Antibody-specific epitope prediction aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity between antibody CDRs and the antigen surface. Existing methods usually leverage PLM embeddings and inject structure through additional graph, surface, or point-cloud encoders, where the positional mechanism inside attention remains largely tied to one-dimensional sequence order. For proteins, the analogue of a token offset is not only sequence separation, but also the three-dimensional displacement between residues after folding. This raises a question, can folded residue geometry serve as the positional mechanism of attention itself? We propose Local-Frame Rotary Attention (LFRA), which expresses inter-residue displacements in backbone-defined local frames and injects them directly into rotary attention. This design preserves continuous directional geometry while ensuring invariance to independent $\mathrm{SE}(3)$ transformations. The code and dataset are available at this https URL.
https://arxiv.org/abs/2608.01092
Music production typically involves multiple editing operations that each require specialized tools and expertise. Existing text-guided music editing systems support few operations or instruments, operate on short clips, or handle only one operation per instruction, unlike real workflows where several changes are requested at once. Here, we present ProCraft, a lightweight 0.5B-parameter autoregressive codec language model that edits 30s music excerpts end-to-end from free-form instructions, including compound requests. ProCraft supports seven operations across eight instruments, from tasks with a unique target (e.g., track removal) to creative ones (e.g., accompaniment generation). We align intermediate representations with pretrained music embeddings and pitch and instrument targets to preserve content outside the edit, and gated cross-attention in every decoder layer to keep generation tied to the instruction. To train on compound requests, we introduce On-the-fly Editing-pair Synthesis, which generates paired instructions and audio combining track-level operations with effect changes. ProCraft performs competitively against task-specific systems on single-task editing, and outperforms four free-text editors on compound instructions for track removal, extraction and denoising on real (MoisesDB) and synthetic (Slakh) recordings. In a user study (16 listeners), ProCraft was rated highest on removal and denoising and on-par with a 16-times larger model on extraction and instrument transfer. Ablations further show that representation alignment and cross-attention reduce leakage from unwanted tracks and raise editing success rates, especially on out-of-domain data.
https://arxiv.org/abs/2611.07423
Solving visual puzzles requires both accurate interpretation of visual evidence and reliable computation under task-specific rules. Embedding visual assumptions and task constraints directly in solving code makes the represented problem difficult to inspect and revise independently. We introduce Vis2State, a training-free agentic framework that abstracts visual puzzles into explicit, revisable problem states linking visual inspection and execution. Visual inspection guides state construction and refinement, while generated programs solve the represented problem. The model constructs both the state and the program without predefined puzzle schemas or solving procedures. Inspection and execution feedback allow it to revise the problem representation and solving procedure independently. Vis2State achieves the state-of-the-art performance on four benchmarks. Cross-model evaluation further demonstrates consistent gains. Ablations, error analyses, and fixed-program state interventions further support the effectiveness of the state-centered design. The code will be made publicly available to facilitate future research.
https://arxiv.org/abs/2611.07397
Registering intraoperative Ultrasound (US) bone-surface point clouds to preoperative Computed Tomography (CT) models can support radiation-free orthopedic navigation. Differences in imaging physics produce distinct surface sampling patterns, complicating cross-modal feature matching. Bone strongly reflects ultrasound and casts an acoustic shadow, so US captures only the probe-facing bone surface and leaves most CT points unmatched. This partial coverage makes correspondences ambiguous on near-symmetric bones. We propose CUFormer, a modality-aware registration framework. We introduce a Modality-Aware Transformer (MAT) that encodes input modality through identity embeddings and updates features through modality-specific adapters within a shared geometric matcher. We model imaging visibility and use predicted reference-side visibility to weight coarse and fine correspondences. CUFormer achieves the lowest mean registration errors among evaluated methods on two CT-US datasets, UltraBones100k and UltraBonesHip, and the CT-RGB-D dataset SpineDepth. On UltraBones100k, it reaches mean rotation error 4.53$^\circ$, translation error 3.19\,mm, and Root Mean Squared Error (RMSE) 2.54\,mm, reducing RMSE by 65.8\% relative to the best-performing baseline by this metric. These results demonstrate CUFormer's effectiveness in aligning partial bone surfaces with preoperative CT across anatomical sites.
