Daily Papers

We propose EMBER, a structure-based framework for TCR--pMHC binding prediction that eliminates the need for a predicted docked complex, and with it the placement error that dominates such predictions. Traditional structure-based predictors utilize the co-folded complex structure of the receptor and the antigen and interpret binding from its contact surface. Consequently, every downstream feature inherits any deviation the structure-prediction tool introduced. Methodologically, EMBER folds the TCR and pMHC independently, encodes them as SE(3)-invariant residue graphs, and compares their learned representations without constructing a shared coordinate frame. A relative pose is therefore not an input of the model, so placement error cannot propagate into the prediction. Computationally, EMBER preprocesses O(N{+}M) monomer folds where a complex-based predictor needs O(NM) operations. Experimentally, under epitope-disjoint evaluation with six retrained baselines, EMBER is first on every metric under all four folding tools, by 0.9 to 14.4% in micro-AUROC, 18.5 to 25.3% in micro-AUPRC and 10.6 to 24.1% in MCC. Its ranking is also up to 85% more stable across folding tools.

General-purpose frontier models are large, expensive to run, and increasingly reluctant to engage with authorised defensive- and offensive-security work. We ask the opposite question: how small can a cybersecurity-specialist transformer be while remaining genuinely useful to a security practitioner? We introduce CT0, a Cybersecurity Transformer architecture, and CT0-Micro, its first incarnation: a compact (~4B-parameter) model built on the open base model, whose backbone is specialised by two-phase on-policy distillation on our Cybersecurity AI (CAI) dataset. CT0 serves two modes from one set of weights: System 1 answers typed security decisions (is this file suspicious, is this request an attack, did the model just refuse) in a single forward pass without generating a token, System 2 is the usual tool-using agent, and a confidence gate spends generation only where the fast path is unsure. Specialisation lifts the agentic path: CT0-Micro solves 21.1% of cybench-subtask against 7.6% for its base, above every open model of comparable footprint and the densest cybersecurity capability per parameter we measured. The fast path is what the architecture buys: CT0-Micro screens eighty files per second for indicators of compromise, catches its own refusals at 96.5% accuracy in 47 ms where the model judging itself reaches 76.5% in 254 ms and misses half of them, flags jailbreak requests at AUROC 0.966 in 8 ms, and, generating only for the facts it is unsure about, extracts vulnerability facts more accurately than either mode alone at a fifth of the generative cost. All of it is built in about 314 RTX PRO 6000 GPU-hours and served from one workstation GPU, with no policy layer between operator and target. Across eighteen benchmarks and use cases run with one checkpoint and head, we report where the design helps, where it does not, and what it still lacks.

ECG foundation models are increasingly popular due to their adaptability across various tasks. However, their clinical applicability is often limited by performance gaps compared to task-specific models, even after pre-training on large ECG datasets and fine-tuning on target data. This limitation is likely due to the lack of an effective post-training strategy. In this paper, we propose a simple yet effective post-training approach to enhance ECG foundation models. We evaluate it on a publicly available Transformer-based foundation model. Experiments across multiple ECG tasks show that our method consistently outperforms baseline fine-tuning. On the PTB-XL benchmarks, it improves macro AUROC by 0.7%-8.9% and macro AUPRC by 23.3%-77.9%, also outperforming several recent state-of-the-art approaches, including task-specific and advanced architectures. Further analyses demonstrate improved training dynamics and data efficiency, with only 30% of the training data outperforming the baseline trained on the full dataset. Ablation studies highlight the importance of stochastic depth and preview linear probing. These findings underscore the potential of post-training strategies to improve ECG foundation models, and we hope this work will contribute to the continued development of foundation models in the ECG domain.

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.

Large language models (LLMs) can generate fluent reasoning traces that nevertheless lead to incorrect answers, making response-level uncertainty estimation important for abstention, human review, and adaptive compute allocation. Existing approaches generally fall into three categories: passive single-trace methods use token-level confidence signals, sampling-based methods compare multiple complete traces at higher generation cost, and active prefix-based methods probe partial traces to study answer stabilization or preference transitions. However, none actively re-elicits an answer from a completed reasoning trace to measure its consistency with and support for the original answer. To address this gap, we introduce Trace-Conditioned Answer Consistency (TrAC), a correctness-supervised uncertainty quantification framework that combines active and passive signals anchored to one completed reasoning trace. Its active component, Prefix-Conditioned Elicitation (PCE), re-elicits a short answer conditioned on the completed trace and represents both its consistency with the original answer and its token-level probabilistic support. Its passive component, Trace Uncertainty Profile (TUP), summarizes how token-level uncertainty evolves throughout the original generation without additional decoding. A lightweight head then integrates the two representations into a response-correctness score. Across five mathematical reasoning benchmarks and three LLM families, TrAC improves macro AUROC by 1.8% and reduces AURC by 3.4% relative to eight-sample self-consistency, while using one complete reasoning trace and a short cached answer probe. When eight samples are already available, augmenting sample consensus with re-elicitation further improves macro AUROC by 4.3% and reduces AURC by 8.3%, without additional full-trace generation.

