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01.
arXiv (CS.AI) 2026-06-17

FllumaOne: A Code-Native Multimodal CAD Dataset with Executable Programs and Kernel-Validated Feature Histories

Authors:

arXiv:2606.17696v1 Announce Type: new Abstract: Parametric computer-aided design records both final geometry and the ordered construction history that determines how a part can be edited. Datasets for editable CAD research should therefore expose modeling operations, parameters, and feature dependencies together with validated geometry. We introduce FllumaOne, a code-native multimodal CAD dataset whose models are generated by executable Python programs in Flluma, a Qt/C++ OpenCASCADE-based CAD system. Each sample aligns its program with a structured feature tree, a training-oriented intermediate representation, STEP geometry, a surface point cloud, natural-language descriptions, metadata, and eight canonical visible-edge renderings. The primary release, FllumaOne-100K, contains 100,000 accepted samples across four template-level complexity regimes. Programs are executed and retained only after kernel geometry, solid validity, and export checks; release reports also record modality completeness and split-level duplicate tests. A Qwen2.5-Coder-1.5B LoRA baseline trained on 80,000 samples achieves 99.98% Python syntax validity, 99.97% Flluma build success, and 99.14% STEP-export validity on the held-out 10,000-sample test split. For the 9,909 predictions converted to surface point clouds, the mean normalized Chamfer Distance is 0.002124. The dataset supports conditioned CAD reconstruction, executable program synthesis, feature-tree prediction, B-Rep analysis, retrieval, design completion, and editable reverse engineering.

02.
arXiv (CS.LG) 2026-06-16

Priority-Aware Shapley Value

arXiv:2602.09326v2 Announce Type: replace Abstract: Shapley values are widely used for model-agnostic data valuation and feature attribution, yet they implicitly assume contributors are interchangeable. This can be problematic when contributors are dependent (e.g., reused/augmented data or causal feature orderings) or when contributions should be adjusted by factors such as trust or risk. We propose Priority-Aware Shapley Value (PASV), which incorporates both hard precedence constraints and soft, contributor-specific priority weights. PASV is applicable to general precedence structures, recovers precedence-only and weight-only Shapley variants as special cases, and is uniquely characterized by natural axioms. We develop an efficient adjacent-swap Metropolis-Hastings sampler for scalable Monte Carlo estimation and analyze limiting regimes induced by extreme priority weights. Experiments on data valuation (MNIST/CIFAR10) and feature attribution (Census Income) demonstrate more structure-faithful allocations and a practical sensitivity analysis via our proposed "priority sweeping".

03.
arXiv (CS.LG) 2026-06-16

Evolutionary Bilevel Reward Shaping for Generalization in Reinforcement Learning

arXiv:2606.16236v1 Announce Type: new Abstract: Reinforcement learning (RL) often suffers from performance degradation when deployed in environments that differ from those encountered during training. Existing techniques such as domain randomization (DR) mitigate this, but require access to diverse training environments and full trajectory observability, assumptions that fail in privacy-preserving or restricted scenarios where only scalar performance metrics are available. We propose Generalization via Evolutionary Reward Shaping (GERS), a bilevel optimization approach to improve generalization on unseen test environments using only scalar feedback from validation environments. At the lower level, an RL agent guided via a reward function shaped by the upper level learns a policy on a limited set of training environments with accessible trajectory data; at the upper level, CMA-ES optimizes the reward shaping parameters to maximize the cumulative unshaped reward on separate validation environments for which trajectory access is unavailable. Results on continuous control tasks indicate that GERS outperforms the standard RL baseline on unseen test environments. GERS performance is comparable to DR, despite DR treating the combined set of training and validation environments of GERS as a single training set that requires trajectory access, whereas GERS cannot access validation trajectories. These results confirm that GERS effectively enhances generalization under restricted data access constraints.

