The total eclipse of bioinformatics: From disruption to convention, and a gentle warning
by Christos A. Ouzounis
Academic Intelligence · Curated Daily
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by Christos A. Ouzounis
arXiv:2508.21720v3 Announce Type: replace Abstract: Automating scientific poster generation requires hierarchical document understanding and coherent content-layout planning. Existing methods often rely on flat summarization or optimize content and layout separately. As a result, they often suffer from information loss, weak logical flow, and poor visual balance. We present PosterForest, a training-free framework for scientific poster generation. Our method introduces the Poster Tree, a structured intermediate representation that captures document hierarchy and visual-textual semantics across multiple levels. Building on this representation, content and layout agents perform hierarchical reasoning and recursive refinement, progressively optimizing the poster from global organization to local composition. This joint optimization improves semantic coherence, logical flow, and visual harmony. Experiments show that PosterForest outperforms prior methods in both automatic and human evaluations, without additional training or domain-specific supervision.
arXiv:2606.13179v1 Announce Type: cross Abstract: In recent years, driven by the computational demands of data-intensive applications such as artificial intelligence and scientific computing, analog computing has gained renewed interest. Given the diversity of computational tasks and recent advancements in analog CMOS circuits and resistive memory technologies, we refer to the evolving landscape as modern analog computing. In this context, we identify three core computational primitives: solving differential equations, solving matrix equations, and performing matrix-vector multiplications, and we explore the connections among them. We also examine various hardware implementations of these analog computing operators, including those built with discrete components, integrated circuits, and resistive memory devices. Among these, resistive memory arrays emerge as particularly promising due to their implementation efficiency. The paper then surveys recent progress in leveraging modern analog computing to solve differential and matrix equations using both advanced analog CMOS circuits and resistive memory arrays. Finally, we discuss the applications of these circuits, the precision and scalability issues and their potential solutions, the relationship with in-memory computing, and the unique computational complexity of analog computing. This paper provides a unified perspective on analog computing, highlighting its strengths, current developments, and challenges, and positioning it as a pivotal enabler of next-generation computational frontiers.
arXiv:2606.18961v1 Announce Type: new Abstract: Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets. To overcome this supervision bottleneck, we introduce unsupervised reward optimization of PLMs, a comprehensive framework for steerable protein generation without ground-truth labels. Our key insight is that task-agnostic rewards, which combine intrinsic model uncertainty with extrinsic semantic consistency informed by protein representation models, exhibit strong correlation with controllability measures across base models and temperature regimes. Building upon this discovery, we propose two offline algorithms: Soft Reward Optimization (SRO) and Binarized Reward Optimization (BRO), which effectively maximize the classical RLHF objective induced by these proxy rewards. Extensive experiments on compositional out-of-distribution prompts demonstrate that both methods significantly outperform competitive baselines (DPO, KTO), while approaching oracle performance across multiple sampling temperatures, model scales and protein families. Moreover, PLMs fine-tuned with unsupervised rewards can achieve consistently higher coverage compared to their base model in pass@k evaluations. By enabling self-improvement of PLMs through their own generated experience, our framework provides a scalable pathway toward controllable biomolecular design in settings where labeled preferences or experimental feedback are scarce or unavailable.
