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01.
Nature (Science) 2026-06-17

<i>CHPO</i> coordinates chilling recovery and nitrogen use in rice

Authors:
Jie Cao↗

Global rice production faces mounting challenges from abnormal temperature fluctuations and nitrogen-fertilizer-driven environmental pollution1–7. Developing varieties that balance chilling resilience and nitrogen-use efficiency (NUE) offers a promising solution, but the molecular networks coordinating these traits remain poorly understood. Here we identify CHILLING PHOENIX (CHPO), a major gene underlying the quantitative trait locus shared by both chilling tolerance and resilience. It encodes a MYB transcription factor that acts as a key regulator coordinating post-chilling recovery with nitrogen use in rice. Natural variation in a GCG-repeat-encoded polyalanine tract alters CHPO DNA-binding preference and redirects regulatory outputs between the japonica-type (CHPOjap) and indica-type (CHPOind), causing opposing effects on chilling tolerance and resilience. This allelic variation is shaped by domestication selection, with the CHPOjap allele probably derived from Chinese wild rice. CHPOjap directly targets OsTCP19 and OsNRT2.4 to fine-tune NUE, thereby enhancing chilling tolerance and resilience. These findings provide a mechanistic framework for a chilling-induced high-nitrogen-utilization module that alleviates the damage caused by chilling stress, and a potential molecular design&nbsp;strategy for breeding rice varieties with both chilling resilience and high NUE at the&nbsp;recovery stage. A rice gene, CHPO, links chilling resilience with nitrogen-use efficiency, revealing a domestication-shaped regulatory mechanism that could guide breeding of climate-resilient, sustainable rice varieties.

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

AfroScope: A Framework for Studying the Linguistic Landscape of Africa

Authors:
Sang Yun Kwon↗AbdelRahim Elmadany↗Muhammad Abdul-Mageed↗

Language Identification (LID), the task of determining the language of a given text, is a fundamental preprocessing step that shapes the reliability of downstream NLP applications. While recent work has expanded African LID, existing systems remain limited in both language coverage and fine-grained discrimination among closely related languages and varieties. We introduce AfroScope, a unified framework for African LID that includes AfroScope-Data, a dataset covering 640 languages, and AfroScope-Models, a suite of strong LID models with broad African language coverage. To address persistent confusions among closely related languages, we propose a hierarchical classification approach that leverages AfroScope-Mirror, a specialized embedding model for targeted disambiguation, improving macro-F1 by 1.57 points on the confusable subset compared to our best base model. We further analyze cross-lingual transfer and domain effects, showing how language-family structure, script compatibility, and domain coverage shape LID performance. We position African LID as an enabling technology for large-scale measurement of Africa's linguistic landscape in digital text, and release AfroScope-Data and AfroScope-Models online.

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03.
medRxiv (Medicine) 2026-06-18

Intra-arterial recombinant human TNK tissue-type plasminogen activator (rhTNK-tPA) thrombolysis for acute medium vessel occlusion (MeVO-TNK): Study rationale and design

Authors:
Deng↗Liu↗C.-C↗Wang↗Y.-H↗Ao↗D.-H↗Huang↗Xie↗Zhang↗Kong↗Q.-Q↗…

Background The optimal management of acute ischemic stroke caused by medium vessel occlusion (MeVO) remains uncertain. Recent randomized trials have failed to demonstrate a clear benefit of endovascular therapy in this population, whereas intra-arterial thrombolysis (IAT) has emerged as a biologically plausible alternative. However, prospective evidence supporting IAT in MeVO is lacking, and the optimal dosing strategy for stand-alone IAT remains undefined. Aim To preliminarily evaluate the efficacy and safety of intra-arterial tenecteplase (IA-TNK) plus standard medical therapy (SMT) compared with SMT alone in patients with acute MeVO stroke, and to explore a stepwise IA-TNK dosing strategy. Design The MeVO-TNK trial is a multicenter, prospective, randomized, open-label, blinded-endpoint (PROBE), exploratory phase II study. A total of 60 participants with imaging-confirmed MeVO will be randomized 1:1 to receive either IA-TNK plus SMT or SMT alone. Participants presenting beyond 6 hours from symptom onset must demonstrate salvageable penumbral tissue on advanced imaging. Those assigned to the intervention group will receive up to two intra-arterial boluses of tenecteplase (0.0625 mg/kg per bolus), with the second bolus administered based on angiographic assessment of reperfusion and safety. Outcomes The primary efficacy outcome is final infarct volume measured at 72{+/-}24 hours after randomization. Secondary efficacy outcomes include the proportions of patients achieving modified Rankin Scale (mRS) scores of 0-1, 0-2 and 0-3 at 90 days, a shift analysis of the mRS distribution at 90 days, early neurological deterioration, and National Institutes of Health Stroke Scale score at 7 days or discharge. The primary safety outcome is symptomatic intracranial hemorrhage within 24 hours. Conclusions This trial will provide preliminary evidence on the biological efficacy, reperfusion potential and safety of stand-alone IA-TNK for acute MeVO stroke, helping to address an important evidence gap and inform the design of future confirmatory studies.