04.
arXiv (CS.CL) 2026-06-19

Apparent Psychological Profiles of Large Language Models are Largely a Measurement Artifact

Psychological instruments designed for humans are increasingly used to assign large language models (LLMs) stable psychological profiles that affect their usability, safety assessment, and use as proxies for human participants in research. Using a formal psychometric framework, we show that these profiles are largely a measurement artifact. Administering a battery of personality and risk-preference instruments spanning self-reports and behavioral tasks to 56 instruction-tuned LLMs alongside large human reference samples, we report four findings. First, differences between models are driven not by the traits an instrument targets but by a directional response bias, a tendency to respond toward one end of the scale, or one labeled option, regardless of item content; a variance decomposition attributes 81-90% of between-model variation to this bias, against 9-16% in humans. Second, the bias declines with model capability but is not eliminated by it. Third, because bias rather than trait drives responding, an instrument's apparent reliability is almost entirely predicted by its response orthogonality, a term we coin for the proportion of items for which trait and bias point in opposite directions. Fourth, the profile a model appears to have shifts with the items used and can be manufactured through item selection. These results demonstrate that the apparent psychological profiles of LLMs are artifacts of the instrument used to measure them, not properties of the models themselves. As instruments borrowed from human psychology are rarely fully orthogonal and may inherently lack validity for LLMs, we call for dedicated assessments centered on response orthogonality.

05.
arXiv (CS.LG) 2026-06-12

A unified complexity bound for logconcave sampling

arXiv:2606.12694v1 Announce Type: cross Abstract: We give a simple, unified, and nearly tight bound for sampling arbitrary logconcave distributions from a warm start using the In-and-Out algorithm along with exponential lifting. The main new ingredient in the analysis is an improved bound on the Poincaré constant of a lifted distribution. As a consequence, the resulting convergence rate is nearly tight for both constrained settings (e.g., Gaussian restricted to a convex body) and well-conditioned settings (e.g., strongly logconcave and smooth densities).

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

InfantFace: Detecting infant faces in neonatal clinical environments

Reliable localisation of the neonatal face is the first step for several video-camera based non-contact assessments such as pain and distress related facial expression analysis, pain scoring, cardiorespiratory signal extraction and cessation of breathing alerts. However, major challenges persist in neonatal clinical environments. Cluttered backgrounds, illumination changes and poor lighting conditions can reduce the accuracy of face detection models. Clinical interventions, monitoring equipment and, in some cases, medical devices can obstruct the face, making visual assessment difficult. We propose a one-stage YOLOv11m-based model tailored for face detection of infants in neonatal clinical environments. We combined multiple publicly available datasets (VGGFace2, CelebA, FDDB, WIDER FACE) to train and evaluate our proposed model. We then fine-tuned our model on a neonatal research dataset involving 228 videos from 114 recording sessions of 113 independent infants. Before fine-tuning, our model achieved an AP50 of 0.87, surpassing the performance of three state-of-the-art general face detectors. Performance improved further to an AP50 of 0.96 after clinical-domain adaptation. Evaluating face detection performance across different datasets remains a challenge due to the lack of publicly available neonatal datasets. Prioritising the creation of such datasets, while upholding appropriate privacy safeguards and ethical standards in their creation and use, would greatly support further progress in this field.

07.
arXiv (quant-ph) 2026-06-16

Optimizing Wigner Negativity in Scattering Processes Using Energetic Cost Functions

arXiv:2606.15101v1 Announce Type: new Abstract: Wigner negativities (WNs) are key signatures of non-Gaussian bosonic states and essential resources for quantum technologies. We study their generation in the scattering of coherent pulses by a two-level atom coupled to a one-dimensional reservoir, a unitary and energy-preserving platform. Optimization in this multimode setting is hindered by the complexity of evaluating Wigner functions. We overcome this challenge by introducing energetic cost functions that identify output modes most likely to host large negativities. First using incoherent energy and then isolating a genuinely non-Gaussian contribution, we demonstrate a strong correlation between these quantities and WNs. This correlation extends beyond short, intense pulses to encompass pulses of finite energy, where photons are scattered while the two-level atom is driven. Focusing on the energy-efficiency of the process, we show that maximally efficient generation takes place for one input photon, on average, spectrally mode-matched with the atom.