The limiting resource for training agents via reinforcement learning (RL) is increasingly frontier task supply: valid, solvable tasks just difficult enough to train the current model. As reasoning and agentic models improve, fixed task distributions saturate, while naive synthetic generation yields tasks that are trivial, impossible, or ill-posed. Training a task generator with RL to optimize validity and learnability can address this bottleneck, but direct optimization requires repeated solver rollouts per candidate. For software-engineering (SWE) tasks, a single rollout can take tens of minutes; solver-in-the-loop generator training is intractable. We introduce PROPEL, a solver-amortized framework for training task generators at the targeted solve rate. PROPEL trains a lightweight activation probe on a one-time labeled corpus of generated tasks and solver outcomes. The probe predicts target-solver pass rate from a frozen generator reference model and serves as a proxy for solve rate during generator optimization, reducing generator evaluation to a single forward pass. Across math, code, and software-engineering at multiple model scales, PROPEL shifts generation toward the targeted solve rate: for coding, tasks generated at the learnable frontier increase from $10.1\% \rightarrow 20.0\%$ for a Qwen2.5-3B-Instruct solver and from $5.3\% \rightarrow 12.6\%$ for a Qwen2.5-7B-Instruct solver. For SWE, PROPEL increases the share of generations at the targeted solve rate from $9.8\% \rightarrow 19.6\%$ for Qwen3.5-27B on repositories not seen during training of probe and generator.
Driver-centric route representation plays a vital role in intuitive driving guidance systems. This paper presents OLRA, a low-cost, map-localization-based framework that derives driver-view-aligned routes by matching map-based navigation routes with camera-detected lane markings. This alignment process mutually enhances vehicle localization accuracy and visual route consistency. To bridge the evaluation gap across different paradigms, we introduce practical route evaluation metrics and benchmark OLRA against OpenPilot, a representative direct-generation approach. Experimental results on the nuScenes dataset demonstrate that OLRA outperforms OpenPilot in complex road segments and in route estimation at distance beyond 20 meters, achieving lower overall Euclidean error. This study is expected to promote future research in low-cost, maplocalization-based route generation methods.
arXiv:2510.02605v2 Announce Type: replace Abstract: While many modern studies are dedicated to ML-based large-sample hydrologic modeling, these efforts have not necessarily translated into predictive improvements that are grounded in enhanced physical-conceptual understanding. Here, we report on a CONUS-wide large-sample study (spanning diverse hydro-geo-climatic conditions) using ML-augmented physically-interpretable catchment-scale models of varying complexity based in the Mass-Conserving Perceptron (MCP). Results were evaluated using attribute masks such as snow regime, forest cover, and climate zone. Our results indicate the importance of selecting model architectures of appropriate model complexity based on how process dominance varies with hydrological regime. Benchmark comparisons show that physically-interpretable mass-conserving MCP-based models can achieve performance comparable to data-based models based in the Long Short-Term Memory network (LSTM) architecture. Overall, this study highlights the potential of a theory-informed, physically grounded approach to large-sample hydrology, with emphasis on mechanistic understanding and the development of parsimonious and interpretable model architectures, thereby laying the foundation for future models of everywhere that architecturally encode information about spatially- and temporally-varying process dominance.
arXiv:2606.13400v1 Announce Type: cross Abstract: While flow-based generative models have demonstrated strong performance across a wide range of domains, deploying them in safety-critical physical systems remains challenging due to strict constraint requirements. Existing approaches typically enforce safety through post-hoc corrections, which incur substantial computational overhead and may distort the learned distribution. We propose PolyFlow, a polytope-constrained flow matching framework that embeds constraints directly into the model and flow dynamics. PolyFlow introduces a discrete-time flow formulation and a projection-free architecture, which eliminate the discretization error and guarantee strict satisfaction of arbitrary polyhedral constraints, without the need for expensive iterative solvers. Experimental results show that PolyFlow achieves zero constraint violation while maintaining high distributional fidelity across a range of planning and control tasks. Compared to state-of-the-art constrained generation baselines, PolyFlow significantly reduces inference latency and demonstrates a favorable trade-off between safety, efficiency, and generative quality. Code is available on https://github.com/MJianM/PolyFlow.
