbed for studying reliable autonomy in economically grounded long-horizon decision-making.

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

Vibe Coding Ate My Homework: An evaluation of AI approaches to greenfield software engineering and programming

arXiv:2606.18293v1 Announce Type: cross Abstract: Thanks to rapid developments in generative AI, we are in the midst of a paradigm shift that may change how we interact with computers forever. We have observed a growth in the use of natural language prompts to build applications and coding infrastructures without underlying knowledge of the field, and this practice has been dubbed `vibe coding.' It arguably represents what the field of programming has been building towards since the beginning, with every higher level of abstraction that is conceived. Vibe coding promises to be the endpoint for the meta of high-level programming as far as method of input is concerned: eliminating a human's use of code syntax entirely in favour of programming in their mother tongue. This paper aims to evaluate the viability of vibe coding for greenfield software engineering tasks, as well as analyse the benchmarks that have been used to measure its software engineering prowess. To this end, we have developed an evaluation suite for analysing an LLM's proficiency in carrying out simple, isolated greenfield programming tasks in Python to provide scoped insight on the matter.

14.
medRxiv (Medicine) 2026-06-17

Treatment of Multi-Drug-Resistant Tuberculosis with Second-Line All-Oral Drugs in Ghana: Incidence of Adverse Events.

Introduction: The treatment of multidrug-resistant tuberculosis (MDR-TB) remains challenging due to the toxicity of second-line medications and suboptimal treatment outcomes. This study aimed to determine the incidence of adverse events and identify factors associated with these events in patients undergoing treatment for MDR-TB with second-line all-oral drugs in Ghana. Methods: This retrospective cohort study reviewed the medical records of 384 MDR-TB patients treated with second-line all-oral drugs at selected health facilities in Ghana, including the Greater Accra Regional Hospital, Eastern Regional Hospital, and Kumasi South Hospital. Data were extracted using the Kobo Collect tool, capturing patient demographics, baseline clinical and laboratory characteristics, treatment regimens, and adverse events. The study period spanned from 2020 to August 2024. Results: The study included a total of 384 MDR-TB patients, with a mean age of 45 years (SD = 15). The majority of patients were male (65.78%), and most were within the 45-64 years age group (33.85%), followed by those aged 25-44 years (31.25%). Regionally, the highest number of cases were reported from the Greater Accra Region (39.06%), followed by the Eastern Region (31.25%) and Kumasi South Hospital (29.69%). Approximately one in four patients (25%) presented with comorbidities, with HIV being the most common (19.5%). The most frequently reported adverse events were diarrhea (14%), dizziness (13.7%), and vomiting (12.3%). Most of these were mild to moderate in severity and tended to decrease as treatment progressed. Severe adverse events, such as leukopenia and acute kidney injury, were rare, occurring in less than 5% of patients. Over the course of treatment, gastrointestinal adverse events such as vomiting and nausea showed a significant decline, indicating possible patient adaptation or improved clinical management. Results from the multivariate Poisson regression analysis revealed that age and comorbidities were significant predictors of adverse events. Patients aged 65 years and above had a 56% lower risk of developing adverse events compared to younger patients (Adjusted Risk Ratio [aRR] = 0.44, 95% CI: 0.25-0.79, p = 0.005). Conversely, patients with comorbid conditions such as diabetes or hypertension were approximately 2.6 times more likely to experience adverse events compared to those without comorbidities (aRR = 2.65, 95% CI: 1.58-4.43, p < 0.001). The effect of sex was not statistically significant after adjustment (aRR = 1.03, 95% CI: 0.70-1.50, p = 0.86). At the end of the treatment period, 74.9% of patients achieved successful outcomes, including both those who were cured and those who completed treatment without being classified as cured. However, 25.1% had unsuccessful outcomes, which included treatment failure, relapse, or death. Conclusion: In conclusion, adverse events are common in the treatment of MDR-TB with second-line All-Oral drugs, with gastrointestinal adverse events being the most prevalent. These findings highlight the importance of monitoring and managing adverse events to optimize treatment outcomes for MDR-TB patients in Ghana.

15.
arXiv (quant-ph) 2026-06-11

Multipartite reference-frame-independent quantum cryptographic communication

arXiv:2606.12284v1 Announce Type: new Abstract: Reference frame mismatch among communication parties introduces errors in quantum cryptographic protocols. As the number of participants increases, aligning reference frames becomes increasingly difficult, complicating multipartite quantum cryptographic implementations. Here, we theoretically and experimentally investigate multipartite reference-frame-independent (RFI) quantum cryptographic communication using Greenberger-Horne-Zeilinger (GHZ) states. We generalize the bipartite RFI security parameter $C$ to an $N$-party parameter $C_N$ and derive the asymptotic secret key rate expressed solely in terms of experimentally accessible quantities. We analyze the key rate under global and local depolarizing noise models and find that increasing the number of parties $N$ enhances robustness against global depolarizing noise while increasing vulnerability to local channel noise. We also present a proof-of-principle experimental demonstration of four-party RFI quantum cryptographic communication using four-photon GHZ states, confirming the reference-frame invariance of both the $C_4$ parameter and the secret key rate under various reference frame rotations.