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

Bootstrapped Monitoring: Leveraging Transparent Reasoning to Oversee Stronger AI Agents

arXiv:2606.11998v1 Announce Type: new Abstract: Trusted monitoring is a cornerstone of AI control. However, as frontier models grow more capable, the increasing capabilities gap between trusted and untrusted models may render trusted models unreliable monitors. We introduce bootstrapped monitoring, a protocol that addresses this by inserting a stronger, intermediate untrusted model with transparent chain-of-thought reasoning into the oversight chain. The untrusted monitor ($U_m$) evaluates the agent's actions, while a weaker trusted model ($T$) oversees $U_m$'s reasoning to detect collusion. We evaluate bootstrapped monitoring on multi-turn software engineering tasks (BashArena) across multiple agents and monitors. Bootstrapped monitoring substantially improves catch rates over trusted-only monitoring, even when the untrusted monitor actively colludes with the agent, provided we have access to its raw chain-of-thought. Our results suggest that bootstrapped monitoring can extend the useful lifetime of trusted models in control as AI capabilities advance.

09.
arXiv (CS.CV) 2026-06-11

CellNet – Localizing Cells using Sparse and Noisy Point Annotations

Counting living cells is an important step in many biological research workflows. Our collaborators at the Wellcome Sanger Institute study vital genes in humans via large scale saturation genome editing screening, which requires repeatedly counting cells a great number of times. Computer Vision based automation is crucial for high throughput and resource efficiency. In this work, we develop a regression-based deep learning computer vision algorithm to detect and count cells in phase-contrast microscopy images. To reduce annotation effort, which in practice often becomes a bottleneck, we focus on counting cells only using sparse point annotations, which are fast and easy to acquire. By comparison to state-of-the-art 0-shot methods, we show that regression-based counting is a promising alternative in low data regimes. Through developing methods to automatically count living cells in microscopy images, we contribute to valuable research on the human genome. The code is available at https://github.com/beijn/cellnet.

10.
arXiv (CS.AI) 2026-06-17

ASTEROID: A Spatiotemporal Information Transformer for Forecasting Multi-Step Time Series of Molecular Dynamics

arXiv:2606.17668v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis. Accurate forecast of the outcomes of a MD simulation is not only an attractive scientific challenge but also has substantial practical value. In this work, we developed a data-driven framework, termed ASTEROID (Advanced Spatiotemporal TransformER fOr Inferring Dynamics), that can directly predict multi-step atomic coordinates, avoiding conventional iterative integration. For this purpose, our ASTEROID reformulates MD trajectories as high-dimensional spatiotemporal sequences and integrates the Spatiotemporal Information (STI) Transformation equation into a Transformer architecture. The core innovation of ASTEROID lies in its ability to model multiscale spatiotemporal dependencies. In particular, for spatial dependencies, a local-global self-attention mechanism captures both short- and long-range interactions. For temporal dependencies, an encoder-decoder structure integrates global context with autoregressive forecasting. ASTEROID was evaluated on several quantum-mechanics derived molecular datasets. Our results indicate that ASTEROID achieved not only a higher level of accuracy in multi-step prediction than existing methods on various benchmarks, but also significantly reduced computational cost of conventional MD simulation. Moreover, the model supports iterative multi-step forecasting over an extended time scale. This work establishes a robust and generalizable data-driven paradigm for accelerating MD simulations.