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

The Benchmark Illusion: Pruned LLMs Can Pass Multiple Choice but Fail to Answer

Authors:
Rui Wen↗Lu Sun↗Jiayang Liu↗Zesheng Xu↗Tianshuo Cong↗Zheng Li↗

Compressing large language models reduces memory use and inference cost, but it can also create failures that standard benchmarks miss. A pruned model may still perform well on multiple-choice evaluations, yet fail to answer the same question in open generation. We ask what pruning changes: does it erase the correct answer, or does it make the answer harder to produce as the top output? We study this question with multilingual question answering, tracking the same questions before and after pruning. We find a benchmark illusion. Under high-sparsity pruning, especially Wanda, models often fail in greedy open generation while still selecting the correct answer under multiple-choice scoring. In these recognition-only errors, the answer is usually not gone, but demoted: it often reappears with beam search, sampling, or one in-context example. Overall, multiple-choice benchmarks can overstate the usability of compressed LLMs, creating an evaluation blind spot. Compressed models should be tested on what they can produce, not only on what they can recognize.

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

Unintended Effects of Geographic Conditioning in Large Language Models

Authors:
Naz Col↗David M. Chan↗

Modern conversational AI systems frequently rely on user metadata to localize responses, yet the unintended regional biases introduced by this hidden context remain poorly understood. In this work, we evaluate location leakage: the phenomenon where a model generates geographic references despite receiving a geographically neutral user prompt. Across both creative writing and open-ended Q&A prompts, even state-of-the-art LLMs systematically favor region-specific outputs when exposed to location metadata, with leakage spiking by up to 793 times above baseline (e.g., from 0.04% to 31.7% for Llama 3.1-8B, and 21.3% and 8.8% for Qwen3-8B and Claude Sonnet 4.6, respectively). Our analysis further shows a novel structural conditioning effect: replacing the injected location with the placeholder "Unknown" still elevates leakage by up to 72 times above baseline, demonstrating that the user profile frame itself, independent of any geographic content, acts as a generative conditioning signal.

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

Reframing AI Loss of Control: What It Is, How to Have It, How to Lose It

Authors:
Ze Shen Chin↗Maurice Chiodo↗Dennis M\"uller↗Coleman Snell↗

arXiv:2606.12442v1 Announce Type: cross Abstract: At present, loss of control risks have gained much prominence in public discussion, particularly in relation to AI, with extensive discourse present among academics, frontier labs, and even governments. However, in the existing literature, the concept seems to rest on surprisingly weak foundations, where even those that discuss loss of control extensively do not first establish what control is and what exactly is being lost. Our paper aims to address these gaps. We establish a working definition of control by anchoring it to the "setting and getting of goals". Then, we discuss various aspects of control, built on foundational concepts from related fields like cybernetics, management control, and control theory. This includes who (or what) can be in control, and the things they require to be in control, such as the ability to set goals, having a functional control loop, having requisite variety, and having sufficient goal alignment. Once a framework for control is established, we then discuss how control can be lost, how AIs can contribute to such loss of control, and offer relevant recommendations for how one can maintain control. One interesting consequence of our work is that humanity, as individuals and as groups, can lose varying degrees of control as a result of AI behaviour that is far below the level of superintelligence; the potential for loss of control scenarios (as we define them) already exist, and have existed for a long time.