Multimodal Foundation Models are increasingly used as reasoning agents, making reliability, knowing when a model may hallucinate, critical. A common intuition, which we call the Attention-Confidence Assumption, holds that reliability follows from "structural" visual perception: tight attention on relevant regions should signal a trustworthy answer, while scattered attention signals confusion. We challenge this through the VLM Reliability Probe (VRP), a systematic cross-family study of reliability signals in contemporary Vision-Language Models (VLMs). We introduce structural-attention metrics, cluster counts (C_k) and spatial entropy (H_s), to quantify the visual encoder's gaze, and track its evolution (Delta H_s) across layers. This reveals a "Symbolic Detachment": models often "Early Lock" visual features only to diffuse attention later, severing early perception from final generation. Contrary to the grounding hypothesis, we find a "Cluster Failure": spatial attention has near-zero correlation (R approx 0.001) with accuracy. Instead, reliability is a phenomenon of generation dynamics and internal-state distributions. Self-Consistency, the agreement rate across sampled reasoning paths, is the dominant predictor of truth (R = 0.429). Scaling causal interventions exposes a sharp architectural divergence: LLaVA locks its prediction in a fragile late-stage bottleneck, whereas PaliGemma and Qwen2-VL distribute reliability globally, staying resilient even when ~50% or more of their most predictive layer is destroyed. For current VLMs, reliability signals are detached from visual grounding maps and are best inferred from generation-time dynamics and hidden-state probes.
The data processing inequality is an information-theoretic principle stating that the information content of a signal cannot be increased by processing the observations. In particular, it suggests that there is no benefit in enhancing the signal or encoding it before addressing a classification problem. This assertion can be proven to be true for the case of the optimal Bayes classifier. However, in practice, it is common to perform "low-level" tasks before "high-level" downstream tasks despite the overwhelming capabilities of modern deep neural networks. In this paper, we aim to understand when and why low-level processing can be beneficial for classification. We present a comprehensive theoretical study of a binary classification setup, where we consider a classifier that is tightly connected to the optimal Bayes classifier and converges to it as the number of training samples increases. We prove that for any finite number of training samples, there exists a pre-classification processing that improves the classification accuracy. We also explore the effect of class separation, training set size, and class balance on the relative gain from this procedure. We support our theory with an empirical investigation of the theoretical setup. Finally, we conduct an empirical study where we investigate the effect of denoising and encoding on the performance of practical deep classifiers on benchmark datasets. Specifically, we vary the size and class distribution of the training set, and the noise level, and demonstrate trends that are consistent with our theoretical results.
TimeLens is an AI-powered bilingual mobile guide for the Grand Egyptian Museum (GEM). Pointing a phone at an exhibit, a visitor sees the artifact recognized in real time and can ask follow-up questions answered in English or Arabic. The work addresses three problems specific to in-gallery deployment: fine-grained visual similarity among 51 catalogued artifacts (many near-identical Ramesside statues), the gap between curated training data and handheld camera conditions, and the risk of an AI guide stating unsupported historical facts. Two engineering contributions are reported. First, an on-device artifact detector was developed through a data-quality-driven iteration study – from foundation-model auto-annotation (YOLO-World), through spatial label-cleaning rules, to a fully hand-annotated dataset – isolating label quality as the decisive factor: the final YOLOv8n model resolves every previously failing class while remaining a 5.97 MB TensorFlow Lite asset that runs in real time on a mid-range phone (mAP@0.5 = 0.995, mAP@0.5:0.95 = 0.924). Second, a bilingual Retrieval-Augmented Generation (RAG) guide, grounded in a 108-record ChromaDB knowledge base, was benchmarked across seven candidate language models, with Gemma 4 E2B (Q4 K M) selected; ten targeted optimizations reduce end-to-end latency from over 30 s to approximately 10 s. Both subsystems are integrated in a production Flutter application with bilingual interface, museum location gating, and text-to-speech support.