11.
Nature (Science) 2026-06-17

Analysis of 173,303 exomes and genomes in the Pakistan Genome Resource

Naturally occurring loss-of-function variants in human genes enable drug target discovery because they mimic pharmacological inhibition of proteins. However, the study of these genetic variants is constrained by their rarity. Sequencing of diverse populations, particularly those enriched in familial relatedness, has been postulated to promote discovery of rare genetic variants1–3. Here we present the Pakistan Genome Resource, a South Asian biobank with high familial relatedness comprising 173,303 participants, who collectively carry naturally occurring homozygous loss-of-function variants in 6,476 genes. We describe the genetic architecture of this population, associations between genes and biomarkers, the distribution of loss-of-function variants across molecular pathways, and recall-by-genotype studies of therapeutically relevant genes. The Pakistan Genome Resource expands the catalogue of human genetic variants, provides a comprehensive genetic reference resource for the Pakistani population, and demonstrates the value of studying diverse cohorts to advance human health. The Pakistan Genome Resource compiles biobank data from 173,303 individuals with high familial relatedness, broadening the catalogue of human genetic variation and establishing a population-specific genomic reference for Pakistan.

12.
Nature (Science) 2026-06-22

Stereoretentive decarbonylative C(sp<sup>3</sup>)-C(sp<sup>3</sup>) cross-coupling

Authors:

While C(sp3)–C(sp3) bond-forming cross-coupling methods have become more common, stereocontrolled bond-formation remains a challenge,1 despite its importance for drug discovery, where there is a emerging demand for molecules with increased sp3 character.2-4 Enantiospecific cross-coupling approaches would complement advances in enantioselective coupling,5-8 but have been limited to specialized substrates with lower availability5,9 because stereospecific oxidative addition of more abundant chiral alkyl electrophiles is unknown.10 Inspired by the classic, stereoretentive Curtius rearrangement,11 herein we disclose a catalytic strategy that proceeds by an analogous stereoretentive decarbonylation step to form a versatile chiral alkylnickel intermediate from easily-available chiral amino-acid and α-hydroxy-acid derivatives. The chiral alkylnickel intermediates decompose and/or racemize on the order of minutes, but are sufficiently stable to enable stereoretentive cross-electrophile coupling12 with alkyl radicals (derived from alkyl iodides) at relatively low temperature (22-40 °C). This mechanistic strategy provides a straightforward approach to stereocontrolled C(sp3)–C(sp3) bond formation, including diastereomers that are inaccessible by stereoselective radical mechanisms. The “metallo-Curtius” strategy described in this study lays a mechanistic foundation for the development many new stereospecific cross-coupling reactions.

13.
medRxiv (Medicine) 2026-06-17

Cardio Heart Connect: Protocol for a Randomized Trial of a Commercially Available mHealth Fitness Intervention for Cardiac Rehabilitation After Transcatheter Aortic Valve Replacement

Background: Despite ample evidence of the benefits of cardiac rehabilitation (CR), few transcatheter aortic valve replacement (TAVR) patients participate. Commercially available mobile health offers an opportunity to deliver activity-promotion content to populations that are challenged to participate in CR. This study aims to test the efficacy of clinically controlled, commercially available fitness programming for improving physical activity and cardiovascular health outcomes designed to be initiated while patients are on waitlists for traditional CR. Methods: The Cardio Heart Connect study is a hybrid type I effectiveness-implementation trial aiming to enroll N=200 patients who have been placed on a cardiac rehab waitlist following a TAVR procedure from the University of Colorado Hospital Heart and Vascular Center. Participants will be randomized 1:1 to the Cardio Heart Connect intervention with commercially available fitness or attention control, designed to control for technology access. At baseline, post-intervention (8 weeks), and follow-up (12 months), we will assess the primary outcome of participants? daily steps as measured by smartwatch accelerometer and secondary outcomes of interest including functional capacity (Duke Activity Status Index; VO2max), quality of life (Kansas City Cardiomyopathy Questionnaire), and cardiovascular health status (Life Essential 8). In addition, we will use mixed methodologies to evaluate the implementation of intervention using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) Framework. Conclusions: Commercially available fitness programs have the potential to provide more accessible opportunities for patients recovering from TAVR to engage in physical activity and may be preferred due to their customizability, convenience, and ease of scheduling. Overall, this study will provide insight into the use of commercial mHealth to promote activity following TAVR.

