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Online handwriting provides a non-invasive and low-cost behavioral biomarker for Alzheimer's disease (AD) detection, as it reflects both cognitive planning and fine motor control. Existing handwriting-based AD detection methods usually rely on global trajectory features or whole-sample representations, which can be strongly affected by individual writing style, task-specific variation, and acquisition noise. In this paper, we propose NormPaST-Risk, a healthy-normative Paper-Air selective trajectory state-space risk network for interpretable AD detection from online handwriting. Instead of treating the entire trajectory as a single holistic representation, our method reformulates AD handwriting detection as local disease-relevant segment discovery. Specifically, a multi-scale temporal encoder captures stroke dynamics at different temporal resolutions, while a selective Paper-Air state-space encoder models long-range handwriting progression and distinguishes on-paper motor execution from in-air planning and transition behaviors. To explicitly characterize abnormal deviations, a healthy normative branch learns normal handwriting dynamics from healthy controls, and a task-aware multi-expert segment-risk module estimates segment-level AD risk calibrated by hidden-state changes and normative deviations. A weakly supervised segment-level objective further enables high-risk segment discovery without manual segment annotations. Experiments on the DARWIN benchmark demonstrate that the proposed framework achieves superior AD/HC classification performance compared with existing methods. Moreover, the discovered high-risk segments can be projected back to the original handwriting trajectory, providing interpretable evidence associated with AD-related handwriting variations.

Cancer registrars, including Oncology Data Specialists (ODSs), must interpret complex and frequently updated coding and staging standards. We developed CRISS (Cancer Registry Intelligent Support System), a retrieval-augmented generation (RAG) conversational assistant that provides rapid, citation-supported access to registry guidance. This study evaluated whether CRISS could (1) support accurate and citation-supported responses, (2) improve access to and interpretation of relevant guidance, and (3) support training/helpdesk use while preserving human oversight of final abstraction decisions. We built a domain-specific knowledge base from national cancer registry standards, segmented into metadata-tagged passages and indexed as dense embeddings. Retrieved passages were used to generate citation-grounded responses through a large language model (LLM). Open-weight, proprietary, and non-RAG baseline models across Gemini and GPT families were evaluated on easy, medium, and hard registry questions using an LLM-as-a-Judge protocols. RAG configurations consistently outperformed non-RAG approaches, especially as question difficulty increased. Mean grounding scores for RAG were 0.62/0.56/0.59 across easy/medium/hard tiers versus 0.29/0.26/0.29 for non-RAG. RAG models also achieved higher semantic-similarity scores overall. Proprietary RAG models performed strongest on easy and medium questions, while local RAG models ranked highest on hard questions and proprietary models were generally more cautious. Domain-specific RAG improved evidence grounding and response quality for cancer registry questions while enabling citation-supported assistance across complexity levels. CRISS demonstrates the potential of human-centered, citation-grounded AI to support cancer registrars while preserving human oversight for final coding decisions.

Speech and voice are multidimensional signals that capture both communicative intent and underlying physiological processes, providing a unique, non-invasive window into health. Analyzing these signals has the potential to yield digital biomarkers that (i) provide scalable, objective measurement tools for research and clinical care and (ii) reflect the presence or progression of diverse conditions, including neurological, psychiatric, respiratory, and cardiovascular disorders. Realizing this promise, however, requires the field to overcome pervasive reproducibility and generalizability issues due to heterogeneous data collection, processing, and analysis practices. A major source of this heterogeneity is how underlying acoustic measures themselves are defined and computed. In this paper, we outline key considerations across the speech biomarker discovery lifecycle, from data collection through machine learning modeling to clinical interpretation, needed to achieve reliable, reproducible, and clinically translatable results. Chief among these is the need for harmonization efforts to start from common, precisely specified measure definitions. As a first step, we therefore provide definitions, physiological correlates, and computational implementations for a minimal, clinically interpretable set of core speech measures spanning respiration, phonation, articulation, and fluency. We close by discussing ongoing standardization efforts and the open challenges that remain in advancing the adoption of speech- and voice-based digital biomarkers.

