Paper Plaza - AcademicHub

01.

arXiv (CS.LG) 2026-06-25 DOI: arXiv:2512.05337

Symmetric Linear Dynamical Systems are Learnable from Few Observations

Authors:

Minh Vu ↗Andrey Y. Lokhov ↗Marc Vuffray ↗

arXiv:2512.05337v2 Announce Type: replace-cross Abstract: We consider the problem of learning the parameters of a $N$-dimensional stochastic linear dynamics under both full and partial observations from a single trajectory of time $T$. We introduce and analyze a new estimator that achieves a small maximum element-wise error on the recovery of symmetric dynamic matrices using only $T=\mathcal{O}(\log N)$ observations, irrespective of whether the matrix is sparse or dense. This estimator is based on the method of moments and does not rely on problem-specific regularization. This is especially important for applications such as structure discovery.

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02.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2604.17805

Ranking Abuse via Strategic Pairwise Data Perturbations

Authors:

Junyi Yao ↗Zihao Zheng ↗Jiayu Long ↗

arXiv:2604.17805v2 Announce Type: replace-cross Abstract: Pairwise ranking systems based on Maximum Likelihood Estimation (MLE), such as the Bradley-Terry model, are widely used to aggregate preferences from pairwise comparisons. However, their robustness under strategic data manipulation remains insufficiently understood. In this paper, we study the vulnerability of MLE-based ranking systems to adversarial perturbations. We formulate the manipulation task as a constrained combinatorial optimization problem and propose an Adaptive Subset Selection Attack (ASSA) to efficiently identify high-impact perturbations. Experimental results on both synthetic data and real-world election datasets show that MLE-based rankings exhibit a sharp phase-transition behavior: beyond a small perturbation budget, a limited number of strategic voters can significantly alter the global ranking. In particular, our method consistently outperforms random and greedy baselines under constrained budgets. These findings reveal a fundamental sensitivity of MLE-based ranking mechanisms to structured perturbations and highlight the need for more robust aggregation methods in collective decision-making systems.

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03.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.04145

EvalStop: Using World Feedback to Detect and Correct Reward Overoptimization in Multi-Tenant RLHF Platforms

Authors:

Guilin Zhang ↗Chuanyi Sun ↗Shahryar Sarkani ↗John M. Fossaceca ↗

arXiv:2606.04145v2 Announce Type: replace-cross Abstract: Cloud LLM fine-tuning platforms increasingly serve RLHF workloads, where a learned reward model is optimized as a proxy for human quality. As Gao et al. (2023) showed, this proxy diverges from world feedback (downstream eval metrics) under sustained optimization pressure, a phenomenon known as reward overoptimization. Existing platform schedulers ignore this divergence: non-clairvoyant schedulers optimize JCT without any quality signal, SLAQ-style quality-aware schedulers use training loss (a weaker proxy that drops monotonically through hacking), and classical per-job early stopping requires human monitoring and does not free shared GPUs. We propose EvalStop, a composable scheduling primitive that terminates jobs on k consecutive eval-score declines, releases GPUs, preserves the best checkpoint, and delegates to any base scheduler. We frame scheduler-level early stopping as a detection problem and evaluate it in a discrete-event simulator whose RLHF workload mixes reward-hacking and structurally healthy runs, with ground-truth labels hidden from schedulers. On RLHF-heavy workloads (80% RLHF, 64 GPUs), EvalStop achieves precision 98% / recall 99% / FPR 1.5% while improving JCT by 9% and cutting wasted compute by 22% over SRTF-Est (p

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04.

arXiv (CS.CL) 2026-06-24 DOI: arXiv:2606.24783

Paying to Know: Micro-Transaction Markets for Verified Product Information in Agentic E-Commerce

Authors:

Filippos Ventirozos ↗Matthew Shardlow ↗

Commercial NLP treats the shopping chatbot as a recommender or a conversion tool: its job is to match a user to a catalogue entry and close a sale. We argue that the arrival of agent-native micro-payment rails (e.g., x402, AP2) changes what is scarce. When the buyer is an autonomous agent that can investigate exhaustively, the bottleneck is no longer matching products but acquiring trustworthy, decision-relevant information about them. We envision agentic e-commerce as a micro-transaction market for verified information: buyer agents spend fractions of a cent to progressively unlock seller- and reviewer-supplied data – service histories, third-party test reports, bills of materials, audited sales and support metrics – paid for a la carte under a freemium model, with reviewer trust scored reputationally. We sketch the architecture of such a market and argue that it rewards genuine product quality and yields truer competition than ranking-based storefronts. We then translate the vision into concrete NLP problems – cost-optimal information acquisition, data pricing and negotiation, real-time entity resolution, grounded value exchange, and privacy-preserving persona modelling – and argue that these, not chat fluency, deserve the field's attention.