The rapid advancement of large language models (LLMs) necessitates effective mechanisms to ensure their responsible deployment by accurately distinguishing unsafe content from benign content. While substantial safety datasets are available in English, multilingual safety modeling remains underexplored due to limited open-source safety datasets in other languages. Even within English datasets, safe yet sensitive corner-case content is scarce, leading to shortcut learning by models and non-trivial false-positive rates. To mitigate these issues, we introduce a novel minimax reinforcement learning (RL) framework wherein a data generator and a classifier model co-evolve, facilitating the production of high-quality synthetic multilingual safety data. We theoretically formalize this interaction as a minimax game and rigorously demonstrate convergence to a Nash equilibrium. Empirical evaluations confirm that our synthetic data generation method significantly enhances the classifier model performance, enabling a substantially smaller model to surpass the state-of-the-art by nearly 10% on English benchmarks while achieving 4.5x faster inference speed. These results establish a scalable and efficient methodology for synthetic data generation, advancing the development of safer and more robust multilingual LLM deployments.
Real-time conversational assistants for procedural manual tasks often depend on video input, which can be computationally expensive and compromise user privacy. For the first time, we propose a real-time conversational assistant that provides comprehensive guidance for procedural manual tasks using only lightweight privacy-preserving modalities such as audio and IMU inputs from a user's wearable device to understand the context. Using a furniture assembly task and a cooking task, we show how this assistant proactively communicates step-by-step instructions to a user performing a procedural task, and answers user questions. We illustrate the data generation method and the system design to achieve such an assistant. On observing that an off-the-shelf language model is a talkative assistant but is not always able to answer questions correctly, we demonstrate how finetuning the model improves its ability to limit unnecessary dialogues with a 50% increase in the precision, while also improving its ability to answer questions correctly, measured by a 150% increase in the recall of answers. We further describe how such an assistant is implemented on an edge device with no dependence on the cloud.
Carbohydrates are among the most abundant and structurally diverse biomolecules in nature, playing central roles in energy storage, molecular recognition, and cell signaling. Within this domain, C-glycosides1-3, in which the oxygen atom of the glycosidic bond in O-glycosides is replaced by carbon, have emerged as valuable motifs in medicinal chemistry due to their resistance to enzymatic hydrolysis2,4. Of particular importance are C-aryl glycosides, exemplified by the SGLT2 inhibitors dapagliflozin, canagliflozin, and empagliflozin, which are frontline therapies for type 2 diabetes5-7. However, scalable syntheses of C-aryl glycosides have traditionally relied on protected sugar derivatives, lengthy sequences, or conventional cross-couplings that often suffer from poor selectivity, limited scope, and extensive protecting-group manipulation6. Herein, we report a practical approach to C-aryl glycosides using glycosyl sulfonyl hydrazides as redox-neutral radical precursors for cross-coupling. Prepared directly from unprotected native sugars, these reagents generate glycosyl radicals under mild conditions and enable efficient access to diverse C-aryl glycosides, including all approved SGLT2 inhibitors, natural products such as salmochelins and neopetrosins, and medicinally relevant probes. Beyond anomeric functionalization, this platform enables C–C bond formation at multiple positions on carbohydrate scaffolds and supports stereoretentive radical coupling that can override inherent stereochemical biases, expanding practical access to carbohydrate-derived therapeutics and chemical tools.
The increasing amount of political debates and politics-related discussions calls for the definition of novel computational methods to automatically analyse such content with the final goal of lightening up political deliberation to citizens. However, the specificity of the political language and the argumentative form of these debates (employing hidden communication strategies and leveraging implicit arguments) make this task very challenging, even for current general-purpose pre-trained Language Models (LMs). To address this, we introduce a novel pre-trained LM for political discourse language called RooseBERT. Pre-training a LM on a specialised domain presents different technical and linguistic challenges, requiring extensive computational resources and large-scale data. RooseBERT has been trained on large political debate and speech corpora (11GB) in English. To evaluate its performances, we fine-tuned it on multiple downstream tasks related to political debate analysis, i.e., stance detection, sentiment analysis, argument component detection and classification, argument relation prediction and classification, policy classification, named entity recognition (NER). Our results show improvements over general-purpose LMs on the majority of these tasks, highlighting how domain-specific pre-training enhances performance in political debate analysis. We release RooseBERT for the research community.