Received OFDM grids preserve both pilot and payload observations, yet wireless foundation models are rarely pre-trained on them. We introduce LWM-TF, a 9.58M-parameter factorized masked autoencoder pre-trained on complex 5G NR uplink grids taken after the FFT and before channel estimation. Each block attends first across OFDM symbols and then across resource blocks and receive antennas, and the mask follows the same two axes. Because the payload phase is unpredictable, the model reconstructs the normalized log-power of each masked token and predicts its scale separately; ablations show that the two terms are complementary and that this target outperforms complex-signal reconstruction. The encoder is pre-trained on 850,496 physical uplink shared channel (PUSCH) slots from a 10^6-slot dataset simulated with the NR transmit chain under various channel conditions. With the encoder frozen, linear probes classify modulation, predict CRC success, and detect UE mobility. On a separately generated test set, 16 labeled slots per class give 0.85 modulation accuracy, 0.82 CRC area under the ROC curve (AUROC), and 0.73 mobility AUROC, ahead of a supervised CNN on every paired draw. With 10,000 labels the probes reach 0.94, 0.96, and 0.92, well above engineered receiver statistics, and detect mobility where the CNN stays at chance. Without any impairment labels, distances in the frozen feature space flag unseen waveform impairments with 0.78 macro AUROC, against 0.68 for receiver statistics. A single pre-trained encoder thus provides receiver features that transfer across tasks, most strongly when labels are scarce.

Sleep is a complex physiological process evaluated through various modalities recording electrical brain, cardiac, and respiratory activities. We curate a large polysomnography dataset from over 14,000 participants comprising over 100,000 hours of multi-modal sleep recordings. Leveraging this extensive dataset, we developed SleepFM, the first multi-modal foundation model for sleep analysis. We show that a novel leave-one-out approach for contrastive learning significantly improves downstream task performance compared to representations from standard pairwise contrastive learning. A logistic regression model trained on SleepFM's learned embeddings outperforms an end-to-end trained convolutional neural network (CNN) on sleep stage classification (macro AUROC 0.88 vs 0.72 and macro AUPRC 0.72 vs 0.48) and sleep disordered breathing detection (AUROC 0.85 vs 0.69 and AUPRC 0.77 vs 0.61). Notably, the learned embeddings achieve 48% top-1 average accuracy in retrieving the corresponding recording clips of other modalities from 90,000 candidates. This work demonstrates the value of holistic multi-modal sleep modeling to fully capture the richness of sleep recordings. SleepFM is open source and available at https://github.com/rthapa84/sleepfm-codebase.

Vision-language models (VLMs) trained on paired chest radiographs and radiology reports learn a shared embedding space that can preserve instance-level image-report correspondence. This poses a privacy risk in settings where radiographs and reports are deliberately kept separate after acquisition, such as image-only data sharing or access-controlled reports, because a de-identified image may be re-linked to its original narrative report through cosine similarity alone. We formalized this as image-to-report retrieval and used public paired cohorts, in which the true pairing is known by design, as ground-truth benchmarks to audit the risk rather than as the privacy scenario. Evaluating VLMs of increasing clinical specialization on 406,241 paired examples from 126,804 patients across MIMIC-CXR (43,793 held-out pairs) and external CheXpert Plus (29,296 pairs), we found that re-linkage rose systematically with specialization: the strongest VLM retrieved the correct report at 15 times chance at a candidate pool of N = 100, 50 times chance at N = 10,000, and well above chance at full-database scale. The signal persisted under pathology-matched hard negatives that removed disease-label shortcuts, indicating correspondence beyond broad diagnostic categories. To reduce it without retraining, we froze both encoders and applied differentially private optimization only to the projection heads defining the alignment layer (epsilon = 0.34, delta = 6x10-6). This reduced Recall@1 by 61.8% at N = 10,000 on MIMIC-CXR and transferred to CheXpert Plus without retraining, while image-side utility was largely preserved: macro AUROC for linear-probe classification across 14 labels shifted only from 79.63% to 79.43%. Targeted DP finetuning of the shared alignment layer can substantially reduce cross-modal re-linkage without materially degrading the image representations that make these models clinically useful.