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

P-K-GCN: Physics-augmented Koopman-enhanced Graph Convolutional Network for Deep Spatiotemporal Super-resolution

arXiv:2606.19303v1 Announce Type: new Abstract: High-fidelity simulation of spatiotemporal dynamics is computationally prohibitive, necessitating efficient super-resolution techniques to reconstruct high-resolution data from coarse-grained inputs. Traditional data-driven methods often lack physical constraints, and simple physics-informed learning struggles with irregular spatial geometries and intricately evolving temporal dynamics. To tackle these challenges, we propose a Physics-augmented Koopman-enhanced Graph Convolutional Network (P-K-GCN) for spatiotemporal super-resolution on irregular geometries. Specifically, a continuous spline-based GCN is first designed to extract spatial dependencies directly from coarse graph, and Koopman operator theory is incorporated to project the nonlinear dynamics into a compact latent space where temporal progression is linearized. Second, we augment the optimization objective with a physics-based loss to force the data-driven reconstructions to adhere to physical laws for improving predictive fidelity and robustness. Finally, we provide a rigorous theoretical analysis, establishing that the physics augmentation and Koopman regularization mathematically guarantees a reduction in super-resolution error by diminishing Rademacher complexity and tightening generalization bounds. We evaluate our framework on reconstructing spatially high-resolution cardiac electrodynamics across a 3D heart geometry from sparse low-resolution measurements. Numerical experiments demonstrate that our method achieves superior accuracy compared to baseline models.

17.
arXiv (CS.LG) 2026-06-19

GB-LSR: A Fast Local Spectral Image Representation with a Single Global Bandwidth for Continuous Reconstruction and Super-Resolution

arXiv:2606.19617v1 Announce Type: cross Abstract: We present GB-LSR (Global-Bandwidth Local Spectral Representation), a fixed-grid local spectral representation for continuous image reconstruction. The image domain is partitioned into non-overlapping square patches, each carrying coefficients for a truncated Fourier basis predicted from shared convolutional-encoder features. A single trainable scalar bandwidth is shared globally across all patches and images, and reconstruction at any continuous coordinate is a fixed-size basis contraction whose cost is independent of image size. We study three bandwidth-handling variants: a trainable global scalar (main), a fixed global scalar, and a per-patch bandwidth field. On a standardized native-reconstruction benchmark across Kodak, Set14, and Urban100, the main variant outperforms matched-budget amortized LIIF / LTE / WIRE re-implementations by 2.8-3.6 dB PSNR and 0.11-0.15 LPIPS, while running at roughly one-quarter of the slowest baseline's inference cost. The single global scalar suffices empirically: per-patch adaptive-bandwidth alternatives do not improve over it on either a closed-form locality diagnostic or an end-to-end ablation. In a separate arbitrary-scale super-resolution (ASR) extension, GB-LSR achieves competitive PSNR-Y under a canonical-style SR protocol and runs 1.44x faster than LIIF-RDN and 3.25x faster than LTE-SwinIR at x4; within the same extension, a variant trained and evaluated without 4-corner local-ensemble averaging gives a 1.77x speedup with 35% lower peak memory and negligible PSNR change, while additionally widening the RDN encoder from 64 to 96 channels gives a small positive PSNR shift with a 1.58x speedup and 31% lower peak memory. Native-reconstruction claims are scoped to the matched-budget amortized protocol, and ASR claims are scoped to a separate canonical-style SR protocol.

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

Latent-Conditioned Parameterized Quantum Circuits as Universal Approximators for Distributions over Quantum States

arXiv:2605.28690v3 Announce Type: replace-cross Abstract: Many applications in quantum simulation, quantum chemistry, and quantum machine learning require not a single quantum state but an ensemble of states characterizing the heterogeneity of a target system. Preparing such ensembles state-by-state is prohibitive in both variational and fault-tolerant settings, thereby motivating a generative modeling approach. We introduce latent-conditioned parameterized quantum circuits (LPQCs), a hybrid quantum-classical framework in which classical neural networks map a latent variable sampled from a prior distribution to the parameters of a parameterized quantum circuit. We prove that LPQCs are universal approximators for probability measures over density operators in the 1-Wasserstein distance, extending classical universal approximation theorems to the quantum-distribution setting. We additionally introduce a multimodal latent prior and a mixture-of-experts circuit architecture, and show empirically that the latent-conditioned parameterization alleviates the barren plateau problem during optimization, a behavior for which we provide rigorous partial guarantees. Numerical experiments validate the framework on a synthetic multi-cluster ensemble of mixed quantum states and on a QM9-derived ensemble of 3-D molecular structures. In these tasks, LPQC outperforms recent quantum generative baselines and matches the generation quality of a classical neural-network baseline, while requiring an output dimension that grows only linearly with the number of qubits rather than exponentially. By leveraging classical expressivity in the latent space, LPQCs offer a tractable route to quantum generative modeling.