New words are invented every day. A human listener can learn a new word by hearing it clearly once and inferring its usage from sentence context. This paper proposes granting ASR a similar ability to learn the contextual representations and spellings of new words from unlabeled test data at test time. A frozen CTC acoustic model provides spellings, a frozen language model provides contextual evidence for out-of-vocabulary (OOV) word detection, and an adaptation module expands the vocabulary by learning the lexical token representations with distributions over CTC-generated candidates. The spelling model of each token is optimized by minimizing a Kullback-Leibler divergence (KLD) objective. We demonstrate that the CTC-weighted language model log likelihood ratio can be interpreted as the KLD between the unknown correct ASR and the unsupervised learned ASR, and that, using a Pinsker bound, the square root of KLD can be interpreted as an upper bound on the total variation distance between the true and estimated spelling of the unknown word. Experiments show relative OOV character-error-rate reductions of up to 14.97% on LibriSpeech and 6.67% on dysarthric Speech Accessibility Project data for recurring OOV words, relative to the corresponding rescoring system.

A language model's confidence in an answer is often read as a proxy for how well it knows the corresponding fact. This manual documents an open toolkit built to test that reading directly: a small causal language model is fine-tuned on a corpus that consistently asserts one fabricated arithmetic answer for each of the 81 single-digit addition pairs, and its post-fine-tuning confidence in each fabricated answer is compared against its own pre-fine-tuning confidence in the corresponding true answer, using an unchanged measurement procedure throughout. We describe and justify every pipeline stage, fact-space generation, token-length-aware confidence measurement, baseline validation, corpus construction, fine-tuning, and paired before/after comparison, together with the confound each is meant to rule out, among them tokenization asymmetry between single- and double-digit answers and the difference between an answer merely losing its edge and one being actively suppressed. This manuscript is a methodological and implementation reference: it documents the instrument and does not report or interpret the outcome of any specific run. The toolkit and its pinned dependency environment are archived separately (Section 9) under a persistent identifier, to be cited as an instrument by work that produces and interprets empirical results with it.

The integration of model-based and data-driven paradigms provides a powerful framework for fault diagnosis by combining the interpretability of analytical redundancy relations, i.e., input-output relations that are used as diagnosis indicators in model-based diagnosis, with the adaptability of learning techniques. DT4X is a recent diagnosis algorithm that uses symbolic regression to generate multivariate relations leveraging some properties of analytical redundancy relations and uses them as split functions in a decision tree. However, its symbolic regression procedure optimizes only the separation between two selected classes at each node, often fragmenting the remaining classes and degrading both interpretability and diagnosis performance. This paper introduces DT4X+, an enhanced version of DT4X that modifies the construction of training sets and the symbolic-regression loss so that expressions separate the target classes while preserving the coherence of non-target classes. The resulting relations become fully consistent with ARR properties and lead to more informative splits, improved robustness, and better performance on dynamic-system datasets. Experiments conducted on several benchmark systems demonstrate the benefits of this enhanced formulation.

Multi-stage LLM-based cyber agents may complete attack workflows while remaining brittle, costly, or reliant on incorrect interpretations of execution evidence. Success rates alone obscure inefficiency, adaptation through retries, and recognition of success or failure. We present an end-to-end diagnostic study of an Autonomous Adversary system with orchestrator, executor, and validator LLMs in enterprise-like lateral-movement scenarios. Six frontier models are evaluated across two scenarios and three modes: expert-defined, self-scaffolded, and fully autonomous. We assess validator consistency and evidence grounding; introduce a subtask-conditioned, cost-aware score for abnormal token use, retries, and runtime; and use comparative LLM-as-a-Judge analysis to identify planning deficiencies, including tool misalignment, plan similarity, over-specification, inadequate probing, and weak recovery. Validators are generally relevant and evidence-grounded but often nonspecific and overly optimistic. Bottlenecks cluster in credential and lateral-movement tasks, spread with scenario complexity, and vary more under full autonomy. Reliable evaluation must assess outcomes, evidence interpretation, resource use, and adaptation after failure.

Reinforcement learning (RL) has emerged as a key paradigm for improving the reasoning capabilities of large language models (LLMs). However, existing reward systems, such as rule-based and reward-model-based, often exhibit issues such as unstable optimization and reward hacking. In this work, we revisit the general reasoning of LLMs from a geometric perspective, conceptualizing it as a coupled manifold composed of three interdependent sub-manifolds: logical deduction, evaluation, and representation. Based on this perspective, response generation in RL can be interpreted as a decoupling process from the evaluation manifold, while reward estimation corresponds to a decoupling process from the logical deduction manifold. The limitations of rule-based and reward-model RL systems can be geometrically interpreted as the mismatch of policy-reward manifolds during RL process. To address the aforementioned misalignment, we propose Decoupling and Coupling Reinforcement Learning (DCRL) framework, which incorporates two key components: (1) a syllogistic logic-based prompt evolution mechanism that dynamically refines reward rubrics to enhance the expressiveness of the reward manifold; and (2) a policy-reward re-coupling mechanism that jointly updates the reward and policy models, ensuring consistent evaluation and mitigating manifold mismatch during training. Theoretical analysis and extensive experiments across multiple reasoning domains demonstrate that DCRL consistently outperforms both rule-based and reward-model baselines. Notably, a Qwen3-4B model trained under DCRL surpasses a Qwen3-32B baseline and approaches the performance of a Qwen3-235B model, highlighting superior effectiveness and generalization in RL.

