Physical Alignment

In data-driven training, multivariate time-series forecasting is usually optimized with a scalar loss averaged over samples, variables, and horizons. This averaging is convenient, but the optimizer sees only the aggregated gradient, which does not reveal whether the variable-wise contributions align or oppose one another. To quantify how often this disagreement arises, we measure the variable-wise gradients directly and find that 30.6% of their pairwise cosine similarities are negative on average across seven datasets. However, conflict and harm are not the same thing. Under shared training 35 of the 64 variables do worse than a full-input single-target oracle, and the harmed fraction is not reliably predicted by how often gradients conflict. We propose Per-Variable Surgery (PV-Surgery), an optimizer-side training strategy for backbones with cache-compatible layers. One backward pass builds variable-wise gradient proxies from output-side signals and keeps the pointwise forecasting loss. Reliability-aware selection targets layers whose proxy sums closely approximate their shared-gradient slices. Conditional pooling forms anchor and conflict pools without dropping variables. Common-direction surgery aligns variable or pooled gradients with their normalized mean and restores input norms to avoid reweighting. In experiments across five backbones, seven datasets, and four horizons, PV-Surgery lowers MSE by 3.61% and MAE by 2.93% on average. For multivariate forecasting, this indicates that the variable-wise structure hidden by mean-loss training is a usable optimization signal.

Ontology alignment (OA) has evolved through several methodological paradigms, ranging from lexical and structural aligners to knowledge graph embedding (KGE) models and, more recently, Large Language Model (LLM)-based approaches. Although modern OA frameworks provide unified ecosystems for deploying these heterogeneous aligners, mechanisms for systematically reconciling their complementary and sometimes conflicting predictions remain relatively underexplored. We present OntoAligner-Ensemble, a modular and aligner-agnostic framework that combines candidate correspondences through a configurable two-stage process comprising voting-based fusion strategies followed by post-fusion selection policies. The framework supports any aligner implemented within OntoAligner that produces candidate correspondences, enabling diverse alignment paradigms to be integrated through a unified decision process. To demonstrate its effectiveness, we instantiate the framework using representative lightweight string-aligner, KGE-based, and Retrieval-Augmented Generation aligners powered by both open-weight and API-based LLMs. We evaluate individual aligners and ensemble configurations across eight benchmark tasks from five OAEI tracks spanning biomedical to beyond-equivalence. The results show that ensemble fusion consistently improves the balance between precision and recall and frequently outperforms standalone aligners across diverse domains. Furthermore, our analysis reveals that ensemble composition directly affects the precision-recall trade-off: heterogeneous cross-paradigm ensembles generally improve precision, whereas homogeneous LLM ensembles more often achieve higher overall F1-scores. These findings demonstrate that systematic ensemble learning offers a robust and reproducible strategy for OA while providing practical guidance for selecting ensemble compositions under different alignment scenarios.

We ask whether language-model pre-training can be decomposed into smaller, independently trainable jobs that can later be recomposed into a coherent larger model. We introduce Mixture of Training (MoT), a scaffolded modular pre-training procedure that partitions a target Transformer into contiguous layer blocks, trains each block inside a frozen pretrained aligner scaffold, and then recomposes the trained blocks with an optional short end-to-end adaptation pass. On a 1.3B-parameter Gemma-style model trained on C4, MoT provides a small-scale proof of mechanism: independently trained depth slices can be recomposed into a usable language model, and a quality-parity schedule reaches the same reported perplexity as the monolithic baseline. This parity setting processes more aggregate tokens and has a shorter idealized layer-equivalent critical path after aligner preparation; its effective compute advantage depends on reusing the aligner across runs. We therefore present MoT not as a general replacement for monolithic pre-training, but as a small-scale framework for studying whether scaffolded sub-runs can act as reusable training units.

