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

Context Compression Is Not One Thing: Readable Symbolic Re-expression vs. Coherent Summary at Matched Budget

We study context compression for multi-hop question answering with small language models. We propose Telegraph English, a readable symbolic format that rewrites retrieved passages into structured entity-relation statements, preserving reasoning evidence at lower token cost. In controlled experiments on MuSiQue, TwoWiki, and HotpotQA, Telegraph English outperforms three matched-budget compression baselines (character-level deletion, truncation, and random sub-sampling) on every dataset, with gains of 13 to 20 F1 percentage point. It also outperforms a coherent prose summary produced by the same encoder on the hardest dataset. A pre-registered depth-interaction hypothesis is null: the advantage does not grow with reasoning depth within datasets. We interpret these results as evidence that readable symbolic re-expression preserves entity content more densely than either natural language or coherent summarization at matched token budget.

02.
arXiv (CS.CV) 2026-06-17

Phys4D: Fine-Grained Physics-Consistent 4D Modeling from Video Diffusion

Recent video diffusion models have achieved impressive capabilities as large-scale generative world models. However, these models often struggle with fine-grained physical consistency, exhibiting physically implausible dynamics over time. In this work, we present Phys4D, a pipeline for learning physics-consistent 4D world representations from video diffusion models. Phys4D adopts a three-stage training paradigm that progressively lifts appearance-driven video diffusion models into physics-consistent 4D world representations. We first bootstrap robust geometry and motion representations through large-scale pseudo-supervised pretraining, establishing a foundation for 4D scene modeling. We then perform physics-grounded supervised fine-tuning using simulation-generated data, enforcing temporally consistent 4D dynamics. Finally, we apply simulation-grounded reinforcement learning to correct residual physical violations that are difficult to capture through explicit supervision. To evaluate fine-grained physical consistency beyond appearance-based metrics, we introduce a set of 4D world consistency evaluation that probe geometric coherence, motion stability, and long-horizon physical plausibility. Experimental results demonstrate that Phys4D substantially improves fine-grained spatiotemporal and physical consistency compared to appearance-driven baselines, while maintaining strong generative performance. Our project page is available at https://sensational-brioche-7657e7.netlify.app/

03.
arXiv (CS.CL) 2026-06-15

Can professional translators identify machine-generated text?

This study investigates whether professional translators without prior specialized training can reliably identify short stories generated in Italian by artificial intelligence (AI). Sixty-nine translators took part in an in-person experiment, where they assessed three anonymized short stories - two written by ChatGPT-4o and one by a human author. For each story, participants rated the likelihood of AI authorship and provided justifications for their choices. While average results were inconclusive, a statistically significant subset (16.2%) successfully distinguished the synthetic texts from the human text, suggesting that their judgements were informed by analytical skill rather than chance. However, a nearly equal number misclassified the texts in the opposite direction, often relying on subjective impressions rather than objective markers, possibly reflecting a reader preference for AI-generated texts. Low burstiness and narrative contradiction emerged as the most reliable indicators of synthetic authorship, with unexpected calques, semantic loans and syntactic transfer from English also reported. In contrast, features such as grammatical accuracy and emotional tone frequently led to misclassification. These findings raise questions about the role and scope of synthetic-text editing in professional contexts.

04.
arXiv (CS.CL) 2026-06-18

Trust Region On-Policy Distillation

On-Policy Distillation (OPD) is a fundamental technique for efficient post-training of large language models (LLMs), with broad applications in agent learning, multi-task enhancement, and model compression. However, OPD training becomes unstable when the teacher and student distributions differ substantially, as teacher supervision on student-generated tokens may yield unreliable policy gradients and even cause optimization failure. This work addresses reliable on-policy token-level supervision through credit assignment strategies, and proposes Trust Region On-Policy Distillation, TrOPD. It features the following characteristics: 1) Trust-Region On-Policy Learning: TrOPD performs OPD only in regions where the teacher provides reliable supervision, mitigating the optimization difficulty of the K1 reverse-KL estimator under distribution mismatch. 2) Outlier Estimation: For outlier regions, we explore gradient clipping, masking, and forward-KL estimation to reduce the adverse effects of unreliable supervision. 3) Off-Policy Guidance: The student continues generation from teacher prefixes and uses forward KL to imitate off-policy guidance, encouraging on-policy exploration toward reliable regions. Experiments show that TrOPD consistently outperforms SoTA OPD baselines, including OPD, EOPD, and REOPOLD, across mathematical reasoning, code generation, and general-domain benchmarks.