We present NV-Reason-CT, a generative vision--language model for chest and abdominal CT combining native 3D visual encoding with radiologist-guided reasoning. The model couples a native 3D vision transformer with a language model, passing all visual tokens and their explicit 3D coordinates into language decoding without further spatial token merging. This retains volumetric spatial information within the vision encoder and through the language model's positional encoding during joint processing with text. We train on a curated corpus of approximately 550,000 multimodal instruction examples from 70,111 unique CT image inputs, combining standardized reports, abnormality-focused and anatomy-specific questions, multi-turn interactions, and radiologist-authored reasoning from recorded and transcribed expert CT interpretations. Expert annotations provide direct supervision and guide additional report-grounded synthetic reasoning. End-to-end supervised fine-tuning (SFT) is followed by Group Relative Policy Optimization (GRPO), with verifiable rewards over chest and abdominal abnormality sets. The model supports abnormality classification, report generation, and interactive reasoning with reviewable observations, differential diagnoses, and uncertainty. Evaluation spans public CT benchmarks and a held-out NIH cohort. On CT-RATE, NV-Reason-CT achieves a macro-F1 of 0.614 and macro-AUROC of 0.871 without a task-specific classification head; generated reports achieve a report-derived macro-F1 of 0.592. In a preliminary study with expert radiologists, AI-assisted review received favorable confidence ratings and was associated with a 50% reduction in average reported interpretation and reporting time. We release the model and training code to support reproducible research on explainable AI for volumetric medical imaging.

Generative image models can produce highly realistic images, raising concerns about potential misuse in creating deceptive content. Current deepfake approaches face several challenges, including limited generalizability, lack of interpretability, and poor actionability. To help address these, we present ASAP, an interactive visualization system designed to empower users in the analysis and summarization of deceptive patterns in AI-generated images. ASAP introduces a novel CLIP-adapted image encoder that generates interpretable representations, enabling the extraction of influential pixel regions via calculated masks. This approach facilitates the identification of key deceptive features through influence measurement techniques. These backend techniques are integrated into a visual analytics dashboard that allows users to quantify and analyze authenticity-indicative patterns in image collections containing both authentic and AI-generated images. This approach also supports the comparative analysis of various generative models, including GANs and diffusion models. We demonstrate ASAP's efficacy through a user study and two application scenarios using established fake image detection benchmarks, showcasing its ability to effectively extract and quantify deceptive patterns.

Real-world molecular design remains challenging for large language model (LLM)-based agents. It requires them to interpret design contexts, satisfy multiple constraints, identify infeasible specifications, and reason over multi-step tool outputs. Existing benchmarks do not capture this complexity, focusing instead on explicit and narrow constraints, only feasible problems, and single-path solutions. To address this gap, we propose MolDesignBench, a scenario-grounded benchmark that more closely reflects real-world molecular design for evaluating tool-augmented LLM agents. MolDesignBench comprises 2K generation and optimization instances that combine implicit requirements embedded in design narratives with explicit property and functional-group constraints, including infeasible cases, and require the effective use of 17 specialized chemistry tools. Experiments across diverse frontier LLMs reveal low success rates--with the best achieving only $\sim43$%--and frequent failures in implicit-constraint reasoning, infeasibility detection, and tool reasoning. The corresponding fine-grained failure-mode analysis identifies implicit constraint interpretation and infeasibility detection as the primary bottlenecks, establishing MolDesignBench as a rigorous testbed to guide future research on chemical agents. The benchmark, tool interface, and evaluation code are publicly available.