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05.

Nature (Science) 2026-06-10 DOI: HASH:4d9d0816507856a65109d54623dac69b

Lignin to adipic acid in a high-yield chemical and biological redox process

Authors:

Kathryn M. Mains ↗

Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin currently around 20 wt% (refs. 1–4). Most existing lignin depolymerization strategies target aryl–ether bond cleavage, which can produce aromatic monomers in yields of only about 30 wt%, and still as complex mixtures with C–C-linked dimers and oligomers5,6. The recalcitrance of these C–C linkages between aromatic moieties fundamentally limits single-product yields from lignin, prompting the development of strategies to efficiently cleave these C–C bonds3,7–9. Here we show how reductive processing of lignin from poplar accesses a hydrocarbon mixture of alkyl-aromatic monomers and oligomers that is privileged for oxidative conversion to monomeric aromatic carboxylic acids, comprising mostly benzoic acid and phthalic acid isomers in up to 73 wt% monomer yields, using a Co/Mn/Br catalyst. The soil bacterium Pseudomonas putida KT2440 was engineered to convert this mixture of aromatic carboxylic acids to muconolactone, a precursor to bio-based nylons, enabling final adipic acid yields up to 26 wt% (gram adipic acid per gram lignin) with a maximum theoretical yield of 57 wt%. This pairing of reductive and oxidative steps with lignin resembles processes in petrochemical refining and shows how lignin may be converted into a single, valuable bioproduct in high yields. A chemical and biological redox process that resembles processes in petrochemical refining is used to convert lignin from poplar into a single, valuable bioproduct, adipic acid, in high yields.

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06.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2601.00921

Geometric and Quantum Kernel Methods for Predicting Skeletal Muscle Outcomes in chronic obstructive pulmonary disease

Authors:

Azadeh Alavi ↗Hamidreza Khalili ↗Stanley H. Chan ↗Fatemeh Kouchmeshki ↗Muhammad Usman ↗Ross Vlahos ↗

arXiv:2601.00921v3 Announce Type: replace-cross Abstract: Chronic obstructive pulmonary disease (COPD) affects hundreds of millions of people worldwide, and skeletal-muscle dysfunction is clinically important. Quantum machine learning is increasingly explored for biomedical prediction, but its value in small biomarker cohorts requires benchmarking against strong classical baselines. We analysed a cigarette-smoke COPD cohort of 213 animals with blood and bronchoalveolar-lavage biomarkers to predict tibialis anterior muscle weight, muscle quality, and force. We developed a kernel-geometric quantum hybrid method in which synthetic symmetric positive definite (SPD) references are mapped through a reproducing kernel Hilbert space, compressed using train-only random projection, normalised, and supplied to low-dimensional quantum regression circuits. We benchmarked this approach against classical ridge/kernel models, SPD relational representations, and quantum-kernel regression (QKR). All methods were evaluated using condition-stratified repeated cross-validation. The largest numerical improvement was observed for muscle weight, where the proposed method had the numerically lowest mean root mean squared error (RMSE), approximately 1.8% below the best classical comparator; paired fold-level testing did not establish statistically significant superiority after Holm adjustment, but the endpoint is biologically meaningful. The method also had the numerically lowest mean RMSE for muscle quality. For force, biomarker-only Ridge performed best, suggesting a more linear endpoint structure.