https://arxiv.org/abs/2611.01536
When a tropical cyclone (TC) threatens several ports, preparedness planning depends on anticipating which ports are likely to be affected and where disruptions may last longest. Limited historical observations at individual ports and uncertainty in landfall location make these relative impacts difficult to estimate. We use a two-stage recommendation framework that first selects candidate ports based on their proximity to the expected landfall location and then ranks them by their estimated number of impact days. Using AIS-derived impact days for 37 ports and 31 TCs in the Gulf of Mexico study region, we compare three ways of representing port--cyclone interactions: pairwise feature interactions, tree-based feature combinations, and explicit feature crosses combined with learned embeddings. In tests on Hurricanes Nicole and Ian, the retrieval stage consistently identifies all observed affected ports under landfall uncertainty. Among the ranking models, Wide & Deep Learning achieves the closest agreement with the observed port rankings. Its mean ranking agreement exceeds that of the distance-based baseline by 85.5% for Nicole and 55.5% for Ian and is less sensitive to uncertainty in the landfall location. These rankings could help port authorities prioritize post-cyclone inspections and allocate recovery resources across ports threatened by the same event.
https://arxiv.org/abs/2611.07296
Diffusion models for video generation have achieved remarkable success, yet precise motion control under explicit user guidance remains challenging. Recent noise-warping methods introduce temporal correlations by warping the noise according to the user-provided motion signal. However, standard spatial warping generally disrupts the noise's i.i.d. Gaussian structure, requiring distribution correction, such as Jacobian-based correction, but at a substantial computational overhead. We propose Householder Motion Embedding (HME), which encodes the motion signal into the noise through a sequence of Householder reflections that together form an orthogonal transformation applied to each location's channel vector. HME exactly preserves the spatial Gaussian structure within each frame while introducing cross-frame correlations that promote temporally consistent video. HME is agnostic to the network architecture and integrates directly into standard video diffusion fine-tuning pipelines. Experiments on different scenarios show that HME matches or outperforms the state of the art, while achieving a 2.7x speedup over noise warping. These results demonstrate that channel-space Householder transformations offer a principled and efficient alternative to noise warping for motion-controllable video generation.
https://arxiv.org/abs/2611.07294
EHR foundation models read medical events within a fixed context window, and long context has so far been measured only in tokens. How far back in time a model must look to capture the earliest predictive signal is unknown. We introduce time-context, the calendar lookback window before the prediction point, and provide, to our knowledge, the first systematic evaluation of decade-scale time-context for an EHR foundation model. We pretrained a decoder-only transformer (34.6M parameters) on 1.4B coded events from 3.6M primary-care patients in North West London and fine-tuned it to predict incident colorectal cancer under a 12-month pre-diagnostic buffer. A frozen cohort of 1,008 cases and 9,582 matched controls, all registered for at least 30 years, was evaluated at 15 nested lookback windows from 2 to 30 years, so that every truncation is compared within the same patients. Discrimination rose from an AUROC of 0.551 at 2 years to 0.590 at 18 years, then plateaued, with about 80% of the gain reached within 10 years; an XGBoost baseline converged to the same level (peak AUROC 0.589). A simulation further suggests that rotary position embeddings (RoPE) over elapsed time alias beyond about 20 years at the default base frequency, motivating a retuned $\theta$. Time-context is a measurable design axis for clinical prediction models, distinct from token-context, and should be reported.
https://arxiv.org/abs/2611.07265
In embedding visualizations, nearby instances are interpreted as semantically related, although neighborhoods derived from input embeddings may not reflect content relationships. Neighborhood-based dimensionality reduction (DR) methods can propagate this limitation by optimizing layouts from embedding-based neighborhood graphs. We propose Knowledge-Guided Neighborhood Graph Construction (KGN), which represents relational knowledge derived from each instance as a set of knowledge graph (KG) triples. It uses the degree of triple sharing as pairwise semantic evidence to adjust embedding distances and reconstruct the top-k neighborhood graph; neither KG extraction nor neighborhood construction uses class labels. We also introduce IDProfile (IDP), which interprets residual mismatches by independently assessing whether the source content supports the assigned class label and the neighborhood-majority class. Across eight text and image dataset-encoder conditions, we characterize KGN over the full guidance-strength sweep and four KG similarity measures. Across this sweep, the maximum NMI and LT_2D each exceed the corresponding kNN baseline in all eight conditions, with the largest gains reaching 0.68 and 1.35, respectively. The gains and the extent of neighborhood reconfiguration vary across conditions and are larger under encoder conditions with lower kNN baseline scores. The IDP analysis shows that the largest reductions are concentrated in Placement Issue candidates, whereas Label Issue and Unresolved Case instances account for a larger share of the remaining review set. These results indicate that KGN can narrow the evaluated gap between embedding-based neighborhoods and content-supported semantic relations, while IDP shows that a residual mismatch should not automatically be interpreted as a projection failure.