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

Can Artificial Intelligence Accelerate Technological Progress? Researchers' Perspectives on AI in Manufacturing and Materials Science

Authors:
John P. Nelson↗Olajide Olugbade↗Philip Shapira↗Justin B. Biddle↗

arXiv:2511.14007v3 Announce Type: replace-cross Abstract: Artificial intelligence (AI) raises expectations of substantial increases in rates of technological progress, but such anticipations are often not connected to detailed ground-level studies of AI use in innovation processes. Accordingly, it remains unclear how and to what extent AI can accelerate innovation. To help to fill this gap, we explore and assess results from 32 interviews with U.S.-based academic manufacturing and materials sciences researchers experienced with AI and machine learning (ML) techniques. We found that AI was primarily used for modeling of materials and manufacturing processes, facilitating cheaper and more rapid search of design spaces for materials and manufacturing processes alike. Benefits included cost, time, and computation savings in technology development. However, AI/ML tools were unreliable outside design spaces for which dense data were already available; they required skilled and judicious application in tandem with older research techniques; and concerns were raised about the potential to detrimentally circumvent opportunities for disruptive theoretical advancement. Based on these results, we suggest there is reason for optimism about acceleration in sustaining innovations through the use of AI/ML; but that support for conventional empirical, computational, and theoretical research is required to maintain the likelihood of further disruptive advances in manufacturing and materials.

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

GenTrack2: An Improved Hybrid Approach for Multi-Object Tracking

Authors:
Toan Van Nguyen↗Rasmus G. K. Christiansen↗Dirk Kraft↗Leon Bodenhagen↗

This paper proposes a visual multi-object tracking method that jointly employs stochastic and deterministic mechanisms to ensure identifier consistency for unknown and time-varying target numbers under nonlinear dynamics. A stochastic particle filter addresses nonlinear dynamics and non-Gaussian noise, with support from particle swarm optimization (PSO) to guide particles toward state distribution modes and mitigate divergence through proposed fitness measures incorporating motion consistency, appearance similarity, and social-interaction cues with neighboring targets. Deterministic association further enforces identifier consistency via a proposed cost matrix incorporating spatial consistency between particles and current detections, detection confidences, and track penalties. Subsequently, a novel scheme is proposed for the smooth updating of target states while preserving their identities, particularly for weak tracks during interactions with other targets and prolonged occlusions. Moreover, velocity regression over past states provides trend-seed velocities, enhancing particle sampling and state updates. The proposed tracker is designed to operate flexibly for both pre-recorded videos and camera live streams, where future frames are unavailable. Experimental results confirm superior performance compared to state-of-the-art trackers. The source-code reference implementations of both the proposed method and compared-trackers are provided on GitHub: https://github.com/SDU-VelKoTek/GenTrack2

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

Evaluation of Alternative-Based Information Systems for Deliberative Polling using an Agentic Simulator

Authors:
Rwaida Alssadi↗Khulud Alawaji↗Balaji Kasula↗Muntaser Syed↗Badria Alfurhood↗Markus Zanker↗Marius Silaghi↗

arXiv:2606.11692v1 Announce Type: cross Abstract: Deliberative polling promises to improve collective decision-making by exposing shareholders to a broad range of arguments before they vote. Yet ensuring that every voter encounters a representative sample of the reason space, the coverage problem, remains an open challenge, particularly at scale and in adversarial or strategically motivated electorates. This paper introduces a way of evaluating solutions using the LLM-based Agentic Bipolar Argumentation Simulator, grounded in a framework which formalises a poll as a six-tuple of endorsing and opposing justifications, attack and enhance relations, and shareholder- and relation-weights. ABAS simulates N autonomous shareholder agents, each assigned a latent opinion according to desired distributions in [-1, 1], who sequentially vote, choose or author justifications, and optionally submit argumentation-graph links. The simulator implements recommendations that rank existing justifications by their observable endorsement mass. It evaluates the mechanism's success by coverage, namely the fraction of the corpus reason-tag set represented in the K recommendations presented to each shareholder, as a solution to the NP-hard Subsuming Justification Problem. Reported experiments characterise how creativity rate (pown), recommendation size (K), argumentation density (plinks), and population size (N) affect coverage and corpus diversity. In an authenticated electorate where Sybil attacks are impossible and only the relation graph is gameable, we stress-test the scoring with coordinated strategic voting attacks: a tag-flood attack collapses coverage, while author-count relation weighting through a reversed-PageRank rule resists the flood markedly better than uniform weights.