Despite their outstanding performance on many NLP tasks, LLMs face serious challenges related to semantic abstraction. In this study, we are interested in understanding how LLMs leverage abstract semantic knowledge in natural language inference (NLI), which requires sophisticated linguistic capabilities to interpret implicit meanings, contextual conceptual relationships, and semantic connections between words and phrases. To this end, we propose a methodological framework for constructing new semantic knowledge at a higher level of abstraction, which we define under the notions of semantic compatibility and incompatibility for NLI. In this framework, the meaning of the lexical-semantic relations between the premise and the hypothesis is reconfigured to achieve a more flexible semantic network that induces different reasoning paths in LLMs. These new pathways show a consistent pattern of responses that allows agreement on a single response. The results demonstrate that our proposal allows to discover and compensate for LLMs' semantic knowledge gaps in NLI, achieving significant improvements in accuracy, exceeding 10% for some models, and in particular for the non-entailment class. It is essential to note that LLMs need structured knowledge and not just more data to bridge reasoning gaps. Our hybrid approach directs attention to overlooked word relationships, allowing models to synthesize missing information. We believe that the future lies not in increasing model size, but in creating a semantic scafolding that mimics the flexibility of human thinking. Hopefully, our proposal will enable the development of more robust agents and interpretable reasoning, guiding AI toward reliable language understanding.

Medical image interpretation is high-volume and time-consuming, and while AI interpretation can reduce workload, fully autonomous deployment carries potential safety concerns and low specificity may in practice lead to increased clinician workload. Learning to Defer (L2D) addresses this by selectively routing cases between autonomous prediction and human experts by learning from input features and AI model and human performance. While theoretical guarantees have been proven for L2D, its performance has not been validated on real-world medical datasets with human reader annotations. We evaluate the predictor-rejector formulation of two-stage L2D, where the AI predictor model is fixed and separate from the trainable routing or rejector model, on Collab-CXR, a multilabel chest X-ray dataset with multiple human annotations per case. This is the first work to look at L2D in the context of real-world medical imaging data with human annotations. We further introduce a new setup, L2D with Guidance, where the decision space is extended to three choices: predict autonomously, defer to a human expert, or defer to a human expert and provide AI guidance. We compare multiple rejector architectures and loss functions, and different input feature availabilities. This is reproduced on two larger datasets, VinDr-CXR and CheXpert. Our results show that two-stage L2D with Guidance outperforms classic two-stage learning to defer, as well as human-alone, AI-alone and AI-guided human baselines. Notably, this performance is achieved with simpler loss functions compared to formally defined L2D surrogate loss functions in current literature.

Analog circuit sizing remains a challenging and time-consuming task due to the large design space, strong performance trade-offs, and increasing circuit complexity in scaled technologies. Although recent large language model (LLM)-based methods show promise in improving sample efficiency and interpretability, existing approaches often lack explicit circuit-topology understanding and are mainly evaluated on relatively simple analog building blocks. This paper presents a multi-agent LLM-based framework for complex analog circuit sizing. The proposed framework first analyzes the circuit topology and decomposes the netlist into functional blocks and substructures. It also extracts lightweight design knowledge for reuse. Based on the extracted topology and knowledge, a planner coordinates multiple role-specialized sizing agents to update design variables and achieve global performance specifications. This workflow mimics the collaborative process of an expert analog design team and provides a structured, interpretable, and simulation-driven optimization procedure. The framework was validated on eight circuits, with the largest design containing up to 55 transistors and 60 sizing variables. Notably, for the LDO benchmark, the proposed method achieved a 60% success rate with an average of 83 iterations, where classical optimizers failed to find feasible solutions. Further, ablation studies demonstrate that topology understanding, design-knowledge infusion, and agent specialization provide complementary benefits. The source code is available to support reproducibility.

Environmental reconnaissance needs mobile platforms that carry sensors, preserve measurement context, and return interpretable evidence under limited energy and communication. We present a literature-informed engineering design for Zephyron, a four-wheel rover with a front manipulator, environmental sensors, distributed computer vision, local recording, and a raised rear solar module. The design keeps the prototype layout but replaces unsupported numerical assumptions with an explicit component and geometry baseline. A reproducible search retrieved 5,000 records (4,858 unique) for screening, followed by targeted review of primary literature and manufacturer documentation. The baseline uses 165 mm wheels, a 12 kg mass budget, a 72 Wh battery-energy basis, and a 20 W photovoltaic module. With rolling-resistance coefficient 0.04, steady ascent of a 10 degree grade needs about 0.517 N m per wheel under equal load sharing. An illustrative 40 W motion load gives 1.44 h from 57.6 Wh usable energy, and a 25 percent driving duty gives 4.19 h without solar input; these are calculated scenarios, not measured performance. Sensor models show how integration time, calibration, temperature, and communication delay constrain interpretation, and a quality-aware stop-and-sample policy links these constraints to mission execution. Lightweight detectors, reference-based sensor learning, and executable data-integrity checks define a reproducible machine-learning evaluation pathway. The contribution is a traceable design and evaluation framework with editable 3D models, subsystem diagrams, and reproducible analytical data. Experimental validation is required before assigning payload, endurance, detection, or field-operating ratings.