https://arxiv.org/abs/2611.07246
Large Language Models (LLMs) are increasingly employed as automated judges for evaluating chatbot responses. While proprietary models can achieve high agreement with human annotators, they remain costly and difficult to deploy in practical settings. Lightweight open-source LLM judges provide an attractive alternative but typically exhibit lower agreement with human ratings. In this paper, we investigate whether soft prompt tuning can align open-source LLM judges more closely with human annotation policy. We train soft prompts on the FairBotBench benchmark and evaluate the adapted judges across the dimensions of bias, toxicity, and personalization. Our findings demonstrate that hybrid soft-prompt tuning, which combines textual prompts with learned continuous prompt embeddings, consistently improves agreement with human annotations over the corresponding untuned baselines. For Qwen 3.5 9B, the adapted judges surpass both hosted reference judges across all three evaluation dimensions.
https://arxiv.org/abs/2611.07126
Few-shot adaptation of vision-language models must balance two competing goals: learning fine-grained visual distinctions from very limited supervision and preserving the efficiency that makes frozen CLIP-like models attractive for deployment. Existing lightweight adaptation methods, including prompt tuning, LoRA, and cache-based adapters, typically supervise global image embeddings and therefore underuse token-level structure. Conversely, structure-aware methods exploit local evidence but often introduce additional inference-time computation. We propose SD-LoRA, a structural distillation framework that uses token-level graph reasoning only during training and transfers its effects into a lightweight LoRA-adapted CLIP model. During training, a heterogeneous graph teacher models patch-patch, global-local, and visual-text relations over high-resolution ViT tokens. Rather than retaining this graph at test time, SD-LoRA transfers its structural bias into the shared CLIP-LoRA backbone through implicit distillation and Prototype Predictive Alignment, which aligns graph-conditioned representations with support-derived class prototypes. At inference, the graph teacher is discarded; prediction requires only a single CLIP-LoRA forward pass and a cache-based classifier. Across 11 few-shot benchmarks, SD-LoRA improves over a strong CLIP-LoRA baseline by 2.4/1.8/3.0/2.4/2.0 percentage points in the 1/2/4/8/16-shot settings, respectively, without additional graph computation at test time. Results on base-to-novel generalization, cross-dataset transfer, out-of-distribution robustness, and calibration further show that training-time structural supervision improves both accuracy and transfer reliability. Code is available at this https URL.
https://arxiv.org/abs/2611.07063
Hierarchical text embedding models offer variable-length representations, while quantization reduces numerical precision; both aim to improve computational efficiency. This work is an empirical benchmark study of how these two orthogonal, already-established techniques interact. We evaluate 38 tasks from the Massive Text Embedding Benchmark (MTEB) using four transformer-based embedding models, covering 1D and 2D hierarchical representations combined with 32-bit, 8-bit, and binary quantization, for 168 configurations per task. We report each efficiency dimension separately: theoretical per-vector storage and end-to-end evaluation time. Under a Friedman test with Nemenyi post-hoc analysis, int8 quantization is statistically indistinguishable from float32 for pair classification and re-ranking and costs at most 1.5 percentage points overall, whereas binary quantization is significantly worse across every task category. Halving the embedding dimension once is not statistically detectable above $m=16$; two successive halvings always are. Combining an 8x dimensionality reduction with int8 yields a 32x reduction in per-vector storage at 94.4% of baseline effectiveness. Because evaluation times were measured once, we treat them as indicative: we find no evidence that quantization speeds up evaluation, whereas sampling from intermediate layers shortens it substantially. Retrieval degrades far faster than every other category, so we report findings per task category.
https://arxiv.org/abs/2611.06859
We present a toolchain for development of ML models on AWS EC2 F2 cloud FPGA infrastructure from high-level language, implementing a complete Vitis HLS to HDK bridge to AFI workflow that has been absent from the academic literature despite eight years of AWS FPGA availability. We introduce a four-level methodology (FP32 PyTorch, bit-accurate quantized Python, HLS C-simulation, physical FPGA) to aid in localizing errors, including FPGA-specific circuit errors. Together these tools allow coding agents to effectively implement FPGA designs from user directions, testing and debugging as needed. We document the deployment workflow, timing closure strategies, and practical HLS engineering decisions that proved crucial. We validate using TinyBERT fine-tuned for address Named Entity Recognition, implementing the embedding layer and the first of four encoder layers on the FPGA hardware. Our implementation streams weights from host DRAM, yielding poor performance compared to CPU/GPU implementations; we discuss forward paths.