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10.
arXiv (CS.AI) 2026-06-19

Interpretable Sperm Morphology Classification via Attention-Guided Deep Learning

Authors:
Zahra Asghari Varzaneh↗Reza Khoshkangini↗Thomas Ebner↗Lars Johansson↗

arXiv:2606.20438v1 Announce Type: new Abstract: Male infertility is a major cause of couple infertility, often linked to abnormal sperm morphology. While deep learning models offer automated analysis, most lack interpretability, limiting their clinical adoption. This study proposes an attention-guided deep learning framework for sperm morphology classification. We combine a pretrained EfficientNet-B0 with a Convolutional Block Attention Module (CBAM) to focus on key areas of the sperm head, improving both accuracy and interpretability. Evaluated on the SMIDS and HuSHem public datasets, our model achieves accuracies of 90.2% and 93.9% (macro F1 scores of 0.913 and 0.948), outperforming SimpleCNN and standard EfficientNet-B0. Furthermore, we use Grad-CAM++ visualizations to highlight features influencing the model's decisions. The results demonstrate that this accurate and transparent framework is a practical tool for automated sperm analysis in fertility clinics.

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

Can Factual Opinions Be Edited (Manipulated) in Large Language Models?

Authors:
Yuanpu Cao↗Ziyi Yin↗Fenglong Ma↗Jinghui Chen↗

Large Language Models (LLMs) are increasingly integrated into various domains, making knowledge editing techniques crucial yet potentially hazardous. Current editing methods primarily target atomic facts, overlooking the significant risks associated with manipulating factual opinions, e.g., documented stances of public figures on societal issues. Such manipulation could reshape public images, influence elections, and alter societal views. To systematically assess this threat, we introduce the Factual Opinion Editing with Evidence (FOE) benchmark, which encompasses 261 public figures, 19 issue categories, and 2,178 complete opinion records. Our evaluations demonstrate that current editing techniques struggle significantly with factual opinions, often achieving only superficial changes while failing to preserve consistency between the edited opinion and the supporting evidence generated by the model. To address this limitation, we further propose a simple yet effective Self-Generated Evidence-Aligned method that achieves opinion-evidence alignment without relying on explicit instructions. Together, our benchmark and method provide a foundation for understanding the emerging security implications of factual opinion editing in LLMs.

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

On Aligning Hierarchical Standardized Embedding for Audio-visual Generalized Zero-shot Learning

Authors:
Zihan Zhang↗Jie Hong↗Siyuan Fan↗Yanghao Zhou↗Pengfei Fang↗

Audio-visual Generalized Zero-shot Learning (AV-GZSL) is a challenging task that aims to classify both seen and unseen objects or scenes by integrating data from audio and visual modalities. Recent studies primarily focus on fusing or aligning audio and visual features to generate more informative audio-visual embeddings. Also, aligning the audio-visual and textual features of most existing methods relies solely on the optimization objectives. However, those methods neglect the inherent distributional and structural differences between audio-visual and textual modalities. To address this limitation, we propose a method termed Aligning Hierarchical Standardized Embedding (AHSE), which enables hierarchical alignment of standardized audio-visual and textual embeddings within a shared embedding space. Specifically, we first apply Z-score standardization to the fused audio-visual and textual embeddings to reduce distributional mismatches. We then introduce a hierarchical alignment strategy that minimizes discrepancies at the semantic, class, and batch levels, thereby constructing a more robust and well-structured embedding space. This strategy not only preserves semantic and inter-class relationships but also maintains spatial consistency within each batch. Extensive experiments on three benchmark datasets: VGGSound-GZSL, UCF-GZSL, and ActivityNet-GZSL, demonstrate that AHSE achieves competitive performance in zero-shot learning.

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13.
arXiv (CS.CL) 2026-06-11

Claw-SWE-Bench: A Benchmark for Evaluating OpenClaw-style Agent Harnesses on Coding Tasks

Authors:
Mengyu Zheng↗Kai Han↗Boxun Li↗Haiyang Xu↗Yuchuan Tian↗Wei He↗Hang Zhou↗Jianyuan Guo↗Hailin Hu↗Lin Ma↗Chao Xu↗Guohao Dai↗…