Rapid intensification (RI) remains one of the most consequential and difficult aspects of tropical cyclone (TC) forecasting. Although full-physics numerical weather prediction models can represent the processes governing RI, resolving storm-environment interactions remains computationally expensive, while purely data-driven approaches often lack physical interpretability. We present FAST-ML, a hybrid framework that bridges data-driven efficiency with physical constraints. A physically informed dual-stream neural parameterization ingests 3D ERA5 fields to diagnose ventilation controls---environmental wind shear and mid-level entropy deficit. By optimizing these parameters end-to-end through a differentiable FAST intensity model, this architecture establishes a robust new paradigm for observation-driven parameter optimization, ensuring storm evolution remains strictly governed by thermodynamic principles. By better capturing the storm's continuous intensity evolution, FAST-ML improves upon its physical baseline, reducing ensemble CRPS across forecast lead times, with a reduction of approximately 31% at 60 h and nearly halving the RI false alarm ratio without sacrificing detection skill. In a 100-member ensemble configuration, FAST-ML produces intensity forecasts comparable to FNV3 for selected storms under the evaluated input configurations. Furthermore, zero-shot tests on selected Eastern Pacific storms provide encouraging evidence of cross-basin transferability. FAST-ML provides a modular intensity forecasting framework that can be coupled with externally supplied storm tracks and environmental fields. It demonstrates that observation-driven parameter learning within physically constrained dynamics simultaneously enhances accuracy, interpretability, and computational efficiency.

Dialogue failures in language models are usually framed as memory failures: context too long, summaries lossy, a constraint forgotten. We argue this misses a deeper problem: in many conversations the model does not forget, it commits too early. An ambiguous early turn collapses into a single hidden interpretation, and later clarification is filtered through that commitment. We call this early posterior collapse: unresolved user intent collapsing into a committed task state before ambiguity is resolved. We study it with controlled dialogue tasks in writing, planning, and coding using Gemini-2.5-Pro and Gemini-2.5-Flash. Across thousands of trials, the same information in different orders yields different outcomes, even when the final dialogue contains equivalent task-relevant information. This order effect suggests later clarification is treated as extra context rather than a corrective signal: it refines a stale task state without invalidating it. Coding tasks are especially vulnerable, suggesting early assumptions get embedded in structured artifacts such as interfaces and control flow. Standard prompting and memory strategies do not reliably help: summaries can collapse ambiguity, and chain-of-thought can reduce explicit wrong commitment in reasoning traces without improving final task success. These findings motivate uncertainty-preserving state management. If assistants cannot let go of early interpretations, robustness cannot rely on post hoc correction alone; it must keep ambiguous early turns from hardening into one task state. Assistants should hold tentative hypotheses while ambiguity remains, ask before executing when high-impact ambiguity persists, and rebuild from a revised state when later evidence invalidates an earlier reading. Rather than one prompting fix, we aim to redirect research for interactive LLMs from retaining more context toward preserving uncertainty.

Reliable uncertainty estimation is essential for deploying object detectors in autonomous systems operating in uncertain environments. Evidential Deep Learning (EDL) provides a principled framework for uncertainty-aware classification by representing network outputs as evidence and interpreting predictions through subjective logic. However, existing evidential object detectors typically combine evidential classification with regression uncertainty models that do not share the same theoretical foundation. In this work, we propose an evidential version of YOLOv8 in which both classification and bounding-box regression are formulated within a common evidential framework. Our approach exploits YOLOv8's distribution-based bounding-box representation, allowing the evidential formulation to be applied not only to classification but also to localisation. As a result, both tasks produce belief, uncertainty, and probability estimates that can be interpreted within the Dempster--Shafer framework. Experiments on KITTI, MUSES, and nuScenes show that the resulting detector remains broadly competitive with standard YOLOv8 in terms of detection accuracy while providing a localisation uncertainty that effectively discriminates between correct and erroneous detections. Moreover, this uncertainty becomes increasingly discriminative under domain shift.