https://arxiv.org/abs/2611.06829
With the growing need for evaluating Large Language Models (LLMs) and their applications to speech, challenges persist in summarizing and evaluating conversations that lack a clear end goal. We introduce SAUCE -- a reference-free, fact-based evaluation pipeline for cross-lingual conversational speech summarization. It measures the accuracy and the fact coverage of a summary through the entailment between conversation and text. We compare SAUCE against several popular summarization metrics and demonstrate the effectiveness of capturing information loss due to transcription and translation error and identifying broken summaries. Crucially, unlike black-box LLM evaluators or dense embedding metrics, SAUCE is inherently explainable: it maps summary scores to discrete, verifiable facts, allowing users to pinpoint exact hallucinations or omissions. We illustrate how this interpretability helps developers systematically profile LLM behaviors and gives end-users an actionable tool to verify summary accuracy in noisy, real-world conditions. Preliminary investigations show SAUCE strongly align with human judgment.
https://arxiv.org/abs/2611.06812
Psychological harms from interactions with large language models cannot be monitored directly because they may emerge over repeated interactions and depend strongly on subjective individual user context. We propose measuring risk, not harm: detecting observable AI behaviors that constitute risk factors for psychological harm at the AI response level and aggregating these signals to support longitudinal monitoring. We operationalize eight such behaviors and construct a synthetic multi-label corpus of 47,062 AI responses and 373,873 response-factor labels, with targeted human annotations for validation and evaluation. We then compare trained embedding-based classifiers, direct LLM judging, and a classifier--judge cascade. All detectors are model-agnostic and operate only on LLM outputs, requiring no access to internal model states. We apply these detectors to several out-of-distribution human-AI conversation data sets from prior research. On held-out human-labeled data, the best cascade achieves macro precision of 0.86, recall of 0.76, and F1 of 0.79. On WildChat, it reduces LLM-judge calls by 97.1\% relative to direct judging. On DelusionEval, risk-factor detections cluster within conversations. Together, our results show that response-level behavioral risk-factor detection can provide a scalable measurement layer for longitudinal psychological-safety monitoring without conflating observable AI behavior with latent user harm.
https://arxiv.org/abs/2611.06806
Efficient benchmarking estimates a system's full benchmark performance from a small number of task executions. Standard approaches rely solely on the binary correctness of executions from a collection of already-evaluated reference systems. An agentic system, however, produces a rich trace for each execution that can reveal substantially more about its capabilities. Leveraging this information requires useful trace representations. We propose representing a trace by extracting a structured summary of it with an LLM and embedding the summary with a standard text encoder. These representations preserve correctness- and task-related signal while minimizing the presence of system identity-, model family- and harness-related signals that dominate raw trace embeddings. Given this representation for each task execution from all reference systems, we construct low-dimensional representations of the systems and predict a new system's score from its position among the reference systems. On SWE-bench Verified and Terminal-Bench 2.0, augmenting an item-response model with this geometry-based prediction reduces mean absolute error from 0.13 to 0.08 (Wilcoxon $p < 10^{-4}$) and from 0.14 to 0.12 (Wilcoxon $p < 10^{-3}$), respectively, when provided a single random executed task. Further, given access to the full set of reference systems, our approach dominates baselines for any given number of executed tasks on both benchmarks.
https://arxiv.org/abs/2611.06803
Message-passing graph neural networks (GNNs) are limited in expressive power by the one-dimensional Weisfeiler-Leman test. Persistent homology (PH) provides topological descriptors that can complement GNN representations, but existing approaches typically compute persistence separately from the representation learning process. In this paper, we introduce Message-Passing Graph Persistence (MGP), a family of topological descriptors that incorporates message passing into graph filtrations. At each filtration step, node embeddings are updated using the current subgraph and associated with persistence events. These embeddings also determine the representatives of connected components during persistence computation. We prove that MGP is invariant under graph isomorphism and that it is strictly more expressive than the PH-based descriptors it extends. We evaluate MGP on an expressivity benchmark and on several graph classification and regression datasets. Experiments show that MGP outperforms other PH-based descriptors on most of these datasets.