General-purpose agents such as OpenClaw are increasingly used as autonomous tool users, but their coding ability is difficult to measure under SWE-bench: a generic agent does not by itself satisfy the clean Docker workspace, patch, and prediction contract required for scoring. We introduce Claw-SWE-Bench, a multilingual SWE-bench-style benchmark and adapter protocol that makes heterogeneous agent harnesses, or claws, comparable under fair settings including a fixed prompt, runtime budget, workspace contract, patch extraction procedure, and evaluator. The full benchmark contains 350 GitHub issue-resolution instances across 8 languages and 43 repositories, drawn from SWE-bench-Multilingual and SWE-bench-Verified-Mini after future-commit cleanup. We also release Claw-SWE-Bench Lite for faster validation, which is an 80-instance subset selected by a cost-aware, rank-aware procedure over 17 calibration columns. On the full benchmark, OpenClaw with a minimal direct-diff adapter scores only $19.1\%$ Pass@1, whereas the full adapter reaches $73.4\%$ with the same GLM 5.1 backbone, showing that adapter design is essential for enabling OpenClaw-style harnesses to perform coding tasks effectively. Across an OpenClaw $\times$ nine-model sweep and a five-claw $\times$ two-model sweep, model choice changes Pass@1 by $29.4$ pp and harness choice by $27.4$ pp under fixed models; systems with similar accuracy can differ substantially in total API cost. Claw-SWE-Bench therefore treats harness and cost accounting as first-class axes of SWE-style coding-agent evaluation, providing both a full benchmark and a low-cost reference set for reproducible comparison. The data is available at https://github.com/opensquilla/claw-swe-bench and https://huggingface.co/datasets/TokenRhythm/Claw-SWE-Bench.

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14.
arXiv (quant-ph) 2026-06-12

Quantized time in quantum walks under weak rank-K measurements

Authors:
Klaus Ziegler↗

arXiv:2606.13552v1 Announce Type: new Abstract: Measurements can be used to monitor the evolution of quantum systems and may lead to a universally quantized time statistics. It is known that the mean return time is quantized for strong and indirect monitoring through the winding number of the return amplitude in a one-dimensional space. Here we discuss that under multi-channel strong or indirect monitoring, where the latter is achieved through ancilla coupling, the mean return time of a quantum walk in the projected subspace is also quantized. This reflects a universal time quantization for a higher dimensional evolution.

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

Quantum Correlation Hierarchy and Teleportation in Dephased Hydrogen Hyperfine System

Authors:
Geerthana Thiyagarajan↗R. Muthuganesan↗

arXiv:2606.11731v1 Announce Type: new Abstract: We study the dynamics of quantum correlations in the hydrogen hyperfine spin system subject to Markovian phase noise. Treating the electron and proton spin degrees of freedom as an open two-qubit system governed by an isotropic hyperfine Hamiltonian and local dephasing, we obtain the exact time-dependent density matrix and derive analytical expressions for the full X-state family. We compute concurrence($C$), trace-distance measurement-induced nonlocality (Trace MIN–$\mathcal{N}_1$), and average steering coherence (ASC) in closed form and establish their strict ordering $ C(t)\leq \mathcal{N}_1(t)\leq \mathrm{ASC}(t) $ at all times. Entanglement is identified as the most fragile resource, undergoing sudden death at a finite time. Trace MIN exhibits dephasing-immune freezing for states with nonzero population imbalance, while ASC is the most robust quantity, persisting longest in every scenario studied.We additionally demonstrate that the dephased thermal hyperfine state serves as a resource for quantum teleportation, deriving a closed-form expression for the average fidelity and establishing that the teleportation advantage window coincides exactly with the entanglement survival interval, $\mathcal{F}_A > 2/3 \Longleftrightarrow \mathcal{C} > 0$, for the full X-state family with maximally mixed marginals. We identify four distinct dynamical regimes and map all three correlation measures onto directly measurable Pauli spin correlators, enabling experimental reconstruction of the full hierarchy without full state tomography.

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

TS-Fault: Benchmarking Time Series Forecasters Against Structural Faults

Authors:
Yuyang Zhao↗Lian Xu↗Hao Miao↗Chenxi Liu↗Hao Xue↗

arXiv:2606.18539v1 Announce Type: new Abstract: Time series forecasting (TSF) underpins consequential decisions in energy, transportation, finance, and healthcare, yet TSF models are almost universally ranked by a single number (e.g., average error) on clean held-out data, under the implicit assumption that it predicts deployed reliability. However, real faults are not i.i.d noise but structured events with temporal shape, broken cross-variable dependencies, regime change coupled with missingness, and causal propagation across a sensing pipeline. Treating TSF robustness as a data-quality problem, we present TS-Fault, a benchmark that evaluates forecasting models under explicit, parameterized fault scenarios with controllable semantic difficulty. TS-Fault organizes recurring failures into four modes along two orthogonal axes (observation- vs mechanism-level; univariate vs multivariate) and injects each fault into the most prediction-critical window via a unified importance score. This design enables robustness to be tested against the structures models actually rely on, rather than reduced to generic noise sensitivity. We evaluate 21 models across 6 datasets, 4 modes, and 5 difficulty levels under a paired clean/corrupt protocol. The results reveal three findings that contradict common leaderboard intuition: (i) clean-data accuracy anti-correlates with robustness; (ii) clean rankings are preserved under observation-level faults but reshuffled under mechanism-level faults; and (iii) all catastrophic failures occur under mechanism-level faults, with foundation models achieving the highest clean-data accuracy yet exhibiting the greatest fragility. The code is publicly available at https://github.com/Ray-zyy/TS-Fault.