14.
Nature (Science) 2026-06-17

Emergent decadal predictability in Antarctic contribution to sea-level rise

Despite large uncertainties associated with future mass loss from the Antarctic Ice Sheet, ice-sheet models show that the rate of sea-level rise from Antarctic ice loss in 2025 is strongly predictive of the rate for the next several decades, regardless of emission pathway or model complexity. This finding is robust across all models that were considered in the Intergovernmental Panel on Climate Change Sixth Assessment Report global mean sea-level projections, including the low-likelihood, high-impact scenarios of sea-level rise. Given this strong near-term decadal predictability, ice-sheet models that can accurately reproduce present-day ice-mass loss provide a reliable basis for near-term sea-level planning and adaptation through to mid-century. The predictability breaks down by the end of the twenty-first century as feedbacks, such as those related to marine ice-sheet retreat, begin to emerge, leading to accelerating ice loss. Drawing on these results, we identify key feedback mechanisms that can account for the transition between near-term decadal predictability and the longer-term, feedback-driven evolution, and suggest priorities for ice-sheet model development aimed at resolving long-term sea-level rise uncertainty. Although Antarctic ice loss projections diverge widely by 2100, this Perspective shows that present-day rates robustly predict mid-century sea level rise, providing a firm basis for near-term planning, while highlighting priorities for model development aimed at resolving longer-term sea level rise uncertainty.

15.
Nature Medicine 2026-06-08

Post-adjuvant chemotherapy in ctDNA-positive patients with resected colorectal cancer: a randomized phase 3 trial

Authors:

Tumor-informed circulating tumor DNA (ctDNA) enables detection of molecular residual disease (MRD) after curative resection of colorectal cancer (CRC), but whether early intervention improves outcomes remains uncertain. ALTAIR was a randomized, double-blind, phase 3 trial embedded in the CIRCULATE-Japan platform evaluating a post-adjuvant ctDNA surveillance strategy with treatment initiation upon molecular recurrence. Patients with resected stage 0–IV CRC who became ctDNA positive after completion of standard-of-care therapy and had no radiological evidence of disease were randomly assigned (1:1) to receive trifluridine/tipiracil (FTD/TPI) or placebo for 6 months. The primary endpoint was investigator-assessed disease-free survival (DFS). Between July 2020 and June 2023, 243 patients were randomized to FTD/TPI (n = 122) or placebo (n = 121). Median DFS was 9.30 months with FTD/TPI and 5.55 months with placebo (hazard ratio = 0.79, 95% confidence interval: 0.60–1.05, P = 0.107), and the primary endpoint was not met. FTD/TPI increased grade 3 or higher hematologic adverse events (73.0% versus 3.3%) without new safety signals. These findings indicate that post-adjuvant intervention with FTD/TPI did not significantly improve DFS in ctDNA-positive patients without radiological disease. ClinicalTrials.gov identifier: NCT04457297 . In the randomized, double-blind phase 3 ALTAIR trial, patients with resected colorectal cancer who became positive for circulating tumor DNA during post-adjuvant surveillance received trifluridine/tipiracil hydrochloride therapy, which did not significantly prolong disease-free survival compared with placebo.

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

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

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.