We introduce the Meaning Intelligence Framework (MIF), a nine-dimension annotation and evaluation schema for Nigerian public discourse that separates surface sentiment from true communicative intent. Existing benchmarks for Nigerian languages, including NaijaSenti and AfriSenti, treat sentiment classification as a three-way polarity task (positive, negative, neutral). We argue that the dominant failure mode of AI systems on Nigerian discourse is not translation failure but context failure: the same utterance carries opposite pragmatic force depending on speaker, audience, and situation. The MIF operationalises this insight across nine scored dimensions: register, surface sentiment, true intent, irony, coded subtext, risk tier, annotator confidence, speaker emotion, and recommended communications action. We construct a 30-item calibration dataset spanning Standard English, Nigerian English, Nigerian Pidgin, and code-mixed registers, and evaluate a frontier language model (Gemini 2.5 Flash) under zero-shot and schema-informed prompting conditions. The headline finding is the Register Gap: zero-shot register classification accuracy is 33.3%, rising to 73.3% (+40 points) when the model receives the MIF schema in-context. The composite Meaning Intelligence Score increases by 5.4 points (73.2 to 78.6) under schema-informed prompting, with the largest practical gains in register identification, coded-subtext detection (+10 points), and strategic action recommendation (+10.3 points). We release the framework specification, annotation guidelines, and the 30-item public calibration set to support reproducibility, while retaining a private holdout corpus for contamination-protected evaluation.
arXiv:2606.07140v2 Announce Type: replace Abstract: We experimentally demonstrate an improved optical biasing scheme for superconducting nanowire single-photon detectors (SNSPDs), which employs a cryogenic InGaAs-InP photodiode (PD) as a local bias source. It is found that, under illumination from a stable external light source, this PD generates a stable photocurrent in a cryogenic environment (~2.3 K), with fluctuations in the photocurrent primarily attributed to fluctuations in the incident optical power. Furthermore, by screening and effectively blocking stray photons leaking from the PD, which give rise to background dark counts, we have achieved an SNSPD exhibiting an ultra-low intrinsic dark count rate of 1e-4 cps. Utilizing this improved optical biasing technique, our SNSPD achieved performance comparable to that obtained under conventional electrical biasing: a system detection efficiency of 80.7%, a background dark count rate of 32.6 cps, and a minimum timing jitter of 57.5 ps. These results indicate that cryogenic-PD-based optical biasing serves as a viable, low-noise, and low-jitter alternative to traditional electrical biasing. Moreover, this work offers useful design guidance for the future development of PD-based low-noise bias sources and for the construction of all-photonic SNSPD systems tailored for high-precision quantum photonics applications.
Characterising the tumour microenvironment (TME) from routine H&E-stained histology images requires simultaneous cell segmentation, feature extraction, and interpretable clinical reporting. We present SEGTME-UNI2, a unified framework addressing these requirements. Its core is UNI2-UPERHOVER, a dual-head segmentation model pairing the UNI2-H pathology foundation model (ViT-Giant, pretrained on >100M tiles from 100K slides) with two parallel UperNet decoders: one for six-class semantic segmentation and one for horizontal-vertical gradient regression enabling watershed-based nuclear instance separation. To address the lack of pixel-level annotations in large real-world repositories, UNI2-UPERHOVER undergoes a three-stage progressive pseudo-label curriculum. Each stage trains a fresh model without weight transfer, driving improvement entirely via increased pseudo-label quality: Stage 1: Uses human-annotated PanNuke (7,901 images, 189,744 nuclei, 0.25 um/pixel). Stage 2: Uses entropy-filtered pseudo-labels from the Stage 1 model on 271,711 TCGA-UT scale-0 patches (0.5 um/pixel). Stage 3: Uses pseudo-labels from the Stage 2 model on all 1,608,060 TCGA-UT patches across six resolution scales (0.5-1.0 um/pixel). Segmentation outputs feed a structured TME feature extraction pipeline computing 20+ per-patch compositional, morphological, spatial entropy, and intercellular distance metrics. These are encoded as JSON and passed to a fine-tuned NVIDIA BioNeMo GPT model to generate clinically interpretable TME narratives. Preliminary validation on held-out PanNuke and TCGA-UT partitions demonstrates framework feasibility and internal consistency. The pseudo-labelled TCGA-UT dataset and UNI2-UPERHOVER checkpoint are publicly released to support large-scale TME profiling and spatial biology research.