Generative traffic video forecasting aims to synthesize long-horizon, temporally coherent future videos of traffic scenes from a short observation history and textual descriptions. In this paper, we present CosmosAlign, a generative traffic video forecasting framework built upon the pretrained Cosmos3-Nano world foundation model. Our approach is motivated by the observation that successfully adapting large pretrained world models to downstream forecasting tasks depends primarily on distribution alignment rather than increased model capacity. To this end, we propose a two-stage LoRA adaptation strategy that first aligns the conditioning-mode distribution with the target forecasting task, and then aligns the training captions with the model's native structured prompting interface through an LLM-based re-captioning pipeline. During inference, we further improve prediction quality using a fully training-free procedure consisting of consensus-based medoid sample selection and motion-adaptive blending of static scene regions. CosmosAlign achieves a final score of 76.49 on the AI City Challenge 2026 Track 5 benchmark, ranking first on the final leaderboard. Our code is publicly available at https://quangminhdinh.github.io/CosmosAlign/.

Computed tomography (CT) remains the reference for 3D osseous morphometry in femoroacetabular impingement (FAI) but requires ionizing radiation and manual measurement. Zero echo time (ZTE) MRI visualizes cortical bone and yields FAI angles that agree with CT, but automated angle extraction remains limited. We developed and validated automated FAI angle computation from ZTE MRI and assessed agreement with expert manual measurements in a cross-sectional study (level of evidence, 3). Pelvic ZTE MRI was acquired in 73 participants (mean age 36.8 +/- 18.5 years; 51 women, 22 men), yielding 135 hips. nnU-Net was trained on 100 manually curated hips to segment the femur, pelvis, and three osseous landmarks. Custom geometric algorithms computed alpha, femoral neck-shaft, Tonnis, coronal and sagittal center-edge, and acetabular version angles from inferred segmentations. Measurements on 35 test hips were compared with the mean of two radiologists' manual measures using intraclass correlation (ICC) and Bland-Altman analysis. Dice exceeded 0.96 for bone and ranged from 0.65 to 0.83 for landmarks. Median landmark error was 0.38 mm (femoral head), 0.82 mm (lateral acetabulum), and <2.5 mm (medial acetabulum, greater trochanter). Interrater ICC was excellent for acetabular version, coronal center-edge, and Tonnis (>=0.82) but poor for alpha and femoral neck-shaft. Model versus rater-mean agreement was excellent for acetabular version, coronal center-edge, and Tonnis (0.92-0.96), good for mid-acetabular sagittal center-edge (0.74), and fair for alpha (0.45) and femoral neck-shaft (0.55). Model Bland-Altman limits of agreement were narrower than interrater limits for most angles. Fully automated morphometric assessment from ZTE MRI is feasible and performs comparably to expert readers for most coverage and version angles.

Registration between cone-beam computed tomography (CBCT) and intraoral scans (IOS) is essential for patient-specific surgical planning. However, disparate imaging modalities, limited overlap, and large pose offsets make automated registration unreliable. Consequently, clinical registration remains dependent on conventional geometry pipelines and manual clinician adjustment. To address these challenges, we propose APCReg, an anatomical-prior-guided coarse-to-fine framework for global registration and reliability-controlled residual correction. Specifically, multi-view anatomical coarse registration (MACR) performs ordered orthogonal projection alignment (buccal, proximal, and occlusal) to decompose the six-degree-of-freedom search before three-dimensional refinement. Overlap-aware residual registration (OARR) combines shared KPConv features, a folded arch-length cue, overlap-gated cross-attention, and Sinkhorn matching. Finally, dental-arch-structured hypothesis selection evaluates diverse poses on held-out reliable correspondences, while a ground-truth-free coarse-retention guard conditionally retains a geometrically reliable coarse pose. On 60 held-out jaw pairs, APCReg achieves a submillimeter mean Chamfer distance of 0.87 mm and a Hausdorff distance of 2.92 mm under this evaluation protocol, and ranks first across the six reported metrics among the evaluated open-source baselines.