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

Open-SWE-Traces: Advancing Dual-Mode Multilingual Distillation for Software Engineering Agents

arXiv:2606.16038v1 Announce Type: cross Abstract: The path toward autonomous software engineering is currently bottlenecked by a severe deficit of diverse, large-scale trajectory data. We address this by introducing \ourdataset, an expansive dataset of 207,489 agentic trajectories spanning nine programming languages (Python, Go, TS, JS, Rust, Java, PHP, C, C++). Sourced from 20,000 real-world PRs via OpenHands and SWE-agent harnesses, the dataset utilizes a hybrid-reasoning synthesis: Minimax-M2.5 generates trajectories with explicit "thinking" processes, while Qwen3.5-122B provides high-quality "non-thinking" traces. Filtered for permissive licenses (MIT, Apache, BSD) from SWE-rebench-V2, this data facilitates the training of models capable of long-horizon reasoning. We validate the dataset by fine-tuning the Qwen3-30B-A3B series (Thinking, Instruct, and Coder). The best performing model achieves resolve rates of 61.7% on SWE-bench Verified, 57.1% on SWE-bench Multilingual, and 36.8% on SWE-bench Pro. These results establish Open-SWE-Traces as a premier resource for distilling human-level software engineering capabilities into efficient, open-source agentic LLMs.

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

ToolGrad: Efficient Tool-use Dataset Generation with Textual "Gradients"

Prior work synthesizes tool-use LLM datasets by first generating a user query, followed by complex tool-use annotations like depth-first search (DFS). This leads to inevitable annotation failures and low efficiency in data generation. We introduce ToolGrad, an agentic framework that inverts this paradigm. ToolGrad first constructs valid tool-use chains through an iterative process guided by textual "gradients", and then synthesizes corresponding user queries. This "answer-first" approach led to ToolGrad-500, a dataset generated with more complex tool use, lower cost, and almost 100% pass rate. Experiments show that ToolGrad models outperform those trained on expensive baseline datasets and proprietary LLMs. The ToolGrad source code, dataset, and models are available at https://github.com/zhongyi-zhou/toolgrad.

07.
arXiv (CS.LG) 2026-06-15

A General Framework for Decision Trees via Bregman Divergences

arXiv:2606.13984v1 Announce Type: cross Abstract: Decision trees are one of the fundamental tools in statistical learning due to their interpretability, flexibility, and their ability to adapt to nonlinear structures. Among them, the Classification and Regression Trees, introduced by Breiman, Friedman, Olshen, and Stone in 1984, became one of the most influential algorithms and remains one of the most widely used methods for classification and regression problems. On the other hand, Bregman divergences, introduced by Lev Bregman in 1967 in the context of convex optimization, provide a broad family of loss functions that naturally generalize the squared Euclidean distance. This family includes, among others, the Kullback-Leibler divergence, the Poisson divergence, and the Itakura-Saito divergence, as well as several losses associated with distributions belonging to the exponential family. Moreover, Bregman divergences possess a rich geometric structure and deep connections with convex analysis and information geometry. In this work, we propose a generalization of the CART paradigm based on Bregman divergences, thereby obtaining a broader family of decision trees adapted to different statistical models and underlying geometries. Although algorithms such as CART or classical implementations such as rpart incorporate different impurity criteria, these are usually introduced in an ad hoc manner for each specific model. In contrast, the Bregman divergence approach provides a unified framework that allows these criteria to be derived and interpreted from common convex and geometric principles. Beyond the algorithmic construction, we also investigate theoretical properties of these trees. In particular, we study how properties of the generating convex function – such as strong convexity or smoothness – influence impurity gains between parent and child nodes, as well as stability and consistency properties of the estimator.

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

Unlocking Diffusion Hierarchies: Adaptive Timestep Selection for Zero-Shot Segmentation

Zero-shot segmentation has recently shown notable improvement by leveraging the rich visual priors in large-scale text-to-image diffusion models, such as Stable Diffusion. However, current diffusion-based methods often face limitations due to the trade-off between spatial resolution and contextual information, as well as their reliance on a single static timestep for feature extraction. To overcome these challenges, our work introduces two key advancements. First, our Contextual Similarity Maps fuse high-resolution attention maps with rich U-Net encoder features, providing both fine-grained and robust per-pixel representations. Second, we identify an emergent hierarchical semantic progression within the denoising process of various diffusion models: representations transition from part-level abstractions at earlier timesteps to object-level abstractions at later stages. Leveraging this insight, we introduce a mechanism to adaptively select the optimal timestep for each pixel. Extensive experiments demonstrate that our method consistently outperforms existing zero-shot segmentation baselines, validating the efficacy of combining contextual features with dynamic, hierarchical timestep selection.