arXiv:2606.19998v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models are increasingly deployed across diverse tasks, yet they remain black boxes whose physical interactions can cause irreversible harm, making generalizable and interpretable failure detection essential. We observe that successful and failed rollouts carry systematically different information-theoretic signatures. Building on this, we formalize VLA control as a closed-loop information pipeline and derive the Triple Information-theoretic (Tri-Info) signals that capture whether actions remain diverse, temporally consistent, and coupled to state transitions. Across six VLA models and three benchmark environments, Tri-Info matches the strongest baselines in-domain. Moreover, Tri-Info transfers across architectures, environments, and the sim-to-real gap without retraining, reaching 83\% accuracy on real-world tasks where prior detectors collapse to chance. This establishes Tri-Info as a simple yet powerful method that not only detects failures with strong cross-domain generalization, but also delivers interpretable diagnostics of the underlying failure modes.
arXiv:2606.11389v1 Announce Type: new Abstract: Let $\lambda = \lambda(\beta,\sigma,a,b)$ denote the top Lyapunov exponent for the linearization along trajectories of the noisy damped non-linear oscillator $\ddot{x}+\beta \dot{x} + ax+bx^3 = \sigma \dot{W}_t$, where $a$, $b$ and $\beta$ are all positive and $\sigma \neq 0$. In 2004 Arnold, Imkeller and Sri Namachchivaya stated without proof that $\lambda(\varepsilon^2 \beta,\varepsilon \sigma,a,b) \sim \overline{\lambda} \varepsilon^{2/3}$ as $\varepsilon \to 0$ with $\overline{\lambda} > 0$. This paper contains a proof of this assertion.
Diffusion large language models (dLLMs) offer an efficient alternative to autoregressive models through parallel decoding, yet existing post-training methods largely rely on random masking strategies that overlook intrinsic token dependencies. In this work, we present an empirical analysis of attention in dLLMs and show that tokens attending more strongly to unmasked context exhibit greater generation stability and play a critical role in reasoning. Motivated by these findings, we propose AGDO, an attention-guided denoising and optimization framework that aligns both training and optimization with attention-derived dependencies. AGDO determines the denoising order based on attention structure and emphasizes attention-critical tokens during supervised fine-tuning and reinforcement learning. Experiments on mathematical and coding benchmarks demonstrate that AGDO consistently improves reasoning performance, outperforming state-of-the-art post-training methods for dLLMs.
LLM agents increasingly rely on external skills – reusable tool specifications – but real-world tasks often require composing multiple skills, not just selecting one. We formalize this as the Compositional Skill Routing problem: given a complex user query and a large skill library, decompose the query into atomic sub-tasks, retrieve the appropriate skill for each sub-task, and compose an executable plan. We present SkillWeaver, a decompose-retrieve-compose framework combining an LLM task decomposer, a bi-encoder skill retriever with FAISS indexing, and a dependency-aware DAG planner. To support evaluation, we introduce CompSkillBench, a benchmark of 300 compositional queries over 2,209 real MCP server skills spanning 24 functional categories, sourced from the public MCP ecosystem. Our experiments reveal that task decomposition quality is the primary bottleneck: standard LLM decomposition reaches only 34.2% category recall at the step level. To address this, we propose Iterative Skill-Aware Decomposition (SAD), a retrieval-augmented feedback loop that iteratively aligns decomposition with available skills. SAD improves decomposition accuracy from 51.0% to 67.7% (+32.7%, Wilcoxon p < 10^-6) in a single iteration; DA-conditioned analysis confirms that correct granularity is the prerequisite for effective retrieval (CatR@1 rises from 34% to 41% when DA=1). SkillWeaver reduces context window consumption by over 99%, and transfer experiments confirm generalization (+35.6% relative DA gain even when target categories are absent from the retrieval pool).