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

The Hidden Evolution of Disguised Visual Context inside the VLM

arXiv:2606.20077v1 Announce Type: cross Abstract: Visual tokens enter Large Language Models (LLMs) as raw, foreign signals. How they are transformed into meaningful representations and interact with the language space depends entirely on the integration architecture. Whether by treating visual tokens as in-context prompts within the input sequence or injecting them directly into the LLM's intermediate layers. A controlled comparison and understanding of how these architectural choices affect visual information and its internal transformation to integrate with the LLM remains underexplored. We provide a fair comparison by evaluating in-context and layer-wise injection VLM integration paradigms under identical training conditions across single image, multi-image, and video benchmarks. In doing so, we uncover a hidden evolution where visual tokens enter the LLM as disguised visual context, raw representations lacking linguistic structure, but are progressively reshaped depending on the integration paradigm, each capturing fundamentally different frequency characteristics of the visual signal. We show that this evolution inside the LLM determines what visual features the VLM can utilize effectively, how visual representations align with the language space, and ultimately how each paradigm performs across different tasks. We further demonstrate that attention allocation alone is insufficient, and that performance is driven by the quality of visual representations at each layer.

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

Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs

arXiv:2606.19374v1 Announce Type: cross Abstract: Graph-based representations are widely used in protein modeling, yet many existing approaches rely primarily on sequence adjacency or geometric proximity, which only partially reflect the principles governing protein folding. Proteins instead adopt complex three-dimensional conformations organized around secondary structure elements, such as $\alpha$-helices and $\beta$-sheets, which encode recurring local motifs and stabilizing hydrogen-bond interactions. In this work, we introduce a secondary-structure-aware graph neural network for protein representation learning. Residue-level node representations are augmented with secondary structure assignments, and graph edges are constructed from hydrogen-bond interactions filtered by their energetic strength. This design enables the model to capture both local structural context and long-range couplings that are central to protein stability and function. We evaluate the proposed approach on commonly used protein benchmarks and observe consistent improvements over existing graph-based methods. In addition, the resulting graph representations offer enhanced biological interpretability, as the learned connectivity aligns with established structural motifs. These findings suggest that incorporating secondary structure and energy-filtered hydrogen-bond topology provides an effective inductive bias for protein representation learning. The code is released at https://github.com/mohamedmohamed2021/SSProNet

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

Data augmented bootstrap: Unifying confidence interval construction by approximate invariance

arXiv:2606.09049v2 Announce Type: replace-cross Abstract: We propose the data augmented bootstrap (DAB), a framework for constructing confidence intervals from approximately invariant transformations of the data. As special cases, DAB recovers popular methods that rely on exact group symmetries, such as conformal prediction, wild bootstrap for Maximum Mean Discrepancy U-statistics and the recently proposed SymmPI. Meanwhile, DAB also recovers the classical bootstrap method, which exploits the dataset's approximate invariance under uniform sampling of data indices as the dataset size grows. For all DAB methods, we establish theoretical coverage results that interpolate between finite-sample and asymptotic guarantees according to the strength of the invariance, and without assuming a group structure. The approximate invariance is measured in the Kolmogorov distance and, for statistics that satisfy Gaussian universality, reduces to conditional mean and variance matching. This allows us to incorporate data augmentation (DA), a widely used machine learning heuristic based on approximate invariances, into known statistical methods. We empirically test the performance of incorporating DA into bootstrap, wild bootstrap and conformal prediction for simulated settings as well as for image, language and scientific data.

20.
arXiv (CS.CL) 2026-06-11

ChartFI: Benchmarking Faithfulness and Insightfulness of Chart Descriptions from Multimodal Large Language Models

Chart descriptions are essential for accessibility, cross-modal retrieval, and assisting readers in extracting insights from complex visualizations. As multimodal large language models (MLLMs) are increasingly adopted for automated chart description generation, a critical question arises: how faithfully and insightfully do these models actually describe charts? Current benchmarks fall short on two fronts: existing datasets consist of simple, homogeneous charts paired with shallow, fact-enumerating descriptions; and prevailing metrics fail to capture the multi-faceted nature of description quality. To address these gaps, we present the Chart Faithfulness and Insightfulness Benchmark (ChartFI-Bench). We first summarize four dimensions that characterize high-quality chart descriptions: factual accuracy, salient feature emphasis, domain-informed guidance, and chart-text complementarity. Guided by these dimensions, we construct a high-quality benchmark comprising 896 chart-description pairs, which feature visually complex charts and semantically rich descriptions. Furthermore, we design four aligned evaluation metrics – Faithfulness, Coverage, Informativeness, and Acuity – to systematically assess the quality of descriptions across these dimensions. Experiments conducted on mainstream MLLMs demonstrate the effectiveness of the proposed framework and reveal common weaknesses among existing models.