09.
Nature (Science) 2026-06-17

Cucurbituril-based anion-conducting membranes with supramolecular nanopores

Authors:

Nanoporous anion-conducting membranes have gained considerable interest for their potential to reduce resistance in electrochemical devices1–4. Current pore-forming methods, such as backbone engineering through polymers of intrinsic microporosity5,6 or covalent organic and metal–organic frameworks7,8, however, suffer from limited structural control, mechanical fragility or demanding synthesis. Here we establish a supramolecular strategy that overcomes these limitations by constructing uniform, dynamic nanopores. Co-assembly of the rigid macrocyclic host cucurbit[7]uril with the cationic polymer guest quaternized poly(piperidinium-terphenyl) yields a robust network of nanometre-scale channels while simultaneously enhancing mechanical and chemical stability. The dynamic host–guest interactions allow the pore structure to fluctuate on picosecond and angstrom scales. This transient environment supports low-friction hydroxide migration through a Grotthuss mechanism, producing a marked enhancement in ionic conductivity. This bottom-up design principle provides a versatile new tool for molecularly engineering transport pathways and promises to advance electrochemical reactors with respect to energy efficiency, operational stability and the production of high-purity products. A supramolecular strategy, in which uniform, dynamic nanopores are constructed, overcomes the limitations of limited structural control, mechanical fragility or demanding synthesis in nanoporous anion-conducting membranes, providing a versatile tool for molecularly engineering transport pathways.

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

AI-enhanced tuning of quantum dot Hamiltonians toward Majorana modes

arXiv:2601.02149v4 Announce Type: replace-cross Abstract: We propose a neural network-based model capable of learning the broad landscape of working regimes in quantum dot simulators, and using this knowledge to autotune these devices - based on transport measurements - toward obtaining Majorana modes in the structure. The model is trained in an unsupervised manner on synthetic data in the form of conductance maps, using a physics-informed loss that incorporates key properties of Majorana zero modes. We show that, with appropriate training, a deep vision-transformer network can efficiently memorize relation between Hamiltonian parameters and structures on conductance maps and use it to propose parameters update for a quantum dot chain that drive the system toward topological phase. Starting from a broad range of initial detunings in parameter space, a single update step is sufficient to generate nontrivial zero modes. Moreover, by enabling an iterative tuning procedure - where the system acquires updated conductance maps at each step - we demonstrate that the method can address a much larger region of the parameter space.

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

Probabilistic Contrastive Pretraining for Multi-task ADME Property Prediction

arXiv:2606.11508v1 Announce Type: new Abstract: Accurate prediction of absorption, distribution, metabolism, and excretion (ADME) properties is critical to drug discovery, but remains challenging because ADME endpoints are noisy, interdependent, and often data-limited. We propose a molecular graph-transformer pretraining framework that combines chemistry-specific self-supervision with contrastive mutual information machine learning (cMIM). Our method encodes molecular graphs into latent variables, reconstructs SMILES strings from the graph-derived latent codes, and augments the contrastive objective with domain-specific self-supervised chemistry tasks. Rather than treating these tasks as auxiliary regularizers with separately tuned loss weights, we formulate reconstruction, contrastive discrimination, and chemistry-specific supervision as unit-weighted log-probability factors in a single probabilistic latent-variable objective. For fine-tuning, we propose a multi-task GNN readout architecture with task-specific multilayer perceptron heads, preserving shared representation learning while mitigating negative transfer and improving the modeling of heterogeneous, nonlinear task relationships. Across Biogen, ExpansionRX, and ChEMBL-MT, the resulting Contrastive KERMT pretraining improves over the KERMT baseline by 7.6%, 9.9%, and 9.5% respectively (averaged over significantly-improved endpoints). Adding ADME-adjacent molecules to the pretraining corpus further improves transfer, and the contrastive component sharpens chemically meaningful latent neighborhoods.