Electricity forecasting often involves spatially related signals observed over regions, substations, and feeders, and Graph Neural Networks (GNNs) provide a natural way to represent these relations. Building a complete GNN forecasting experiment is nonetheless laborious, because graph construction, model selection, training, aggregation, and interpretation sit in incompatible tools. We present GraphToolbox, an open-source Python framework that unifies these stages in one configurationdriven pipeline built on PyTorch Geometric. It offers data-driven graph construction, an adapter that instantiates and trains 51 of the 65 PyTorch Geometric convolutions together with the recurrent cells of PyTorch Geometric Temporal, online expert aggregation, forecasting interpretability, and significance testing on cached forecasts. We evaluate the pipeline in two case studies. On French regional load, the 48 convolutions included in the complete forecasting sweep fall in a band from 1.14% to 1.60% error, online aggregation lowers this to 0.98%, and the graph models improve on classical additive and boosting baselines. On net-load, direct graph models are less accurate than a classical additive model, while forecasting each physical component separately improves them without closing that gap. Both comparisons use the same experimental interface, illustrating the role of GraphToolbox in systematic architectural evaluation.

Self-attention is central to modern Transformer architectures, but its dense dot-product formulation makes it difficult to identify which internal directions are structurally important and which can be modified without disrupting the model. SVD-Inspired Attention (SVDA) addresses part of this problem by introducing a learned diagonal spectrum into the query-key score interaction, making latent attention directions explicitly inspectable through indicators such as spectral entropy, effective rank, sparsity, alignment, selectivity, and perturbation response. This paper examines the transition from diagnostic interpretation to operational intervention. A diagnosis--intervention--verification framework is proposed, and one intervention is evaluated: spectral energy retention in the attention-score pathway. Across FashionMNIST, CIFAR-10, CIFAR-100, and Food-101, the $ρ=0.90$ prescription removes 24.5--53.7% of score directions, reduces parameters by 2.6--4.3%, and reduces estimated MACs by 2.8--5.4%. The paired mean accuracy change of the dimension-reduced model ranges from $-0.03$ to $+0.05$ percentage points over three seeds. These results support SVDA as an intrinsically interpretable attention mechanism whose learned spectrum exposes an operational coordinate system for deterministic and verifiable modification of attention-score formation.

6D object pose estimation is fundamental to robotic manipulation and automation. Recent zero-shot methods have significantly improved generalization to unseen objects, but most still rely on large-scale pretrained models with substantial GPU computation and memory demands. These requirements complicate deployment on robotic platforms where perception, planning, and control share limited computational resources, while learned intermediate representations offer limited geometric interpretability for task-specific adaptation. To address these limitations, we propose G6D, a learning-free, geometry-driven RGB-D 6D pose solver. Given an RGB-D observation, an object instance mask, camera intrinsics, and a CAD model, G6D generates pose hypotheses through template-based geometric matching and refines them using silhouette and depth consistency, forming a purely geometry-driven pose estimation paradigm. This paradigm requires neither pretrained visual models nor target-specific training and preserves interpretable geometric representations throughout pose estimation. Moreover, adjustable hypothesis counts provide flexible accuracy-computation trade-offs, while a CPU-only configuration supports deployment without GPU resources. Experiments on LineMOD and five BOP19 datasets demonstrate advanced performance. Real-world pick-and-place experiments further demonstrate G6D's applicability to robotic manipulation. The complete project is publicly available at https://ai4control.github.io/G6D-Project-Page .

Multi-omics sequences contain complex biological patterns, yet deciphering their mechanisms for automated scientific discovery remains challenging. As large language models (LLMs) interpret these sequences, evaluating both predictions and scientific reasoning is critical. However, existing benchmarks for multi-omics sequence tasks rely on classification and regression metrics, neglecting whether models grasp the underlying biological evidence. We introduce OmicsBench, the first reasoning benchmark for multi-omics sequences, comprising 1,160 expert-validated questions across six tasks spanning DNA regulation, RNA processing, and protein function. OmicsBench requires traceable evidence chains, evaluated using instance-specific rubrics developed with domain experts. Evaluating 17 LLMs reveals an inverse relationship: while scientific LLMs outperform general-purpose LLMs in sequence classification accuracy, they fail to provide valid evidence to support their predictions. One plausible interpretation is shortcut learning: specialized models may rely on statistical patterns rather than the biological mechanisms needed for scientific discovery. Motivated by this finding, we introduce tool-augmented on-policy distillation (TA-OPD), a post-training method to align sequence prediction with evidence-grounded biological reasoning. Across five Qwen3.5 models spanning 0.8B to 27B parameters, TA-OPD consistently strengthens biological evidence grounding while improving predictive performance on most tasks. These gains persist across model scales, indicating that stronger sequence reasoning does not arise solely from increased model capacity, but can be improved through evidence-aware training. Together, OmicsBench and TA-OPD provide a framework for diagnosing reasoning failures in multi-omics LLMs and a path toward models whose predictions are better grounded in biologically meaningful evidence.