21.
arXiv (CS.AI) 2026-06-16

LLM Jaggedness Unlocks Scientific Creativity

arXiv:2605.10574v3 Announce Type: replace Abstract: As artificial intelligence advances, models are not improving uniformly. Instead, progress unfolds in a jagged fashion, with capabilities growing unevenly across tasks, domains, and model scales. In this work, we examine this dynamic jaggedness through the lens of scientific idea generation. We introduce SciAidanBench, a benchmark of open-ended scientific questions designed to measure the scientific creativity of large language models (LLMs). Given a scientific question, models are asked to generate as many unique and coherent ideas as possible, with the total number of valid responses serving as a proxy for creative potential. Evaluating 19 base models across 8 providers (30 total variants including reasoning versions), we find that jaggedness manifests both across models and within models. First, in a cross-task comparison between general and scientific creativity, improvements in general creativity do not translate uniformly to scientific creativity, revealing divergent capability profiles across models. Second, at the prompt level, stronger models do not improve uniformly; instead, they exhibit high variability, with bursts of creativity on some questions and limited performance on others. Third, at the domain level, individual models display uneven strengths across scientific subfields, reflecting fragmented internal capability profiles. Finally, we show that this jaggedness can be harnessed. We explore mechanisms of inference-time compute, knowledge pooling, and brainstorming to combine models effectively and construct meta-model ensembles that outperform any single model. Our results position jaggedness not as a limitation, but as a resource, a structural feature of AI progress that, when understood and leveraged, can amplify LLM-driven scientific creativity.

22.
arXiv (CS.CL) 2026-06-15

Verbatim Chunks Beat Extracted Artifacts: A Controlled Ablation of Memory Representations for Long LLM Conversations

Authors:

A growing class of conversational-memory systems compresses dialogue history into structured artifacts – extracted facts, decisions, or events – on the premise that distilled structure retrieves better than raw text. We test this premise with a controlled ablation: within one fixed retrieval-rerank-reasoning pipeline, we swap only the stored representation – LLM-extracted typed artifacts versus verbatim conversation chunks – holding the model, retriever, reranker, and judge constant. Verbatim chunks win by 15.9 points on LoCoMo (43.9% vs. 28.0%) and 22.0 points on LongMemEval-S (67.4% vs. 45.4%); a 1-hop semantic graph does not recover the gap, and five confound controls reproduce the effect. The mechanism is lossy distillation: extraction discards verbatim detail that chunks retain for free, and the extracted-artifact pipeline never beats naive RAG in overall accuracy. Concurrent positive results with near-verbatim, provenance-preserving units fit the same account: retrieval accuracy tracks how far the representation departs from the source. For the extraction designs we test, structured memory should augment verbatim text rather than replace it: a chunks $\cup$ artifacts union store matches chunks on both benchmarks while artifacts alone forfeit the gap. Code and data: https://github.com/tao-hpu/cog-canvas

23.
arXiv (CS.CL) 2026-06-11

Causal Emotion Recognition in Conversation: Context Saturation and Discourse-Marker Evidence