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

Provable quantum speedups for computing persistence in topological data analysis

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

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

Experimental Analysis of Neural Network-Based Image Classification on the CIFAR-10 Dataset

An experimental investigation of neural image classification on the CIFAR-10 benchmark is presented through fully connected and convolutional network formulations. The analysis emphasizes the complete learning pipeline: image vectorization, normalization, one-hot class encoding, supervised loss minimization, learning-rate selection, mini-batch training, convolutional feature extraction, max-pooling, and validation-based generalization assessment. A convolutional architecture with six convolutional layers and three max-pooling stages is evaluated for ten training epochs using a batch size of 128 and an Adam optimizer with a learning rate of 0.001. The validation accuracy reaches approximately 74.77%, while the validation loss begins to increase after the middle of training despite continued reduction in training loss. The resulting behavior illustrates the practical difference between representation learning and memorization, and it provides a compact experimental baseline for future studies on regularization, data augmentation, deeper architectures, and reproducible image-classification education.

14.
arXiv (CS.CV) 2026-06-12

Adaptable Segmentation Pipeline for Diverse Brain Tumors with Radiomic-Guided Subtyping and Lesion-Wise Model Ensemble

Robust and generalizable segmentation of brain tumors on multi-parametric magnetic resonance imaging (MRI) remains difficult because tumor types differ widely. The BraTS 2025 Lighthouse Challenge benchmarks segmentation methods on diverse high-quality datasets of adult and pediatric tumors: multi-consortium international pediatric brain tumor segmentation (PED), preoperative meningioma tumor segmentation (MEN), meningioma radiotherapy segmentation (MEN-RT), and segmentation of pre- and post-treatment brain metastases (MET). We present a flexible, modular, and adaptable pipeline that improves segmentation performance by selecting and combining state-of-the-art models and applying tumor- and lesion-specific processing before and after training. Radiomic features extracted from MRI help detect tumor subtype, ensuring a more balanced training. Custom lesion-level performance metrics determine the influence of each model in the ensemble and optimize post-processing that further refines the predictions, enabling the workflow to tailor every step to each case. On the BraTS testing sets, our pipeline achieved performance comparable to top-ranked algorithms across multiple challenges. These findings confirm that custom lesion-aware processing and model selection yield robust segmentations yet without locking the method to a specific network architecture. Our method has the potential for quantitative tumor measurement in clinical practice, supporting diagnosis and prognosis.

15.
arXiv (CS.AI) 2026-06-19

RIVET: Robust Idempotent Voice Attribute Editing

arXiv:2606.19629v1 Announce Type: cross Abstract: Voice attribute editing models modify characteristics such as age and gender while preserving speaker identity. In large-scale speech datasets, however, attribute annotations are often noisy or inconsistent, which can cause conditional generative models to produce unstable edits. In this work, we show that idempotency provides an effective mechanism for improving robustness to noisy labels. An idempotent operator is one for which repeated application does not change the result, i.e., f(f(x)) = f(x). Enforcing this property acts as an implicit regularizer that reduces sensitivity to mislabeled examples. We introduce RIVET, a training framework that incorporates an idempotency objective to improve robustness to label noise. We evaluate RIVET under controlled label noise and on the GLOBE dataset with naturally noisy annotations. RIVET improves editing success and better preserves speaker identity than standard training, showing that idempotency improves robustness in voice editing models.

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

Learning to Prompt: Improving Student Engagement with Adaptive LLM-based High-School Tutoring

LLMs can personalize education, although current static-prompt tutoring systems struggle to adapt to diverse academic disciplines. We develop and test a system with subject-aware prompting, based on 14 pedagogical features (e.g., tutor scaffolding, student understanding) extracted from raw transcripts. We first train a prompt routing model in a simulation environment, and then deploy it for online adaptation with actual high-school students. The simulation benchmark shows the router outperforming two static baselines ($0.694$ vs. $0.647$ and $0.64$, $p

17.
Science (Express) 2026-05-06

A 481-meter-high landslide-tsunami in a cruise ship–frequented Alaska fjord | Science

Authors: Unknown Author

Early in the morning of 10 August 2025, a >64 × 10 6 m 3 landslide struck Tracy Arm fjord in Alaska. The landslide was preconditioned by glacial retreat caused by climate change. The resulting 481 m runup megatsunami followed an initial 100-m-high breaking wave traveling >70 m s −1 . The landslide was preceded by several days of microseismicity, which increased in rate and magnitude until ~1 hour before failure. The landslide produced globally observed long-period seismic waves equivalent in size to a M5.4 earthquake. A long-period (~66 s) global seismic signal, produced by a landslide-induced seiche trapped within the fjord, persisted for up to 36 hours, the second time a days-long seiche has been thus observed. With fjord regions increasingly visited by cruise ships, and climate change making similar events more likely, this unanticipated, near-miss event highlights the growing risk from landslides and tsunamis in coastal environments.