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07.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.12279

Mathematical perspective on genetic algorithms with optimization guided operators

Authors:

Anna Brandenberger ↗Ilan Doron-Arad ↗Elchanan Mossel ↗

arXiv:2606.12279v1 Announce Type: cross Abstract: Recent work in ML applies genetic algorithms at inference time to iteratively improve solutions to optimization problems. The basic mutation and recombination operators involved are qualitatively different from those studied classically. Mutations are no longer random; an ML algorithm mutates a solution with the goal of improving an objective. Similarly, recombination is not based on random collages of parent solutions. Instead, it is an ML optimization-based operator whose goal is to synthesize improved solutions from its inputs. Thus, these mutation and recombination operators are more likely to improve the objective, but their computational cost is much higher. We introduce a general model of genetic algorithms and formulating optimization in this model as a query-complexity problem, using the language of reinforcement learning. We then study specialized models. We show that some optimization problems require generation, mutation, and recombination to be solved. We then obtain qualitatively tight algorithms for a family of problems within this framework that captures the nontrivial role of diversity in the solution pool, a key feature of practical ML genetic algorithms.

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08.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2410.16089

Multi-Sensor Fusion for UAV Classification Based on Feature Maps of Image and Radar Data

Authors:

Nikos Sakellariou ↗Antonios Lalas ↗Konstantinos Votis ↗Dimitrios Tzovaras ↗

arXiv:2410.16089v2 Announce Type: replace Abstract: The unique cost, flexibility, speed, and efficiency of modern UAVs make them an attractive choice in many applications in contemporary society. This, however, causes an ever-increasing number of reported malicious or accidental incidents, rendering the need for the development of UAV detection and classification mechanisms essential. We propose a methodology for developing a system that fuses already processed multi-sensor data into a new Deep Neural Network to increase its classification accuracy towards UAV detection. The DNN model fuses high-level features extracted from individual object detection and classification models associated with thermal, optronic, and radar data. Additionally, emphasis is given to the model's Convolutional Neural Network (CNN) based architecture that combines the features of the three sensor modalities by stacking the extracted image features of the thermal and optronic sensor achieving higher classification accuracy than each sensor alone.

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09.

arXiv (CS.AI) 2026-06-15 DOI: arXiv:2606.14476

When the Tool Decides: LLM Agents Defer Blindly to Graph Neural Network Tools, and Stronger Backbones Defer More

Authors:

Zhongyuan Wang ↗Pratyusha Vemuri ↗

arXiv:2606.14476v1 Announce Type: new Abstract: A growing line of work equips large language model (LLM) agents with graph neural networks (GNNs) as callable tools, assuming the agent exercises judgment over when and how much to rely on such a tool. We test this directly. We expose a frozen GNN to a ReAct-style LLM agent as an explicit tool and measure, on node classification over a text-attributed graph (ogbn-arxiv, replicated on WikiCS), whether the agent uses the tool or merely obeys it. We find the agent does not exercise judgment: its predictions agree with the raw GNN's 97.6-99.2% of the time (5 seeds), collapsing into a GNN parrot that adopts the tool's output wholesale and bypasses its own reasoning. Sweeping backbone capability (Qwen2.5 0.5B-7B), the deference is not a weak-model artifact: among models able to invoke the tool, agreement rises with capability (0.60 to 0.98 from 1.5B to 7B). Crucially, the cost of deference does not shrink as capability grows and grows where alternatives emerge: a per-node oracle over the available actions beats the parrot by 0.09-0.18 at 3B and 0.12-0.22 at 7B, roughly doubling at high homophily, because the parrot is pinned to the frozen GNN while the agent's alternatives improve; at 7B a simple neighbour-label tool overtakes the GNN at high homophily (0.81 vs 0.71) yet the agent still defers. A simple selective-invocation gate recovers about half of that high-homophily gap (0.71 to 0.83) but yields no net global gain, and held-out estimates bound the best achievable gate over standard test-time features to at most a third of the oracle headroom: reliable selective invocation looks limited by available information, not merely router design. Our results are a cautionary measurement: evaluations of agent+tool systems cannot assume the agent adds judgment on top of the tool, and selective invocation must be designed in rather than expected to emerge from scale.