arXiv:2606.19894v1 Announce Type: new Abstract: The remarkable success of score-based diffusion models has spurred significant efforts to establish their theoretical foundations. However, existing complexity bounds for score approximation rely heavily on restrictive assumptions like Lipschitz continuous densities or smooth manifold supports, which are routinely violated by the singularities, sharp boundaries, and disjoint clusters inherent to real-world perceptual data. This work establishes a universal score approximation theorem that works for any distribution supported on any compact set of upper Minkowski dimension $d$. Using a novel discrete-mixture formulation, we prove that the score function can be approximated with a ReLU network whose complexity grows exponentially only with $d$, thus breaking the exponential curse of ambient dimensionality. Combined with existing theories on accurately solving the backward diffusion SDE for arbitrary compact distributions, our work shows that diffusion models readily adapt to irregular, non-smooth data structures, explaining their competence in real-world generative tasks.
Background: Veterans face an elevated risk of suicide compared to the general population, motivating national efforts to develop predictive models that can guide proactive care. Current models used by the U.S. Department of Veterans Affairs (VA) rely primarily on structured electronic health record (EHR) data, though clinical notes contain rich contextual information that can be quantified using natural language processing (NLP) to derive psychosocial variables that may improve risk detection. Machine learning methods, particularly classification and regression trees (CART), can also uncover interactions between clinical and psychosocial variables, enabling identification of patient characteristics that modify suicide risk factors. However, integrating structured and unstructured data presents challenges because NLP features often greatly outnumber traditional clinical variables, potentially biasing interaction discovery. In prior work, we addressed this imbalance by introducing a weighted CART framework that balances structured variables with NLP-derived psychosocial features from semantic lexicons (SEANCE). While effective, semantic approaches summarize language into predefined constructs and may overlook important lexical variation present in clinical narratives. Methods: In this study, we extend that framework by replacing semantic features with a high-dimensional bag-of-words (BoW) representation of clinical notes and by evaluating models across cohorts defined by structured suicide risk stratification (low, medium, high) and varying temporal lookback windows. Using a cohort of 27,241 veterans, we analyzed clinical documentation collected up to 30, 90, or 270 days prior to death (or a matched index date for controls), enabling temporally flexible risk modeling. XGBoost models were trained to balance structured and unstructured features and identify cross-modal interactions between textual and clinical variables. Results: When incorporated into generalized linear models, these interactions improved predictive performance, particularly among low- and medium-risk patients, and substantially reduced the performance gap between interpretable and more complex models. Notably, the BoW representation outperformed our prior semantic index-based approach. Discussion and Conclusions: Together, these findings demonstrate the utility of interpretable NLP methods for uncovering clinically meaningful interactions between psychosocial and demographic factors in suicide risk and establish a strong benchmark for future deep learning approaches aimed at capturing richer contextual and temporal information from clinical narratives.
arXiv:2604.26819v2 Announce Type: replace Abstract: We prove that any random variable $X$ whose moment generating function is point-wise upper bounded by that of $ G \sim \mathcal{N}(0,1) $ must be dominated by $ G/\mathbb{E}[|G|] $ in convex order, meaning $ \mathbb{E}[f(X)] \le \mathbb{E}[f(G/\mathbb{E}[|G|])] $ for all convex $f$. This is sharp as witnessed by $ X \sim \mathrm{Unif}(\{-1,1\}) $ and $ f(x) = |x| $.