18.
arXiv (CS.CV) 2026-06-19

U$^2$Mamba: A Two-level Nested U-structure Mamba for Salient Object Detection

Mamba-based models have emerged as a promising alternative for salient object detection (SOD), offering significant advantages in modeling long sequences. However, existing models often fail to explore contextual information and the depth of the entire architecture. This paper introduces U$^2$Mamba, a powerful and innovative U-structured network for salient object detection. We propose multiscale Mamba U-blocks (MMUBs) that enhance the model depth to improve local feature extraction capabilities. Our newly developed nested U-structure, incorporating MMUBs, enables the network to integrate various receptive fields from shallow and deep layers, thereby collecting richer contextual information and longer-range data without being constrained by resolution. Instead of using the traditional deep supervision scheme and top-level supervised training, we propose a hierarchical training supervision method where the loss is computed at each level during the training process. Extensive experiments demonstrate that U$^2$Mamba achieves highly competitive performance against state-of-the-art methods. The source code is available at \url{https://github.com/JL021/U2Mamba}.

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

Enhancing Visual Feature Attribution via Weighted Integrated Gradients

arXiv:2505.03201v4 Announce Type: replace-cross Abstract: Integrated Gradients (IG) is a widely used attribution method in explainable AI, particularly in computer vision applications where reliable feature attribution is essential. A key limitation of IG is its sensitivity to the choice of baseline (reference) images. Multi-baseline extensions such as Expected Gradients (EG) assume uniform weighting over baselines, implicitly treating all baseline images as equally informative. In high-dimensional vision models, this assumption often leads to noisy or unstable explanations. This paper proposes Weighted Integrated Gradients (WG), a principled approach that evaluates and weights baselines to enhance attribution reliability. WG introduces an unsupervised criterion for baseline suitability, enabling adaptive selection and weighting of baselines on a per-input basis. The method preserves the core axiomatic properties of IG in a generalized weighted-baseline form. Under an expected, proxy-based fitness–relevance monotonicity assumption, WG provides a probabilistic justification for assigning larger weights to more informative baselines. Experiments on commonly used image datasets and models show that WG improves over EG under our protocol, with up to 36% gains across evaluated convolutional and Transformer architectures. These gains come with additional fitness-evaluation cost, so WG should be viewed as an attribution-fidelity trade-off rather than a faster alternative to EG. By moving beyond the assumption that all baselines contribute equally, Weighted Integrated Gradients offers a clearer and more reliable approach to explaining computer-vision models, improving both understanding and practical usability in explainable AI.

20.
Nature (Science) 2026-06-10

Gene ancestries reveal diverse microbial associations during eukaryogenesis

The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4–6 and the role of interactions with viruses7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes. Phylogenomic reconstruction of the proteome of the last eukaryotic common ancestor sheds light on the origin of eukaryotes, indicating an important role of horizontal transfer of genes from diverse bacterial and viral donors.

21.
arXiv (quant-ph) 2026-06-11

An Introduction to the Foundations and Interpretations of Quantum Mechanics

arXiv:2603.09818v2 Announce Type: replace Abstract: This article surveys a selection of key conceptual and interpretational developments in quantum mechanics, tracing the theory from its foundational postulates to contemporary discussions of measurement, nonlocality, and the emergence of classicality. Beginning with the structure of Hilbert space and the postulates governing state evolution and measurement, the epistemic stance of the Copenhagen interpretation and its modern reformulations are examined. The Einstein-Podolsky-Rosen argument, Bell's theorem, and Hardy's paradox are then discussed as probes of locality and realism, alongside the deterministic but explicitly nonlocal de Broglie-Bohm theory. The measurement problem and the implications of contextuality are analyzed in relation to objective collapse models, which introduce new physical dynamics to account for definite outcomes. Finally, the role of decoherence in the suppression of interference and the emergence of classical behavior is explored, together with the interpretational frameworks of many-worlds and consistent histories. This material aims to provide a coherent introductory overview of how several of the most prominent interpretations address the central concern of what quantum mechanics tells us about the nature of physical reality.