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

NeuronFabric: A Software Reference Architecture for On-Chip Transformer Training with Local Adam

Authors:
Evgeny Ukladchikov↗

arXiv:2606.16440v1 Announce Type: cross Abstract: Publicly documented accelerator architectures generally separate training computation from optimizer-state updates or rely on external memory and host orchestration. This paper presents NeuronFabric, a software reference architecture intended for future FPGA and ASIC implementations of transformer training with local Adam updates. A complete C# prototype implements forward pass, backpropagation, and Adam optimization without external machine-learning frameworks. The goal is to validate numerical correctness and memory requirements before hardware implementation. The evaluated model is a 334K-parameter autoregressive transformer (d=88, H=4, f=264, L=4, vocab=256) trained on the Shakespeare corpus. The BF16W configuration achieves evaluation loss 1.5426 after 80K samples, compared with 1.5224 for an FP32 GPU reference, while producing coherent character-level text. The paper introduces BF16W, which stores weights in BF16 while retaining Adam optimizer moments in FP32. This reduces memory requirements for on-chip training. A 334K-parameter FP32 model with Adam moments requires approximately 4.0 MB, matching the BRAM capacity of a Xilinx ZCU102 device. The BF16W variant requires approximately 3.34 MB, leaving memory available for activation storage. We describe the vocabulary-budget constraint observed during earlier experiments, quantify BF16W memory savings, and outline FPGA training as the next stage of development. No FPGA measurements are included in this paper. This publication serves as a public architectural disclosure and software reference implementation for future FPGA and ASIC exploration of the NeuronFabric architecture.

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

Can Post-Training Turn LLMs into Good Medical Coders? An Empirical Study of Generative ICD Coding

Authors:
Ziqing Wang↗Weihao Li↗Shijie Chen↗Yuan Luo↗Kaize Ding↗

Automated International Classification of Diseases (ICD) coding is a core medical-coding task for billing, epidemiology, and clinical decision support. Generative large language models (LLMs) are often reported as weak medical coders, but this finding mainly comes from inference-time settings such as prompting, retrieval, reranking, or tool use, leaving the role of task-specific post-training underexplored. We present a controlled empirical study of post-training for generative ICD coding, comparing discriminative baselines with LLM coders across prompting, supervised fine-tuning, and reinforcement learning under a common protocol and metric set. To our knowledge, this is the first study to evaluate RL-based post-training for generative LLM coders in ICD coding. We further introduce PHI, a diagnostic curriculum that extends GRPO to refine missed-code cases. Our results show that prompting-only evaluation substantially underestimates the potential of LLMs for ICD coding. SFT provides the main capability jump, GRPO further improves code-set prediction beyond SFT, and PHI provides targeted gains on macro-level performance. These findings suggest that the main bottleneck is not the generative formulation alone, but how the model is adapted and optimized for full-taxonomy recall. We release our code, data splits, and checkpoints at https://github.com/AlexandreWANG915/LLM4ICD.

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19.
bioRxiv (Bioinfo) 2026-06-11

OCOO-T : A SIMPLE AND SCALABLE VIRTUAL CELL MODEL FOR TRANSCRIPTIONAL PERTURBATION RESPONSE PREDICTION

Authors:
Zhao↗Lai↗Jiang↗An↗

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

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20.
bioRxiv (Bioinfo) 2026-06-19

StickForStats: automated statistical assumption validation for reproducible computational biology