https://arxiv.org/abs/2611.06801
Sign language generation (SLG) maps written sentences into signing motion while preserving both lexical content and fine-grained articulation. This requires a model to decide what signs should be expressed and to realize them through precise handshape, trajectory, facial expression and body coordination. Existing pose-based systems and reconstruction-only motion tokenizers often entangle these two decisions, leaving the generator without an explicit text-aligned intermediate target for what to sign before refining how to sign it. To address this issue, we introduce Semantic Residual Vector Quantization (SRVQ), a framework for SLG that frames generation as a two-level process moving from semantics to kinematics. The newly introduced SRV Quantizer learns a hierarchy in which the first residual level encodes sign content and subsequent levels refine pose, handshape, trajectory, and body coordination, all within a single quantizer and without separate semantic representations or external planning stages. Through word-aware conditioning for hierarchical code generation, a masked semantic generator predicts semantic codes and a kinematic generator completes the residual codes for full SMPL-X motion synthesis. We evaluate using retrieval and FID in a shared text-motion embedding space, alongside standard geometric metrics. On CSL-Daily and Phoenix-2014T, SRVQ achieves R@1 of 82.3 and 70.3, outperforming the previous SOTA by 30 and 46 points, respectively.
https://arxiv.org/abs/2611.06781
When a language model answers, we can usually only estimate why. We build a transformer in which every step is a Born measurement - attention $|\langle q|k\rangle|^4$ normalised over each row, a measured product in place of the feed-forward nonlinearity, and a Born readout. With its denominators held at their values for the input, each class probability is a polynomial in the word amplitudes, so its integrated-gradient evidence is computed by a finite quadrature with no quadrature error: the words' contributions sum to the class probability above its no-information share, to $10^{-11}$ or better. On e-SNLI natural language inference, with about 98k parameters outside the embedding, the model reaches $76.98 \pm 0.17$% test accuracy, level with a softmax transformer of the same size ($76.62 \pm 0.36$%). Deleting the word its evidence ranks first changes the answer in 45% of test pairs, out of the 53% any single deletion can change, against 32% for the softmax model explained the same way and 40% by its attention x gradient. Attention can look as much like the words annotators highlighted as the evidence does, yet accounts for the answer less well: deleting the word it ranks first changes the Born Transformer's answer in 32% of pairs. The same weights compile exactly to optoelectronic optics and to qubits, and a coherent attention layer becomes one circuit equal to the model (852 CNOTs on 23 qubits). On IBM's ibm_kingston, reading only the attention overlaps by Hadamard tests, the device gave the model's answers, also when a word was deleted. With calibration circuits as deep as the overlaps, each word's evidence with the device's attention row sums followed the exact evidence (correlations 0.997 and 0.932 on two pairs chosen in advance); where a pair's evidence is a small total of large opposite terms the earlier runs say it does not, and we say why.
https://arxiv.org/abs/2611.05355
Large language model (LLM) agents typically append raw tool outputs to their context. Over multi-step interactions, long and noisy observations incur substantial context overhead and dilute the agent's attention to task-relevant information. Existing token pruning and summarization methods remain constrained by discrete text representations, limiting the achievable compression ratios. In this work, we challenge the prevailing assumption that agents must consume tool observations as explicit text tokens. To this end, we propose Coca-Cola, a continuous latent context compression model for LLM agents. Coca-Cola compresses tool observations into latent tokens and embeds them into the input embedding space of the agent. We further introduce Action-Preserving Training, which aligns the agent's next-action distributions under full and compressed observations. This trains the compression model to learn action-sufficient latent tokens that retain decision-critical information. Experiments with web-search agents on four QA benchmarks and two model families show that Coca-Cola reduces the agent's token consumption by 70.01%-89.24% and end-to-end runtime by 24.45%-55.97%, while consistently improving task performance. These results suggest that Coca-Cola offers a promising approach for context compression in agents. Our code is available at this https URL.
https://arxiv.org/abs/2611.06500
QA-based text embeddings represent texts as vectors consisting of 1/0 answers to yes/no questions. Although these embeddings provide detailed information for interpretation and achieve high task performance, they often require humans to examine a large number of questions. Furthermore, the relationship between the number of questions and the appropriate level of question granularity has not been sufficiently studied. To address these challenges, we propose a method for constructing hierarchical questions for text embeddings. As the hierarchy deepens, questions become more specific and their number increases. During interpretation, we reduce the number of questions that humans need to examine by replacing questions at deeper levels with aligned questions at shallower levels. The question hierarchy is constructed through recursive clustering, contrastive prompting, and question alignment. Experimental results on general-purpose tasks show that our method improves interpretability while maintaining task performance. It is also found that, when only a limited number of questions are available, questions at shallower levels tend to achieve higher task performance than those at deeper levels, even with the same number of questions.
https://arxiv.org/abs/2611.06402