19.
bioRxiv (Bioinfo) 2026-06-11

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individual cells, offering new opportunities to characterize cellular states as integrated biological systems. However, developing a unified framework that can seamlessly integrate diverse omics modalities and remain robust to heterogeneous modality missingness remains challenging. Here we present HoloCell, to our knowledge the first generative foundation model for joint representation learning and generative modeling across all three major single-cell omics modalities, i.e., epigenomics, transcriptomics, and proteomics. HoloCell contains over 860 million parameters and is pretrained on the Human-Multi-Omics-Corpus, which comprises approximately 468 million single-cell profiles across these three omics layers, corresponding to over 425 billion tokens. HoloCell introduces a simple yet biologically grounded hierarchical tokenization strategy that encodes cis-regulatory elements, genes, and proteins as structured tokens within a shared modeling framework. We evaluated HoloCell across single-omics representation learning, paired multi-omics integration, unpaired multi-omics alignment, and cross-modal generation via iterative diffusion and remasking, demonstrating its superior performance and flexibility across diverse omics tasks. From a representation perspective, HoloCell provides a unified digital mapping of cellular states across multiple omics layers, capturing cell heterogeneity as an integrated system. From a generation perspective, its iterative diffusion and remasking framework accounts for the inherently unordered nature of biological features, enabling in silico simulation of multi-omics information flow. Together, these capabilities position HoloCell as a versatile foundation model toward the emerging concept of a virtual cell, offering both systematic characterization and generative simulation of cellular systems within a unified framework.

20.
arXiv (CS.CL) 2026-06-16

DEEPRUBRIC: Evidence-Tree Rubric Supervision for Efficient Reinforcement Learning of Deep Research Agents

Deep research agents synthesize long-form reports by searching and reasoning over retrieved evidence. Reinforcement learning with rubric-based rewards improves these agents by optimizing them against checkable criteria that translate report quality into reward signals, but its efficiency depends on whether those criteria reliably capture the task scope and evidence needs. Most existing studies ask an LLM to generate rubrics for a given query, but when the model fails to infer the underlying information needs, the generated rubrics may be incomplete and reduce RL efficiency. To obtain more reliable query–rubric supervision, we introduce DeepRubric, a data construction framework that reverses this process: instead of inferring evaluation criteria for a given query, it first determines what an evidence-backed report should be evaluated on and then synthesizes aligned query–rubric pairs from those evaluation targets. Starting from a sampled seed topic, DeepRubric builds an evidence tree by recursively expanding evidence-backed sub-questions, whose leaves serve as atomic and verifiable evaluation targets. It then uses the evidence tree to synthesize the training query and rubrics, ensuring that the reward evaluates exactly the information requested by the query. Using DeepRubric, we construct 9K query–rubric supervision examples and train DeepRubric-8B with rubric-based GRPO, achieving comparable performance to prior open state-of-the-art deep research models across three benchmarks with roughly 13x fewer RL GPU-hours.

21.
medRxiv (Medicine) 2026-06-11

Corticospinal tract risk modifies motor recovery after minimally invasive surgery for intracerebral hemorrhage: a secondary analysis of MISTIE-III

Objective: Outcome after surgical hematoma evacuation for intracerebral hemorrhage (ICH) depends on hematoma location. As corticospinal tract (CST) integrity affects motor recovery after stroke, we hypothesized that CST integrity drives heterogeneity in surgical outcomes and investigated this in a secondary analysis of MISTIE-III participants. Methods: Risk of CST injury was categorized into four levels, based on the interaction between the CST, the hematoma, and perihematomal edema (PHE) on automatically segmented stability CT: no risk, PHE infiltration, hematoma infiltration, and complete interruption of the CST. Associations with outcome were tested using multivariable linear regression for motor National Institutes of Health Stroke Scale (NIHSS) at day 180 and ordinal regression for modified Rankin Scale (mRS) at day 365, introducing an interaction term between CST risk and treatment group. Results: Day 180 motor NIHSS was significantly lower for 'no risk' ({beta}:-3.77, [95% confidence interval [CI]: -5.8 to -1.70], p=0.0003) and 'PHE infiltration' ({beta}:-2.3, [95%CI: -3.5 to -1.1]; p=0.0002) vs. 'complete interruption'. Surgery was associated with lower Day 180 motor NIHSS in participants with hematoma infiltration ({beta}:-2.07, [95%CI: -3.8 to -0.4], p=0.016). Compared to complete interruption, 'no risk' (adjusted odds ratio [aOR]:0.27, [95%CI: 0.10 to 0.74], p=0.01) and 'PHE infiltration' (aOR:0.41, [95%CI: 0.23 to 0.74]; p=0.003) were associated with lower odds of unfavorable day 365 mRS. Surgery was associated with lower mRS in participants with no risk (aOR:0.23, [95%CI: 0.05 to 0.97, p=0.045). Interpretation: Increasing CST risk is associated with worse motor recovery (day 180) and disability (day 365). CST risk modifies the effect of the MISTIE-III procedure on motor recovery and disability.