Authors:
Bharti↗Chakraborty↗

Reproducible computational biology depends on statistical decisions that routine workflows often skip: verifying that a differential-expression test's assumptions hold across all genes, that a strategy-comparison ANOVA is robust to non-normality, or that a meta-analysis is not distorted by publication bias. Surveys consistently find that fewer than 20% of published biomedical studies report checking these assumptions, and existing statistical software leaves validation to the analyst as an optional step. We present StickForStats, an open-source web platform that reframes assumption validation as a default precondition for every analysis. Its Guardian system–a middleware pipeline of eight validators (normality, variance homogeneity, independence, outliers, sample size, modality, linearity, homoscedasticity)–checks assumptions before execution and, on critical violations, reroutes to an appropriate nonparametric alternative with a documented decision trail. At genome scale, applying Guardian to a 91-sample synovial-sarcoma RNA-seq study (GSE271517) cascaded 90.6% of 27,221 genes to a rank-based test and flipped the differential-expression verdict for 553 genes–479 rescued from an under-powered t-test and 74 outlier-driven false positives rejected–materially changing the gene list a biologist would act on. The same automatic validation generalizes across domains: a CRISPR editing-strategy comparison (ANOVA F = 1122, with Guardian recommending Kruskal-Wallis H = 36.6), an ordinal correlation (Pearson r = 0.476 corrected to Spearman {rho} = 0.479), and a sixteen-trial clinical meta-analysis revealing severe publication bias (Egger's t = -5.78, p < 0.001); a complementary module extends the same validators to published manuscripts, checking claims against CONSORT, STROBE, ICH-E9, and JARS-Quant reporting standards. By making assumption validation automatic and transparent, StickForStats targets a tractable, under-served contributor to irreproducibility. The platform is MIT-licensed, validated against SciPy and R, and freely available at https://github.com/visvikbharti/stickforstats_new.

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21.
arXiv (CS.AI) 2026-06-17

Beyond Parallel Sampling: Diverse Query Initialization for Agentic Search

Authors:
Sidhaarth Murali↗Jo\~ao Coelho↗Jingjie Ning↗Jo\~ao Magalh\~aes↗Bruno Martins↗Chenyan Xiong↗

arXiv:2606.17209v1 Announce Type: new Abstract: Test-time scaling for agentic search typically increases depth (i.e., more turns and tokens per trajectory) or breadth (i.e., more parallel rollouts). Here we focus on breadth scaling, showing that standard parallel sampling yields diminishing returns, tracing this to query redundancy at the first turn. When models issue similar first queries across rollouts, the threads retrieve overlapping evidence, and subsequent turns are conditioned on this shared retrieval. We address this limitation with DivInit, a training-free intervention at the first turn. Rather than sampling k independent first queries, DivInit draws n candidates from a single call, picks k < n diverse seeds, and runs them as parallel trajectories. Across five open-weight models and eight benchmarks, DivInit consistently improves over standard parallel sampling, with average gains of five to seven points on multi-hop QA at matched compute. Code available at https://github.com/cxcscmu/diverse-query-initialization

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22.
arXiv (CS.AI) 2026-06-18

AdsMind: A Physics-Grounded Multi-Agent System for Self-Correcting Discovery of Adsorption Configurations on Heterogeneous Catalyst Surfaces

Authors:
Zongmin Zhang↗Yuyang Lou↗Bowen Zhang↗Junwu Chen↗Ryo Kuroki↗Xuan Vu Nguyen↗Edvin Fako↗Lixue Cheng↗Philippe Schwaller↗

arXiv:2606.19152v1 Announce Type: cross Abstract: Identifying the lowest-energy surface-adsorbate configuration is critical for modeling heterogeneous catalysis, yet exhaustive exploration with ab initio calculations is computationally prohibitive. Machine-learning force fields (MLFFs) accelerate structural relaxation but leave the search over the vast configurational space a major bottleneck, and open-loop large language model (LLM) agents lack a physics-grounded feedback mechanism to correct erroneous initial guesses. We propose AdsMind (Adsorption configuration discovery with Machine intelligence and relaxation feedback), a closed-loop multi-agent framework that enables autonomous error correction through MLFF relaxation feedback. Across four LLM backends, AdsMind achieves consistently high search reliability, with success rates of 100% and 98.8% on the benchmarks AA20 and OCD-GMAE62. Relative to its single-pass (1-Shot) ablation it reduces cross-backend energy dispersion, and it uses only 4.11 and 4.67 MLFF relaxations per case, respectively – an approximately 14-fold reduction over heuristic enumeration baselines. Density functional theory (DFT) validation using VASP/PBE on six representative AA20 systems shows that the reported open-loop Adsorb-Agent outputs exhibit qualitative adsorption-energy sign errors for molecular adsorbates, whereas AdsMind preserves the correct sign in all tested cases with closer quantitative agreement. AdsMind thus delivers reliability, self-reflection, and interpretability simultaneously, supporting more DFT-informed autonomous chemistry workflows.