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10.

arXiv (CS.CL) 2026-06-19 DOI: arXiv:2606.19534

PerceptionDLM: Parallel Region Perception with Multimodal Diffusion Language Models

Authors:

Yueyi Sun ↗Yuhao Wang ↗Jason Li ↗Ye Tian ↗Tao Zhang ↗Jacky Mai ↗Yihan Wang ↗Haochen Wang ↗Jinbin Bai ↗Ling Yang ↗Yunhai Tong ↗

Multimodal large language models (MLLMs) have achieved remarkable progress in visual understanding tasks. However, most existing MLLMs rely on autoregressive generation, which limits their efficiency for perception tasks that require captioning multiple regions. In this work, we propose PerceptionDLM, a multimodal diffusion language model optimized for efficient parallel region perception. Built upon PerceptionDLM-Base, a strong foundational baseline that achieves state-of-the-art performance among open-source diffusion MLLMs, our architecture fully leverages the parallel decoding nature of DLMs. Specifically, we introduce efficient prompting and structured attention masking to enable simultaneous perception of multiple masked regions, allowing the model to generate region descriptions in parallel at both the sequence and token levels. This design significantly improves inference efficiency compared with existing approaches that process regions sequentially. To systematically evaluate the parallelism property of visual perception capability for DLMs, we construct a new Parallel Detailed Localized Captioning Benchmark (ParaDLC-Bench) by scaling the DLC-Bench to include multiple region masks per image, enabling joint evaluation of both caption quality and inference efficiency. Experiments demonstrate that PerceptionDLM maintains competitive performance in region captioning while achieving substantial speed improvements for multi-region perception tasks. Our results highlight the potential of multimodal diffusion language models for efficient, parallel visual perception. To the best of our knowledge, we are the first to achieve parallel region caption and perception by leveraging the advantages of diffusion language models. Code, models, and datasets are released.

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11.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2603.02668

SorryDB: Can AI Provers Complete Real-World Lean Theorems?

Authors:

arXiv:2603.02668v2 Announce Type: replace Abstract: We present SorryDB, a dynamically-updating benchmark of open Lean tasks drawn from 78 real world formalization projects on GitHub. Unlike existing static benchmarks, often composed of competition problems, hillclimbing the SorryDB benchmark will yield tools that are aligned to the community needs, more usable by mathematicians, and more capable of understanding complex dependencies. Moreover, by providing a continuously updated stream of tasks, SorryDB mitigates test-set contamination and offers a robust metric for an agent's ability to contribute to novel formal mathematics projects. We evaluate a collection of approaches, including generalist large language models, agentic approaches, and specialized symbolic provers, over a selected snapshot of 1000 tasks from SorryDB. We show that current approaches are complementary: even though an agentic approach based on Gemini Flash is the most performant, it is not strictly better than other off-the-shelf large-language models, specialized provers, or even a curated list of Lean tactics.

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12.

PLOS Computational Biology 2026-06-15 DOI: HASH:4da4e9508751e62538097eab4d2ad8f4

WormSORT: A detection-based multiple object tracking model for individual silkworms in breeding environments

Authors:

Hongkang Shi ↗

by Hongkang Shi, Linbo Li, Shiping Zhu, Haibo He, Minghui Zhu, Jianfei Zhang Variety breeding has long been a cornerstone of high-quality agriculture, and recent advances in artificial intelligence have opened new avenues for accelerating biological breeding. In this study, we applied multiple object tracking (MOT) technology to silkworm breeding to achieve efficient, non-invasive, and dynamic individual monitoring. Unlike pedestrian or vehicle tracking, silkworms pose unique challenges for MOT due to their small size, dense distribution, and high inter-individual similarity, which complicate accurate tracking and behavioral analysis. To address these issues, we propose WormSORT, an enhanced tracking method based on a tracking-by-detection framework with an optimized data association strategy. A pre-trained detection model identifies silkworms in each frame, and deep feature vectors are extracted using a re-identification network. Identity association is first performed using Intersection over Union (IoU) matching, followed by deep feature similarity for unmatched cases, improving both tracking accuracy and reliability. To further enhance tracking stability, we introduce a candidate input padding mechanism, including IoU padding and feature padding, ensuring that high-confidence unmatched trajectories and detections remain involved in the matching process. To validate the proposed tracking strategy, we constructed two multiple silkworm tracking (MST) datasets: MST-50, containing approximately 50 individuals over 1000 frames, and MST-100, containing approximately 100 individuals over 1200 frames. Experimental results demonstrate that WormSORT outperforms existing methods, including DeepSORT, StrongSORT, OCSORT, ByteTrack, and BotSORT, achieving superior tracking performance. This study provides a valuable reference for silkworm tracking and behavioral analysis, contributing to the advancement of high-quality silkworm rearing and management.