Recent breakthroughs in self-supervised learning (SSL), such as the Latent-Euclidean Joint-Embedding Predictive Architecture (LeJEPA), alongside successes in integrating visual encoders with language models, have driven the demand for adaptable, high-capacity vision encoders in Computed Tomography (CT). In this work, we explore 2D slice-based architectures as a flexible alternative to native 3D models for processing volumetric CT data. Using the CT-RATE dataset, we trained DALE-CT (Depth-Aware Latent-Euclidean Computed Tomography), a 2D model family built entirely from scratch using LeJEPA, and compared its performance against a continually pre-trained DINOv2 baseline. To enhance representation quality, we developed a novel 3D depth-aware pre-training strategy anchored by dense auxiliary supervision from both automated anatomical masks and human-annotated abnormalities. Under linear probe evaluation with Multiple Instance Learning (MIL) for multi-abnormality detection, the frozen backbone of this dual-supervised model (DALE-CT-2S) achieves a Macro AUROC of 0.833. This performance demonstrates near-parity with state-of-the-art 3D vision-language models, achieved entirely from scratch with significantly less data and no textual supervision. To ensure reproducibility, all training code, evaluation scripts, and model weights have been made publicly available.

Time-series foundation models have demonstrated strong cross-domain transfer, yet their common architectural assumptions remain poorly aligned with wearable physiological signals, which are multichannel, irregularly sampled, noisy, and governed by coupled continuous-time dynamics spanning distinct spectral scales. We present SOTER, a generative foundation model for wearable physiological time series that unifies cross-channel coupling, spectrum-guided expert specialization, and continuous-time latent evolution within a single pre-training framework. SOTER combines a spatial feature-aware backbone that models inter-signal dependencies, a power spectral density (PSD)-guided mixture-of-experts layer that routes representations to experts associated with fixed spectral bands through an inspectable, non-learned rule, and a neural controlled differential equation decoder that supports prediction and imputation at arbitrary timestamps. We pre-train SOTER on 226 billion time points from five public physiological datasets and evaluate the same pre-trained model across out-of-distribution zero-shot forecasting, frozen-encoder linear-probe classification, and continuous-time imputation on wearable benchmarks. SOTER achieves the best RMSE on 4 of 6 datasets and the best MAE on 5 of 6 in zero-shot forecasting, the highest average Macro-AUROC in classification, and the lowest imputation error on all six datasets at 75% missingness. It further remains robust to additive acquisition noise, matching or surpassing baselines evaluated on clean inputs even under the strongest corruption. These results indicate that domain-specialized foundation models for wearable physiology benefit from jointly modeling channel structure, spectral scale, and continuous-time dynamics.

Predicting whether a trained model will generalize under distribution shift remains difficult, especially when target-domain data are unavailable. We introduce STAMP (Semantic Temporal Augmented Model Prediction), a source-only, target-label-free criterion that estimates out-of-distribution (OOD) performance from paired source-domain images. STAMP computes the output-space correlation ratio η^2=S_B/S_T by contrasting semantically stable pairs with random pairs: higher η^2 indicates that model outputs vary with semantic identity rather than nuisance variation. On 44 chest X-ray models spanning CNNs, ViTs, MetaFormers, foundation models, and SSL/VLM probes, temporal STAMP attains Spearman correlations of 0.844--0.855 with macro AUROC on VinDr-CXR, CheXpert, and MIMIC-CXR; a class-matched variant improves single-class RSNA from 0.311 to 0.663. STAMP attains the best average source-only medical ranking and outperforms the target-domain ATC and AoTL estimators without any target data. On 27 ImageNet models, temperature-scaled STAMPTS attains ρ{=}0.984 on ObjectNet and ρgeq0.905 on four additional distribution shifts, with partial correlations of 0.662--0.949 after controlling for ImageNet accuracy. Requiring approximately 12s per model on one GPU, STAMP is a practical pre-deployment model-selection and auditing tool.

Large language models (LLMs) progressively revise their predictions across Transformer layers, yet we typically observe only the final output, discarding the trajectory through which it is formed. We introduce Belief-Trajectory Energy(BTE), a model-grounded measure that characterizes an input through the layerwise predictive revisions it induces in a model. By mapping intermediate states into a shared predictive space, BTE provides a principled measure of belief change that can be summarized as either a scalar or a structured depth profile. Theoretically, we show that local BTE corresponds to predictive revision under the Fisher-Rao geometry, while the sequence of revisions captures information beyond the initial-to-final belief change. Empirically, scalar BTE provides a model-relative signal of difficulty across diverse reasoning tasks, while richer BTE representations support human-LLM review detection and fine-grained generator attribution, reaching up to 0.998 macro-AUROC and 95.6% eight-way attribution accuracy. Further analysis shows that BTE develops throughout pretraining and is selectively reshaped by targeted training, demonstrating that the resulting measurement reflects what the scoring model has learned. Together, our results establish belief trajectories as a principled model-grounded signal and suggest a broader perspective in which learned models can themselves serve as instruments for characterizing the data they process. More demonstrations can be found at https://yingjiahao14.github.io/BTE-web/.