22.
arXiv (CS.AI) 2026-06-12

Decoding Insect Song: A Multitask Semisupervised Orthoptera Bioacoustic Classifier

arXiv:2606.13236v1 Announce Type: cross Abstract: Passive acoustic monitoring holds great promise for ecological inference, yet existing automated tools are typically narrowly trained and non-transferable. We address these limitations with PULSE, a semi-supervised, multi-task framework for Orthoptera bioacoustics, combining weakly-supervised species classification, self-supervised learning on unlabelled field audio, and knowledge distillation from a general-purpose bioacoustic model. Our domain-adapted specialist model outperforms a state-of-the-art general model across all metrics (macro F1: 0.21 vs. 0.07; AUC: 0.74 vs. 0.45; AP: 0.32 vs. 0.19), with active learning further raising F1 to 0.34 and AUC to 0.84. Beyond classification, the learned embeddings encode ecologically meaningful structure, exposed through an interactive visualisation tool for ecological discovery.

23.
arXiv (CS.LG) 2026-06-15

Beyond a Single Explanation of the Adam–SGD Gap

arXiv:2606.14259v1 Announce Type: new Abstract: Prior work has identified several factors that can contribute to the performance gap between Adam and SGD, spanning data aspects, architecture design, and optimization properties. Yet these explanations are often studied in isolation, leaving their relative importance unclear. In this work, we revisit these hypotheses through a controlled empirical study across vision, language, genomics, and graph tasks, spanning modern and classical architectures, and carefully designed training setups. Our results suggest that no single factor consistently explains the Adam–SGD gap. For instance, the Adam advantage can (1) persist under a uniform vocabulary distribution yet nearly disappear under a heavy-tailed one; (2) reverse in favor of SGD in softmax-attention models; and (3) become larger under soft architectural modifications, e.g., when ReLU is replaced by a GeLU nonlinearity. This suggests that the gap arises from nontrivial data and architecture interactions, rather than from a single common factor. Yet, we observe a pattern across our settings: a crossover batch size at which the relative advantage shifts from SGD to Adam as the batch size scales. These empirical results are captured by our theoretical gap model, which predicts this batch-size-dependent crossover. Our perspective helps reconcile several existing hypotheses while offering practical insights across domains.

24.
arXiv (math.PR) 2026-06-11

Second-order PACF asymptotics and discrimination between fractional Gaussian noise and $\operatorname{FARIMA}(0,d,0)$

作者:

arXiv:2605.31416v2 Announce Type: replace-cross Abstract: Fractional Gaussian noise and $\operatorname{FARIMA}(0,d,0)$ have the same long-memory pole $|\theta|^{-2d}$ and hence the same leading PACF law $\alpha(n)\sim d/n$. We show that this agreement breaks at the first non-universal order. For $0

25.
arXiv (CS.AI) 2026-06-19

What Do Safety-Aligned LLMs Learn From Mixed Compliance Demonstrations?

arXiv:2606.20508v1 Announce Type: new Abstract: Prior work has shown that in-context demonstrations can jailbreak language models, but it remains unclear how models interpret different types of compliance demonstrations. We study this by mixing benign compliance demonstrations (non-harmful request, helpful response) with harmful compliance demonstrations (harmful request, helpful response) and testing three hypotheses about how demonstration composition drives harmful compliance. Across four models, we find that benign and harmful demonstrations are not interchangeable: benign demonstrations can either reduce or increase harmful compliance depending on the model. We further show that preference optimization is the critical training stage that prevents benign demonstrations from increasing harmful compliance, that demonstration ordering exhibits strong recency bias, and that models differ in how refusal interacts with in-context learning: some adopt demonstrated formatting even when refusing, while others override all in-context signals upon refusal. Taken together, this work moves beyond showing that demonstration-based jailbreaking works to characterizing how it works: what models extract from compliance demonstrations depends on demonstration content, ordering, and training methodology.