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13.

bioRxiv (Bioinfo) 2026-06-18 DOI: HASH:2e76c8e1562952ec829b18fc544963dd

Looking beyond stereotyped neuron structures reveals links between beading and morphological rearrangements in aging phenotypes.

Authors:

Gomez ↗Nguyen ↗Lagergren ↗Flores ↗San Miguel ↗

Understanding how neuronal morphology changes during aging and acute stress is essential for elucidating mechanisms of neurodegeneration. The highly branched PVD neuron of Caenorhabditis elegans provides a powerful model for studying dendritic remodeling and degeneration-associated phenotypes such as dendritic beading. However, the complexity of this arbor presents substantial challenges for automated segmentation and quantitative analysis. In this study, we adapted a convolutional neural network (CNN)-guided region growing framework for automated dendrite tracing, coupled with two topology-based algorithms for categorizing dendritic segments by branching degree. The segmentation algorithm achieved high accuracy relative to manual tracing, with a median Dice coefficient of 0.82, while reducing analysis time by approximately tenfold. Automated dendrite categorization demonstrated strong agreement with manual annotations across branching orders, though position-based mapping performance declined with age due to progressive morphological distortion. Leveraging this platform, we investigated mechanistic differences in dendritic beading patterns observed during aging and cold shock. Consistent with prior work, aging was associated with decreased inter-bead spacing, whereas cold shock produced increased bead dispersion with stress severity. Structural analysis revealed that these trends were not driven by dendritic pruning or reduced arbor complexity. Instead, while a traditional anatomically unflexible paradigm falsely implicated lower-degree dendrites as highly vulnerable, our branching-informed framework revealed that age-dependent beading is fundamentally dictated by a segments history of successive branching events. Conversely, acute cold shock triggered systemic beading that expanded across all dendritic orders in a severity-dependent manner. Together, these findings demonstrate that chronic aging and acute stress engage distinct degenerative pathways (compartment-specific lineage vulnerability versus global architectural collapse) rather than gross morphological loss, as well as highlighting the need for paradigms that enable reliable analysis of changing morphologies.

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14.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2601.20361

TINNs: Time-Induced Neural Networks for Solving Time-Dependent PDEs

Authors:

Chen-Yang Dai ↗Che-Chia Chang ↗Te-Sheng Lin ↗Ming-Chih Lai ↗Chieh-Hsin Lai ↗

arXiv:2601.20361v2 Announce Type: replace Abstract: Physics-informed neural networks (PINNs) solve time-dependent partial differential equations (PDEs) by learning a mesh-free, differentiable solution that can be evaluated anywhere in space and time. However, standard space-time PINNs take time as an input but reuse a single network with shared weights across all times, forcing the same features to represent markedly different dynamics. This coupling degrades error performance and can destabilize training when enforcing PDE, boundary, and initial constraints jointly. We propose Time-Induced Neural Networks (TINNs), a novel architecture that parameterizes the network weights as a learned function of time, allowing the effective spatial representation to evolve over time while maintaining shared structure. The resulting formulation naturally yields a nonlinear least-squares problem, which we optimize efficiently using a Levenberg-Marquardt method. Experiments on various time-dependent PDEs show up to 4 times improved relative error and 10 times faster convergence compared to PINNs and strong baselines.

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15.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2508.13313

Flow Matching for Efficient and Scalable Data Assimilation

Authors:

Taos Transue ↗Bohan Chen ↗So Takao ↗Bao Wang ↗

arXiv:2508.13313v4 Announce Type: replace-cross Abstract: Data assimilation (DA) estimates a dynamical system's state from noisy observations. Recent generative models like the ensemble score filter (EnSF) improve DA in high-dimensional nonlinear settings but are computationally expensive. We introduce the ensemble flow filter (EnFF), a training-free, flow matching (FM)-based framework that accelerates sampling and offers flexibility in flow design. EnFF uses Monte Carlo estimators for the marginal flow field, localized guidance for observation assimilation, and utilizes a novel flow path that exploits the Bayesian DA formulation. It generalizes classical filters such as the bootstrap particle filter and ensemble Kalman filter. Experiments on high-dimensional benchmarks demonstrate EnFF's improved cost-accuracy tradeoffs and scalability, highlighting FM's potential for efficient, scalable DA. Code is available at https://github.com/Utah-Math-Data-Science/Data-Assimilation-Flow-Matching.