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23.
arXiv (quant-ph) 2026-06-12

Unifying spacetime approaches to quantum mechanics

Authors:
N. L. Diaz↗M. Cerezo↗Paolo Braccia↗

arXiv:2606.12539v1 Announce Type: new Abstract: Recent efforts to formulate quantum mechanics in a way that treats space and time on a more equal footing have led to a large variety of spacetime-oriented approaches. In this work we present a detailed study of spacetime states, the objects that play the role of quantum states in the recently introduced framework of spacetime quantum mechanics, and show that the main proposals in the literature are different manifestations of the same underlying object. Path integrals, quantum states over time, pseudo-density matrices, the Page and Wootters mechanism, superdensity operators, and timelike-entanglement proposals all arise from spacetime states through particular evaluations, reduced information, linear maps, or quantum channels. This unification provides explicit mathematical representations of these formalisms, reveals relations among them, and clarifies the spacetime information each one captures. We also study the broader relevance of the spacetime-state point of view for Leggett-Garg inequalities, OTOCs, temporal tensor networks, fermionic systems, relativistic QFTs, quantum reference frames, and classical physics, together with additional insights and perspectives revealed by the common unifying framework.

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

Elastic ODYN: Differentiable Optimization for Infeasible Control and Learning in Robotics

Authors:
Aristotelis Papatheodorou↗Jose Rojas↗Ioannis Havoutis↗Carlos Mastalli↗

arXiv:2606.16564v1 Announce Type: cross Abstract: Robotic systems routinely encounter conflicting objectives, modeling errors, and degenerate contact conditions that render quadratic programs (QPs) infeasible. Yet most optimization solvers and differentiable QP layers assume feasibility, leading to numerical failures, unstable gradients, or solver breakdown when constraints cannot be simultaneously satisfied. We present Elastic ODYN, a primal–dual non-interior-point QP solver that handles infeasibility through smooth squared-$\ell_2$ elastic relaxations. The resulting formulation remains well posed under ill-conditioning and degeneracy, supports warm starting, and converges to closest-to-feasible solutions when no feasible point exists. A lightweight refinement stage recovers physically meaningful dual variables from the elastic solution. Building on this framework, we develop Elastic OdynLayer, a differentiable QP layer with stable gradients under infeasibility, and Elastic OdynSQP, an infeasibility-aware SQP method that resolves inconsistent subproblems and intrinsically infeasible optimal control tasks through selective constraint relaxation. We evaluate the framework on benchmark QPs, singular contact mechanics, differentiable parameter identification, and quadrupedal and humanoid trajectory optimization. Across all settings, Elastic ODYN consistently outperforms state-of-the-art elastic QP solvers in robustness, warm-start performance, and convergence reliability, enabling optimization, simulation, control, and learning beyond the feasibility assumptions of existing methods.

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25.
arXiv (CS.AI) 2026-06-17

Counterfactual Optimization of Baseball Pitch Sequences and Estimation of Its Impact on Season-Level Statistics

Authors:
Ryota Takamido↗Hiroki Nakamoto↗

arXiv:2606.17345v1 Announce Type: cross Abstract: Although pitch sequencing is a central topic in baseball analytics, previous studies have primarily focused on optimizing the final pitch within a single plate appearance, leaving the role of preceding setup pitches and their impact on long-term season-level performance insufficiently examined. To address these issues, this study conducted counterfactual analyses using MLB Statcast data. A Transformer-based machine-learning model was trained to predict whether a target pitch would result in an in-play outcome or swing-out. Counterfactual pitch sequences were then generated by replacing either the final pitch or the preceding setup pitch with alternative pitch types and locations while keeping the surrounding contextual information fixed. Optimal counterfactual selections were defined as those that minimized the predicted in-play probability, and their expected effects on pitchers' seasonal statistics were estimated using regression models linking model outputs to season statistics. The results suggest that the optimization of both final and setup pitches may substantially influence season-level performance, including improvements of more than 1.0 in K/9. The analyses also provided several practical insights, including velocity-band-specific effective locations, the importance of pitch commands, and the expansion of pitch-selection options through middle-velocity pitches. These findings quantitatively support the strategic importance of pitch sequencing in baseball.

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