Interpretable EEG biomarkers with bag-of-waves: Spatial and temporal waveform dictionaries for low-data regimes

Electroencephalography (EEG) is widely used to diagnose neurological conditions, but its analysis usually relies on either predefined spectral features or deep neural networks. Predefined features carry a strong bias, since they fix in advance what counts as informative, while deep neural networks and foundation models are hard to interpret and need large amounts of data and compute. We present bag-of-waves, an interpretable framework that learns a small dictionary of recurring EEG waveform templates, called atoms, using shift-invariant k-means without labels. The continuous EEG is then turned into a sequence of atom tokens, whose counts feed a simple downstream classifier or clustering step. We extend this representation in two ways: we add atom-to-atom transitions, which we call n- grams, to capture temporal structure, and we move from single-channel atoms to regional and cross-channel spatial atoms for the multichannel case. We test the method on three complementary datasets, each probing a different aspect: single-channel mouse genotype clustering with only sixteen animals (the low-data and temporal case), resting-state dementia classification (the spatial case), and the TUEV benchmark, a six-way classification of clinical EEG events (a high-data comparison against strong deep and foundation baselines). Across all three datasets, bag-of-waves achieves performance competitive with state-of-the-art deep and foundation models. Yet, it operates with a fraction of the parameter count and provides full interpretability: because every atom corresponds to an inspectable waveform, the method explicitly recovers known clinical morphologies that a neurophysiologist can directly validate. Its main advantage is that it works in the low-data regime where heavier models are a poor fit.

TD-DPO: Difference-Aware Preference Optimization for Mitigating Sycophancy in Clinical Autism Intervention Dialogue

The sycophancy of large language models can increase the safety risk in intervention dialogue for autistic children. Supervised fine-tuning can somewhat reduce sycophancy, but relying solely on positive examples is often insufficient to identify and correct failure patterns. We observe that sycophancy behaviors can often be localized to a limited span within the model response. In this regime, sequence-level preference optimization can over-update preference-irrelevant tokens and degrade intervention ability. To address this, we propose the \textbf{M}inimal \textbf{E}dit \textbf{D}ata \textbf{A}ugmentation (MEDA) strategy to construct controlled, stable, minimal edit preference pairs and \textbf{T}oken-level \textbf{D}ifference \textbf{D}irect \textbf{P}reference \textbf{O}ptimization (TD-DPO), which upweights difference tokens between chosen and rejected responses while downweighting shared tokens to suppress background drift. Extensive experiments across multiple backbones and evaluators show that TD-DPO achieves a better trade-off between sycophancy mitigation and intervention ability retention in our offline settings, highlighting its potential as a practical alignment approach for autism intervention.

xHC: Expanded Hyper-Connections

Hyper-Connections (HC) expand the residual stream of Transformers into $N$ parallel streams, providing a form of memory scaling beyond model width and depth. Manifold-Constrained HC (mHC) stabilizes this formulation at scale. The large gains from $N{=}1$ to $N{=}4$ suggest residual-stream expansion as a promising scaling axis. However, existing HC-family methods typically stop at $N{=}4$. Our experiments reveal why: scaling mHC beyond this point yields diminishing performance gains and rapidly increasing training cost. We attribute this limitation to two bottlenecks: insufficient write-back information for an expanding number of streams and residual-mixing generation whose cost scales cubically with $N$. To address both bottlenecks, we propose xHC (Expanded Hyper-Connections), the first HC-family method to achieve meaningful expansion beyond $N{=}4$. xHC combines temporal feature augmentation for richer write-back with a sparse residual-stream architecture that updates only $k=4$ of the $N=16$ streams while retaining dense access to the full residual state. Across 18B and 28B MoE models, xHC delivers strong and consistent downstream improvements. On an 18B MoE model, xHC improves the average downstream score by 4.0 points over mHC, while adding only modest training FLOPs over the vanilla baseline. Scaling-law experiments show that the vanilla and mHC require $1.50\times$ and $1.19\times$ the compute of xHC, respectively, to reach the same loss. Practical large-$N$ training also requires controlling memory traffic from the expanded residual state. We therefore introduce xHC-Flash, which reduces the per-sublayer memory traffic from $73.5C$ to $40C$, comparable to the $34C$ required by mHC at $N{=}4$, while retaining the gains of full xHC. Together, xHC and xHC-Flash make large-$N$ residual-stream expansion effective and practical for LLM pre-training.