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16.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.15452

PHINN: Persistent Homology Inspired Neural Network for Rare-Event Time Series Generation

Authors:

Emre Yusuf ↗Ren Takahashi ↗Jayabrata Bhaduri ↗

arXiv:2606.15452v1 Announce Type: new Abstract: Rare events in time series are critical to model but hard to learn due to data scarcity. Current generative models struggle with extreme values. We observe that rare events leave distinct topological fingerprints - transitions in Betti numbers from point-cloud embeddings - that are more stable and discriminative than statistical moments. We introduce PHINN, a flow-matching framework using dynamic Betti curves as conditioning signals and a persistence landscape loss for homology consistency. It scales to multivariate data, includes a natural-language interface to set Betti targets, supports cross-domain meta-learning and few-shot generation, and provides certified adversarial robustness. On financial, epidemiological, and multi-modal benchmarks, PHINN outperforms statistical and diffusion baselines in topological fidelity (beta-RMSE down 41-63%, transition accuracy up 84%) and matches jump-diffusion models in tail coverage while exceeding them in shape fidelity. All results have 95% confidence intervals.

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17.

bioRxiv (Bioinfo) 2026-06-24 DOI: HASH:6440ce47915ee35459c5c479ccaca0a6

Development of Deep-Learning Models that Predict Quantitative Protein-Ligand Interac-tions in Glycobiology as a part of a Capstone Course

Authors:

Yin ↗Liu ↗Zhou ↗Chang ↗Carpenter ↗E. J ↗Satyajith ↗Haregu ↗Greiner ↗Derda ↗

Glycans coat the surface of all cells, and every glycan is recognised by specific glycan-binding pro-teins (GBPs). There are no general tools that can accurately estimate the binding strength between glycan and GBP from the amino acid sequence of the GBP and the molecular structure of the glycan, represented as SMILES string. We describe models for predicting such binding strengths developed as a part of a Capstone Course at the University of Alberta. The models are trained on a dataset that combines BindingDB, a published database of small-molecule protein interactions, and data from glycan arrays measured by Consortium of Functional Glycomics (CFG). In this hybrid dataset of protein-ligand interactions the ligands are both glycans from CFG and small molecules from BindingDB; similarly, proteins include GBP and proteins from BindingDB. Three models are presented (i) ProMax which fuses ESM-2, MolFormer, and MolCLR features; (ii) APEX which constrains learning to a predetermined form, a physical model of binding; (iii) UltraMax adds inter-atomic distances for the ligands. To address the dataset's severe long-tail distribution, the models employ tail-aware losses for rare high-binding instances. Trained and evaluated on approximately one million protein–ligand pairs using hold-out splits for unseen molecules, the three models provide a unified framework for quantitative glycan-protein binding prediction. We observed that learning glycan-protein binding is harder than the similar task of learning small-molecule-protein interactions. Simple mirror-inversion tests led us to postulate that insufficient use of chiral features is an important source of difficulty in learning these interactions.

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18.

arXiv (CS.AI) 2026-06-18 DOI: arXiv:2606.18672

scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

Authors:

Jinke Wu ↗Yifan Wang ↗Siyu Yi ↗Caiyang Yu ↗Ziyue Qiao ↗Nan Yin ↗Jiancheng Lv ↗Wei Ju ↗

arXiv:2606.18672v1 Announce Type: cross Abstract: Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.

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19.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2606.19542

Tracking Representation Dynamics in Large Language Models with Persistent Homology

Authors:

Naman Malhotra ↗Jay Ambadkar ↗Abhinav Gupta ↗Kushal Kasivel ↗Abbas Schwarz ↗Kamillo Ferry ↗Anthea Monod ↗

arXiv:2606.19542v1 Announce Type: new Abstract: Large language models are commonly aligned through supervised fine-tuning, yet little is known about how their internal representations evolve during this process. We study alignment dynamics using persistent homology by tracking the topology of activation spaces throughout fine-tuning. Across four transformer language models ranging from 1B to 7B parameters and three alignment objectives corresponding to helpful, harmless, and mixed training data, we find that the majority of topological reorganization occurs during the earliest stages of training. A dense checkpoint analysis reveals a transient peak in topological activity followed by rapid stabilization. We further show that different alignment objectives induce distinguishable topological trajectories, while instruction-tuned and pretrained models exhibit qualitatively different patterns of evolution. Our results suggest that persistent homology provides a complementary perspective on alignment, revealing representation-level changes that are not apparent from behavioral metrics alone.