Decodability and successful activation steering do not, by themselves, establish what an internal direction represents. This gap is especially consequential for welfare-relevant interpretations, where a proposed functional state must be distinguished from correlated features of the extraction contrast. We study this question for a good-bad outcome direction in a maze task, using controlled interventions that separate the realised outcome from the informational history through which it became known. Across multiple LLM checkpoints, directions fitted on one explicit outcome encoding transfer well to another, indicating that the readout is not tied to surface form. In contrast, when the same realised outcome is reached through announced and unannounced histories, transfer degrades substantially: even after both histories receive the same explicit outcome, the post-event readout remains strongly conditioned on the earlier announcement. In a matched maze-RL run, the post-RL direction becomes substantially more predictive of reference-MDP remaining return and the policy becomes more dependent on it at the tested sites, while this history dependence persists. These results support a functional, value-related interpretation of the direction, but not its identification with a history-invariant scalar valence state.

Data attribution methods using gradient similarity are widely used to analyze and select training data for large language models, but what gradient similarity actually measures is debated. Some interpret it as identifying task-relevant skills, while other work reports that surface form is the main factor. We resolve this debate for supervised fine-tuning examples by varying task and answer format independently. Specifically, we render benchmarks in different answer formats, such that datasets can share a task without a format or a format without a task. We find that gradient alignment follows the answer format, as benchmark pairs sharing an answer format align strongly (disattenuated cosine near 0.4), while same benchmarks rendered with different answer format classes show no alignment (near 0.0). We demonstrate that this ordering holds from the earliest pretraining checkpoints through post-training, and across model scales and families. We then analyze the released selections of LESS, a gradient-based data selection method for instruction tuning, and find that each target's selections over-represent the target's own answer format. Hence, we demonstrate that gradient-based attribution methods track format similarity more than task semantics, meaning that such methods, as well as the semantic interpretation of the gradient, should be tested on data where answer format and task vary independently for greater robustness and reliability.

Artificial intelligence for plant disease analysis has advanced from task-specific classifiers to multi-modal models capable of jointly interpreting visual and textual information. However, practical deployment in precision agriculture remains limited because most existing approaches treat disease understanding as isolated prediction tasks, failing to capture the complementary relationships among symptom recognition, severity assessment, and question-driven diagnostic reasoning. In tomato pathology, accurate interpretation of diseased leaves requires more than label prediction; it demands integrating visual symptoms with semantic context to support a comprehensive and explainable understanding. Here, we present SOLAR, a multimodal generative model that understands tomato disease spanning six question-answering tasks. SOLAR learns to align visual features with task-aware language representations by Fusion Expert module based on mixture-of-expert, enabling it to generate contextually relevant answers across diverse diagnostic tasks. By formulating tomato disease analysis as a generative Visual Question Answering (VQA) task, SOLAR provides a flexible framework that supports multi-task inference within a single model while improving performance and cross-task knowledge sharing. We evaluate SOLAR on $41,677$ images, including $216,209$ Question-Answering (QA) pairs to understand tomato leaf disease under both closed and open-ended QA settings. Experimental results show that SOLAR consistently outperforms state-of-the-art vision-only, vision-language, and task-specific models across all tasks, demonstrating superior accuracy, robustness, and multimodal reasoning. These findings highlight the potential of generative multimodal modeling as an effective direction for understanding of plant disease. The code for this study is available at https://github.com/EnalisUs/SOLAR.

Accurate prediction of nitrous oxide (N2O) emissions from agriculture is important for assessing environmental impacts and supporting sustainable farming. However, prediction remains difficult because N2O emissions result from complex interactions among soil properties, climate, biochemical processes, and management practices, while high-quality observations are limited. Deep learning models can capture nonlinear relationships but often lack physical interpretability and may generalize poorly across environmental conditions. We propose the Knowledge-enhanced Agriculture-informed Neural Network (KAINN), a hybrid neural-mechanistic framework that extends the Agriculture-informed Neural Network by incorporating domain knowledge about fertilizer diffusion, soil respiration, and water-filled porosity. We evaluate KAINN using CNN, LSTM, and Transformer architectures across multiple growing seasons and input-feature configurations. The results show that KAINN generally provides lower root mean square error and mean absolute error and higher R-squared values than purely data-driven models and the original AINN. Analysis of the learned interfaces also shows smoother and more physically consistent parameter trajectories with reduced uncertainty. These findings demonstrate that incorporating environmental knowledge into neural networks can improve the reliability, interpretability, and generalization of agricultural N2O-emission predictions.