TEDDY: A Pediatric Foundation Model for Risk Forewarning from ICD-Coded Diagnostic Histories

Pediatric electronic health records capture developmentally structured clinical trajectories, yet their potential for generative healthcare foundation models remains largely unexplored. Here we present TEDDY (Temporal Event Decoder for Disease in Youth), a 1.84-million-parameter decoder transformer trained on approximately 73 million ICD-10 diagnoses from 1.6 million children at a single pediatric institution. TEDDY models longitudinal diagnosis trajectories and visit timing. Predictions were made before visit codes were revealed, limited to first occurrences, and evaluated against sex- and age-matched controls. Across 797 disease-onset prediction tasks spanning 16 ICD-10 chapters, TEDDY achieved a median AUC of 72.0%, outperforming same-data DenseNet (50.0%), CNN (57.2%), RNN (60.1%), and LSTM (62.7%) baselines on 96-99% of tasks. Performance held across sex and age and was strongest among lower-prevalence diagnoses; 202 of the 225 rarest conditions (90%) had 95% confidence intervals above chance. Predictive signal remained detectable more than two years before first recorded diagnosis, with median AUCs of 59.7% in the unrestricted analysis and 64.4% in a fixed-cohort sensitivity analysis. In asthma and attention-deficit/hyperactivity disorder benchmarks, AUCs were 79.3% and 84.7%, compared with 62.7% and 71.7% for the strongest comparators, including a general-purpose language model three orders of magnitude larger. Visit-timing predictions had a 3.0-day mean absolute restricted mean survival-time error over 365 days, although median and long-tail return intervals remained miscalibrated. Together, these results establish pediatric diagnostic histories as a substrate for compact generative models supporting broad, rare-disease, and long-horizon risk forecasting without population-scale data or billion-parameter models.

Don't Commit Alone: Joint Token Commitment in Diffusion Large Language Models

Diffusion large language models (dLLMs) commit multiple tokens per denoising step by decoding each selected position independently from the shared context; when those positions are dependent, the resulting factorization error is captured by conditional total correlation, which confidence-based selection cannot observe from marginals alone. We propose CoCommit, a marker-gated coordination pass that briefly defers commitment: after the usual bundle selection, a learned marker announces the commit set and the backbone's last-$n$ layers are re-applied so marked positions coordinate -- approximating joint-mode decoding -- before greedy argmax writes tokens. The method reuses existing weights with one extra partial forward pass and no auxiliary model. On LLaDA2.1-mini with LoRA adapters and matched greedy inference, joint commitment improves accuracy on all six benchmarks we evaluate, with the largest gains on reasoning and exact-answer tasks.

Self-Generated Error Training for Token Editing in Diffusion Language Models

Token-to-token (T2T) editing lets LLaDA2.1 revise committed tokens during block-diffusion decoding. The released recipe trains this editor on random vocabulary corruptions, but at inference the editor sees the model's own fluent, high-confidence draft errors instead. We study this training-inference mismatch and propose self-generated T2T, which performs a no-gradient draft pass, fills masked positions with predicted tokens, and supervises recovery in a second pass under these self-generated corruptions. We implement the update as a short LoRA continued-pretraining pass on LLaDA2.1-mini and evaluate on several benchmarks under the official Q-Mode T2T procedure with unchanged inference parameters. The method generally improves accuracy while reducing T2T edit intensity, mitigating failure modes such as final-digit transcription errors after otherwise correct reasoning and excessive self-correction before short factual answers.