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

LEDGER: A Long-Context Benchmark of Corporate Annual Reports for Grounded Financial Retrieval and Extraction

Finance reporting is a natural proving ground for large language models, and the very-long-context capabilities of recent models across all sizes make rigorous evaluation in this domain an increasingly pressing need. Yet most public financial resources reduce the task to plain-text SEC 10-K filings paired with a handful of question-answer items. We release LEDGER (Long-context Evaluation of Documents for Grounded Extraction and Retrieval), a corpus of 4,999 digitized corporate annual reports - full documents with figures, tables, and narrative, not just regulatory filings. Each report is labeled with 31 consolidated financial KPIs to be extracted and linked to the market's reaction at the earnings date. From this data we derive three evaluation benchmarks spanning the difficulty spectrum: a pure page-level KPI retrieval task with TREC-style relevance judgments over 118,048 questions in natural language, a conversational "needle-in-a-haystack" single-value lookup, and a full KPI extraction task, both from long, numerically dense reports. We additionally provide human OCR-quality annotations with inter-annotator agreement and the complete extraction, validation, and scoring toolchain. We further demonstrate the dataset's research utility with a case study linking CEO-letter rhetoric to post-publication market impact.

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

CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

arXiv:2606.13713v1 Announce Type: cross Abstract: Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.

24.
arXiv (CS.AI) 2026-06-12

Physics-Guided Spatiotemporal Learning for Coastal Wave Peak Period Estimation from Video

arXiv:2606.13302v1 Announce Type: new Abstract: Wave parameters in the nearshore are crucial for coastal engineering, shoreline protection, marine hazard assessment, and coastal management for climate resilience. Traditional monitoring systems like buoys and radar platforms offer accurate monitoring but can have high installation and maintenance expenses and limited spatial coverage. Passive ocean monitoring using video has been achieved by leveraging deep learning, however, many methods are not physically interpretable, feasible, and validated for oceanography. In thiswork, a Physics-Guided Deep Spatiotemporal Learning Framework for direct estimation of nearshore wave peak periods from passive coastal video stream is proposed. The framework combines automated temporal-variance based region-of-interest detection, multi-stage Sim-to-Real transfer learning, and physics-informed regularization to enhance the predictive accuracy and physical consistency. A variety of spatiotemporal architectures were assessed, such as transformer-based and recurrent-convolutional ones, alongside synthetic pretraining,silver-label adaptation, and expert fine-tuning. The results show that transformer-based architectures outperformed in terms of the accuracy of the instantaneous prediction, while lightweight recurrent-convolutional architectures achieved higher temporal stability and operational oceanographic skill. Ablation studies also demonstrated the benefits of physics-guided regularization in terms of trend-following consistency, and physically implausible predictions. Explainability auditing also helped to focus attention in hydrodynamically active surf-zone regions and showed good agreement with the physically derived wave propagation behavior. In general, the proposed framework shows the promise of physics-guided video-based deep learning systems for long-term coastal wave monitoring that are cost-efficient and operationally feasible.

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

CoMNeT: A MedNeXt-CorrDiff Framework for Volumetric Brain Tumor Segmentation

Accurate brain tumor segmentation from multiparametric magnetic resonance imaging (MRI) is critical for treatment planning, response assessment, and quantitative neuro-oncology research. However, automated segmentation remains a difficult task in computer vision because of variation in tumor appearance and MRI protocols across patient scans. Moreover, clinically important regions such as enhancing tumor (ET) and tumor core (TC) are often small relative to the full brain volume, furthering increasing the difficulty of achieving high voxel-level precision. In this paper, we show that combining a modern 3D convolutional segmentation model with corrective diffusion-based refinement and ensembling improves volumetric glioma segmentation on the UTSW-Glioma dataset. We propose CoMNeT, a MedNeXt-CorrDiff framework that uses four MRI modalities as input and predicts ET, TC, and whole tumor (WT) regions for automated brain tumor segmentation. MedNeXt is used as the primary segmentation model with Global Response Normalization for feature learning, while CorrDiff is trained as a postprocessing residual refinement method to correct errors in the probability maps before final thresholding. Using five-fold cross-validation, CoMNeT achieved the highest Dice score for most tumor regions, with ET, TC, WT, and average Dice scores of 0.7543 +/- 0.0261, 0.6806 +/- 0.0166, 0.9049 +/- 0.0128, and 0.7798 +/- 0.0184, respectively. CoMNeT outperformed two selected baseline models: SegResNet (0.7555 +/- 0.0190 average Dice) and standalone MedNeXt (0.7697 +/- 0.0154 average Dice). Our findings support the use of corrective diffusion and fold-level probability ensembling as practical additions to existing state-of-the-art 3D convolutional models for automated glioma segmentation.