Small clinical tabular datasets require interpretable machine learning because deep learning is often impractical and ensemble models can be difficult to inspect. A key pitfall is that statistical significance does not necessarily imply predictive utility. Using data from the Panama Aging Research Initiative--Health Disparities (PARI-HD) cohort (n=165), we implemented a leakage-safe threshold-likelihood Bernoulli/Categorical Naive Bayes (BNB/CNB) classifier. Within every training fold, each continuous predictor was reduced to a supervised chi-square-derived state, while income entered the model through a categorical likelihood. All data-dependent steps were performed within repeated stratified 10-fold cross-validation with 30 repeats. The demographic baseline achieved a ROC-AUC of 0.630 +/- 0.017. I-309 (CCL1) was the dominant incremental feature, increasing AUC by 0.110, with paired DeLong tests yielding p<0.05 in 100% of repeats. In the pre-specified primary analysis, I-309 produced a fixed-partition DeLong p=0.0018, with robustness assessed across 200 random partitions, where the median p-value was 0.0011. Within the exploratory family of 18 candidate markers, I-309 achieved a Benjamini-Hochberg-adjusted q=0.032 on the frozen partition and satisfied q<0.05 in 85% of random partitions, whereas no other marker demonstrated reliable incremental predictive value. Because the fitted model is an inspectable table of thresholds and class-conditional probabilities, these results identify I-309/CCL1 as an interpretable candidate feature for tabular prediction of cognitive impairment, pending external validation.

Radiologists follow heterogeneous reporting practices. Two radiologists examining the same image and identifying the same clinical findings might nevertheless compose superficially distinct reports, varying in terminology, shorthand, formatting, and level of detail. These variations in reporting norms represent an under-appreciated obstacle in efforts to evaluate AI-based radiology report generation (RRG) models, where machine-generated reports are typically assessed based on their concordance with human-generated references. In this paper, we quantify the sensitivity of established evaluation metrics to variations in reporting practices, revealing impacts large enough to alter the rankings of models. We introduce a radiologist-informed taxonomy of variations in radiology reporting practice and a method (ReRef) that rewrites reference reports along the axes of our taxonomy while preserving clinical interpretation. For instance, when comparing the performance of nine RRG models on MIMIC-CXR using RadCliQ-v1, condensing the discussion of normal findings in the reference reports causes Libra to drop from first to second place while CheXOne rises from third to first. Our results suggest that many current metrics fail to decouple clinical interpretation from conformity to reporting practices and that choosing the ``right'' references that accurately reflect the desired reporting practices can be important in practice. To support future research, we release MIMIC-CXR-Ext-ReRef, a radiologist-validated dataset of 120 (original, alternative) reference report pairs derived from MIMIC-CXR.

Text-to-music (TTM) systems are increasingly used to generate musical audio from natural-language descriptions. Robust evaluation is therefore essential, yet reliable performance comparison remains challenging. This difficulty stems from differences in system architecture, supported conditioning information, and access mode, as well as heterogeneous and fragmented metrics that cannot be applied uniformly across systems. To address these challenges, we introduce TTM-Bench, a framework that defines a common protocol for systematic, reproducible performance benchmarking of contemporary TTM systems. It evaluates performance along two dimensions: musical-content alignment, quantified by interpretable semantic, genre, and musical-descriptor agreement scores against a common musical specification and summarized by an aggregate score; and computational efficiency, characterized by generation latency and real-time factor, alongside resource use for local models and cost for hosted services. We demonstrate the framework through a preliminary comparative case study, illustrating the complementary evidence captured by these dimensions. The results show that higher musical-content alignment does not systematically coincide with lower computational demands, highlighting the importance of assessing TTM performance through distinct, interpretable measures rather than a reductive overall indicator.

Model explainability is essential for understanding and trusting machine learning models. Existing explainable AI methods often explain predictions through feature importance, counterfactual explanations, or rules. However, a region-level characterization of when and only when a prediction behavior arises remains less explored. This paper proposes Causal Sufficient and Necessary Regional Explanations (SNRE), a framework that learns an input region $A$ and output region $B$ such that membership in $A$ is both sufficient and necessary for the model output to fall in $B$. Motivated by the classical Probability of Necessity and Sufficiency (PNS), we formulate a region-level PNS measure through stochastic interventions and derive a differentiable finite-sample estimator for optimization. SNRE parameterizes the input-output region pair with explicit and interpretable algebraic region families, together with a learnable feature mask, balancing expressiveness and interpretability. Experiments demonstrate that SNRE learns region pairs with strong sufficiency-necessity performance, robust explanation behavior, and practical utility for model analysis.