Decoding in Order-Agnostic Language Models: Chain-Rule Deviation and Uniform Spreading

Order-agnostic language models (OALMs), including discrete diffusion language models (dLLMs), are trained to predict masked tokens under arbitrary conditioning sets, allowing sequences to be generated or scored under arbitrary reveal orders at inference time. In LLaDA-2.1, we report three findings. First, the learned conditionals are not exact factorizations of a coherent joint distribution: changing only the reveal order shifts target log-likelihood by up to 0.49 nats/token, so likelihood alone mixes content difficulty with path-dependent artifacts. Second, although confidence-first (CF) decoding is order-agnostic, its reveal orders are close to left-to-right (L2R) on content tokens. Third, we propose a complementary diagnostic based on the shape of the confidence trace. A uniform-spreading theorem shows that, at fixed total likelihood, target recoverability is maximized when per-step confidence is spread uniformly; the resulting deviation motivates $\mathrm{Var}(\log q_t)$ as a diagnostic for comparing decoding paths. Across C4 and four downstream benchmarks, low variance separates structured paths from random ordering, and variance is consistently associated with downstream correctness. These results support reporting mean confidence and confidence variance jointly when comparing OALM decoding paths.

Remask, Don't Replace: Token-to-Mask Refinement in Masked Diffusion Language Models

Masked diffusion language models such as LLaDA2.1 rely on Token-to-Token (T2T) editing to correct their own generation errors: whenever a different token crosses a confidence threshold, the committed token is overwritten. We identify three structural failure modes of this rule. The trigger cannot fire when no single alternative is confident enough; the replacement is computed under a context that may itself contain errors; and the uniform perturbations used to train the T2T stream do not resemble the coherent, semantically plausible mistakes that the model actually makes at inference. As an alternative, we propose Token-to-Mask (T2M) remasking. Rather than overwriting a suspect token with a new guess, T2M resets the position to the mask state, so that the next denoising step re-predicts it from an in-distribution context. The method is training-free, modifies only the editing rule, and introduces no new parameters. We pair it with three detection heuristics and give a short theoretical account of why a mask is a better conditioning signal than an erroneous token. Across 8 benchmarks, T2M improves accuracy on tasks that require exact token-level output. Its largest gain is +5.92 points on CMATH, where we attribute 79.9% of baseline errors to last-mile corruption (correct reasoning followed by a garbled final answer); T2M repairs 41.3% of these cases.

JTok: On Token Embedding as another Axis of Scaling Law via Joint Token Self-modulation

LLMs have traditionally scaled along dense dimensions, where performance is coupled with near-linear increases in computational cost. While MoE decouples capacity from compute, it introduces large memory overhead and hardware efficiency challenges. To overcome these, we propose token-indexed parameters as a novel, orthogonal scaling axis that decouple model capacity from FLOPs. Specifically, we introduce Joint-Token (JTok) and Mixture of Joint-Token (JTok-M), which augment Transformer layers with modulation vectors retrieved from auxiliary embedding tables. These vectors modulate the backbone via lightweight, element-wise operations, incurring negligible FLOPs overhead. Extensive experiments on both dense and MoE backbones, spanning from 650M (190M + 460M embedding) to 61B (17B + 44B embedding) total parameters, demonstrate that our approach consistently reduces validation loss and significantly improves downstream task performance (e.g., +4.1 on MMLU, +8.3 on ARC, +8.9 on CEval). Rigorous isoFLOPs analysis further confirms that JTok-M fundamentally shifts the quality-compute Pareto frontier, achieving comparable model quality with 35% less compute relative to vanilla MoE architectures, and we validate that token-indexed parameters exhibit a predictable power-law scaling behavior. Moreover, our efficient implementation ensures that the overhead introduced by JTok and JTok-M remains marginal.

Innovator-VL: A Multimodal Large Language Model for Scientific Discovery

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.