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20.

medRxiv (Medicine) 2026-06-17 DOI: HASH:b57b4288dd9142d14f75f4a7ba4b834e

Cross-Device Adaptation of Mirai for Mammography-Based Breast Cancer Risk Prediction

Authors:

Sistig ↗Rothstein ↗J. H ↗Gadgil ↗Achacoso ↗Alexeeff ↗S. E ↗Gerstley ↗L. D ↗Klein ↗R. J ↗Margolies ↗…

Fine-tuning can adapt pretrained medical imaging models to new clinical datasets, but device-specific domain shifts may limit generalizability. We evaluated Mirai, a mammography-based deep learning model for breast cancer risk prediction, in a large screening cohort containing Hologic and General Electric (GE) full-field digital mammography systems, including GE Premium View (GE PV) and Tissue Equalization (GE TE) post-processing software. Native Mirai showed lower performance on TE images than on Hologic or PV images. Fine-tuning on TE images improved TE performance, particularly for short-term risk prediction, but substantially reduced performance on Hologic images, consistent with catastrophic forgetting. To mitigate this effect, we developed a device-invariant model using interleaved multi-device sampling and conditional adversarial training. This approach largely restored Hologic performance while maintaining improved TE performance, providing better robustness across heterogeneous imaging platforms. Comparison of cumulative and annual risk AUCs over a five-year time horizon further showed that performance gains were driven mainly by short- and intermediate-term predictions. These findings highlight both the value and dangers of device-specific fine-tuning and support balanced domain-adaptation strategies for deploying mammography-based risk models across diverse clinical imaging environments.

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21.

arXiv (CS.CL) 2026-06-16 DOI: arXiv:2510.13940

Less is More: Improving LLM Reasoning with Minimal Test-Time Intervention

Authors:

Zhen Yang ↗Mingyang Zhang ↗Feng Chen ↗Ganggui Ding ↗Liang Hou ↗Xin Tao ↗Ying-Cong Chen ↗

Recent progress in large language models (LLMs) has focused on test-time scaling to improve reasoning via increased inference computation, but often at the cost of efficiency. We revisit test-time behavior and uncover a simple yet underexplored phenomenon: reasoning uncertainty is highly localized-only a small subset of high-entropy tokens dominantly affects output correctness. Motivated by this, we propose Minimal Test-Time Intervention (MTI), a training-free framework that enhances reasoning accuracy and stability with minimal overhead. MTI includes: (i) Selective CFG intervention, applying classifier-free guidance only at uncertain positions; and (ii) Lightweight negative-prompt guidance, reusing the main model's KV cache to approximate unconditional decoding efficiently. MTI yields consistent gains across general, coding, and STEM tasks-e.g., +9.28% average improvement on six benchmarks for DeepSeek-R1-7B and +11.25% on AIME2024 using Ling-mini-2.0-while remaining highly efficient.

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22.

arXiv (CS.LG) 2026-06-25 DOI: arXiv:2606.24991

Solving Markov Decision Processes with Future Information via MPC

Authors:

Shambhuraj Sawant ↗Akhil S Anand ↗Dirk Reinhardt ↗Sebastien Gros ↗

arXiv:2606.24991v1 Announce Type: cross Abstract: Model Predictive Control (MPC) is widely used in industrial and robotic systems for enforcing constraints and embedding domain knowledge through finite-horizon optimization-based planning. However, despite these strengths, an MPC scheme typically does not yield optimal policies for sequential decision-making problems formulated as Markov Decision Processes (MDPs). Recent combinations of MPC with Reinforcement Learning (RL) alleviate this issue by treating MPC as a parameterized model of the optimal policy of an MDP and adjusting its parameters using data. While these approaches typically consider classical MDPs, many real-world problems include future information–such as forecasts, prices, or reference trajectories–at decision time, which must be included in the MDP state for optimal decision-making. Current MPC-RL approaches do not directly account for this augmented-state structure, raising the question of how to incorporate future information into MPC to obtain an optimal policy. This work establishes the structural requirements under which a parameterized MPC can exactly represent the optimal value functions and policy of an MDP with future information. We further demonstrate that such a parameterized MPC can serve as a structured function approximator, with its parameters learned using RL. The approach is illustrated on a point-mass racing task with future reference information.