We address two persistent gaps in Emotion Recognition in Conversation: which modeling choices materially affect performance, and how recognition findings connect to interpretable discourse-level patterns. We study both through a systematic investigation on IEMOCAP with cross-dataset validation on MELD. For recognition, we run controlled ablations with 10 random seeds and paired significance tests with multiple-comparisons correction, yielding three findings. First, conversational context is the dominant factor, but performance saturates quickly: roughly 90% of the gain is captured within the most recent 10-30 preceding turns, depending on the label set. Second, hierarchical sentence representations help most in utterance-only settings and show a clear advantage on MELD, but their benefit disappears once turn-level context is available, suggesting that conversational history subsumes much of the intra-utterance structure. Third, integrating an external affective lexicon does not improve results, consistent with pretrained encoders already capturing most of the affective signal needed for ERC. Under a strictly causal setting, our simple models achieve strong performance (82.69% 4-way; 67.07% 6-way weighted F1), showing that competitive accuracy is achievable without future turns. For linguistic analysis, we examine 5,286 discourse-marker occurrences and find a reliable association between emotion and marker position (p < .0001). Sad utterances show reduced left-periphery marker usage (21.9%) relative to other emotions (28-32%), consistent with accounts linking left-periphery markers to active discourse management. This aligns with our recognition results, where Sad benefits most from conversational context (+22 percentage points), suggesting sadness may be more context-dependent than emotions with stronger local pragmatic cues.

24.
bioRxiv (Bioinfo) 2026-06-11

Amylo-Pipe: an integrated web server for mechanistic and kinetic prediction of protein and peptide aggregation

Protein aggregation is central to amyloid-related disorders and remains a major developability challenge for protein therapeutics. Over the past two decades, significant advances have been made to predict aggregation-prone regions (APRs) and estimate aggregation propensity in proteins and peptides. In contrast, the prediction of aggregation kinetics has received relatively less attention due to the limited availability and heterogeneity of experimental data. Consequently, aggregation propensities from APR prediction algorithms were widely accepted as a means to predict relative changes in the aggregation kinetics of proteins and mutants. Previous studies have demonstrated, using large-scale datasets, that aggregation propensity shows a weak or inconsistent correlation with aggregation kinetics. In the present study, we have integrated complementary state-of-the-art mechanistic and kinetic prediction tools for protein aggregation into a unified, user-friendly web framework entitled "Amylo-Pipe". Amylo-Pipe also implements practical features that are especially useful for protein engineering, such as gatekeeper-residue mutational scanning to support the design of aggregation-resistant variants. By consolidating multiple prediction tasks in a single interface, Amylo-Pipe enables a more comprehensive assessment of aggregation behavior than APR-only workflows. The web server is freely accessible at: https://web.iitm.ac.in/bioinfo2/amylopipe/.

25.
arXiv (CS.CL) 2026-06-11

BioMamba: Domain-Adaptive Biomedical Language Models

Background. Biomedical language models should improve performance on biomedical text while retaining general-language-modeling fluency. For Mamba-based models, this trade-off has not been systematically studied across biomedical literature and clinical text. Methods. We developed BioMamba, a family of biomedical Mamba2 models at five scales obtained by continued pretraining of released public Mamba2 checkpoints on a balanced 80%/10%/10% mixture of PubMed abstracts, the Colossal Clean Crawled Corpus (C4), and Wikipedia. The contribution is the adaptation recipe and the accompanying open-weight checkpoints. Results. Across five scales, BioMamba consistently lowered PubMed perplexity, improved Wikipedia-style held-out perplexity by 1.46-4.72 PPL, and left C4 perplexity essentially unchanged. On six out-of-domain multiple-choice benchmarks, BioMamba stayed within +/-3 percentage points of Mamba2 with no systematic regression. After supervised fine-tuning, BioMamba+SFT matched or exceeded Mamba2+SFT on MIMIC-IV note completion and discharge summary generation at every evaluated scale, and improved PubMedQA at every scale. The strongest model (BioMamba-2.7B) reached a PubMed perplexity of 5.28 and accuracies of 90.24% and 73.00% on BioASQ and PubMedQA, respectively. Conclusions. A balanced domain-adaptive continued pretraining recipe strengthens Mamba2 language models on biomedical literature and clinical text while preserving general-language-modeling fluency.