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23.

medRxiv (Medicine) 2026-06-23 DOI: HASH:c81d16df04b4080dc51da5bfeaf7cf78

What Is the Optimal Timing and Frequency of Workload-Matched Postprandial Physical Activity Breaks? A Randomized Controlled Crossover Study of Cardiometabolic and Cognitive Responses During Sedentary Behavior

Authors:

Euring ↗Niederer ↗Groneberg ↗Engeroff ↗

Purpose Postprandial sedentary behavior is associated with negative health effects and constitutes a large part of daily life in modern society. This study investigated how the timing of physical activity after eating influences glucose levels, cerebral and muscle oxygenation, cognitive performance, and well-being during subsequent sitting. Methods In a four-armed randomized crossover trial, healthy adults consumed four standardized meals separated by 48-hour washout periods. Each meal was followed by 2 hours of sitting combined, in random order, with one of four interventions: (1) sitting only, (2) 15 minutes of moderate intensity cycling immediately after eating, (3) 15 minutes of cycling 20 minutes after eating, or (4) three workload-matched five-minute cycling bouts during sitting. Interstitial glucose (continuous glucose monitoring), cerebral and muscle oxygenation (Functional near infrared spectroscopy), cognitive performance (Stroop test), heart rate, blood pressure, and subjective ratings were assessed every 30 minutes. Data were analyzed using repeated-measures ANOVA. Results Twenty participants (mean age 27.1{+/-}10.3 years, 12 females) completed the study. Cycling immediately after eating reduced mean glucose levels during postprandial sitting, while both 15-minute cycling bouts increased cerebral oxygenation. All active conditions enhanced muscle oxygenation. Heart rate and arousal increased with delayed cycling and active breaks. No effects were observed for blood pressure, cognitive performance, focus, or well-being. Conclusion A short bout of physical activity immediately after eating reduces postprandial hyperglycemia and improves brain oxygenation during sitting, whereas delayed activity and brief breaks increase physiological activation without cognitive or perceptual benefits.

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24.

arXiv (CS.CV) 2026-06-19 DOI: arXiv:2606.19584

Language-Instructed Vision Embeddings for Controllable and Generalizable Perception

Authors:

Chengzhi Mao ↗Xudong Lin ↗Wen-Sheng Chu ↗

Vision foundation models are typically trained as static feature extractors, placing the burden of task adaptation onto large downstream models. We propose an alternative paradigm: instead of solely feeding visual features into language models, we use language itself to dynamically guide the vision encoder. Our method, Language-Instructed Vision Embeddings (LIVE), leverages language as high-level guidance to produce task-centric embeddings at inference time, removing the need for task-specific retraining. This enables the encoder to focus on contextually relevant aspects of the input, yielding more controllable and generalizable representations. Empirically, LIVE reduces visual hallucinations (+34 points on MMVP), surpasses vision-language models with orders of magnitude more parameters on visual question answering, and generalizes to unseen instructions and tasks – offering a direct path toward adaptive, instruction-driven visual intelligence.

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25.

arXiv (CS.LG) 2026-06-12 DOI: arXiv:2606.13454

Optical Implementation of Equilibrium Propagation Using Spatial Photonic Ising Machines

Authors:

Dimitri Vanden Abeele ↗Daniele Veraldi ↗Davide Pierangeli ↗Claudio Conti ↗Serge Massar ↗

arXiv:2606.13454v1 Announce Type: cross Abstract: Equilibrium Propagation offers a compelling alternative to traditional machine learning for training energy-based networks. Here we demonstrate a hybrid optical-digital implementation of EP using a Spatial Photonic Ising Machine (SPIM). The SPIM exploits the gauge transformation method to optically encode both continuous neuron states and rank-1 binary trainable patterns as phase modulations via a spatial light modulator, with inference realized using a finite difference scheme. The experimental system is evaluated on the Wine classification dataset. The potential of this approach, including the use of continuous couplings and structured coupling matrices, is evaluated numerically on the more complex MNIST dataset. Our work provides a concrete pathway toward energy-efficient physical implementations of Equilibrium Propagation.

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