In digital dentistry and oral surgery, the registration of jawbone CT and intraoral scanner (IOS) data is essential for integrating internal bone structure with high-resolution dental surface geometry. However, this registration is challenging because the two modalities share only a limited region in common, and their true correspondence is generally unknown. This uncertainty has prevented rigorous quantitative evaluation of registration accuracy. In this study, we propose a pseudoIOS evaluation framework in which a point cloud emulating an intraoral scan is generated from CT data within the same coordinate frame, so that the transformation between them is known by construction and can serve as a true ground truth. Using this framework, we propose a coarse-to-fine registration method that combines a domain-generalizable local descriptor (GeDi) for initialization-independent global alignment with the iterative closest point (ICP) algorithm for local refinement, and also evaluate the influence of metal artifacts on registration. In experiments on seven cases, ICP alone frequently converged to local minima from a perturbed initial position, whereas GeDi$+$ICP maintained submillimeter mean absolute error (MAE) across all evaluated jaw and artifact conditions (0.55-0.69 mm). A three-way repeated-measures analysis confirmed that GeDi$+$ICP was significantly more accurate than GeDi alone. Metal artifacts had a statistically detectable overall effect, but their absolute impact on GeDi$+$ICP was small.

General-purpose humanoid trackers can execute diverse references, but their zero-shot coverage depends on large embodied corpora that are costly to extend. Text-to-motion generators offer scalable supervision, yet models trained on human motion or retargeted data inherit a gap between kinematic plausibility and robot executability. Existing one-way pipelines fix either the generated corpus or the reward tracker. We introduce GenTrack, an online generator--tracker framework that alternates execution-grounded, group-relative generator alignment with tracker training on newly generated references; anchoring and rehearsal constrain drift. On Unitree G1, we evaluate GenTrack with ProtoMotions and SONIC backbones across three zero-shot tracking splits including public AMASS and LAFAN benchmarks, and a private out-of-distribution test set of 1,024 prompt-motion pairs in the wild. The online co-training strategy consistently produces generators that output more robot-executable motions with strong semantic alignment, and trackers with markedly broader zero-shot coverage and improved tracking accuracy, especially on out-of-distribution references. These results demonstrate that joint online post-training effectively narrows the executability gap between retargeted references and robot-native motion, advancing zero-shot humanoid control without additional data collection and beyond the limitations of a static reference pool.

Articulated portrait mesh estimation is fundamental to 3D understanding, avatar generation, and immersive interaction. Existing approaches primarily rely on 3D Morphable Models (3DMMs). However, face-centric models suffer from the "floating head" assumption, conflating head pose with global rotation due to the lack of neck kinematics. Conversely, body-centric models lack high-fidelity facial expression capabilities. Furthermore, current methods struggle to disentangle jaw articulation from expression blendshapes, often over-relying on expressions for mouth opening. These limitations make monocular portrait recovery difficult across representation, supervision, and anatomical parameter estimation. To address these limitations, we introduce GRAPE(Graduated Routing for Articulated Portrait mesh Estimation). We build a Portrait Parametric Model (PPM) with an explicit torso-to-head kinematic chain and a canonical injection step to merge FLAME and the SMPL-X torso. We propose a Progressive Anatomical Alignment (PAA) network, which is composed of a pretrained portrait encoder, a Graduated-Mask Router, and coarse-to-fine experts that follow the portrait anatomical prior. We then train this network with multi-source supervision that combines sparse anatomical keypoints, feature distillation, foreground mask constraints, and relative geometry constraints. Experiments show that GRAPE improves portrait mesh recovery quality, pose alignment, and jaw--expression disentanglement over prior methods. We also demonstrate that our method can benefit the downstream tasks of audio-driven talking-head generation and 3D portrait generation.

Phonetic forced alignment is a key technique in phonetic research, yet existing alignment systems lack specialized models for low-resource language varieties. We address this by training text-dependent and text-independent aligners for Chengdu Mandarin using a 17-hour corpus and a custom G2P dictionary. We trained a text-dependent GMM-HMM model (Chengdu-MFA) and fine-tuned a pretrained audio encoder on frame classification with Chengdu-MFA's pseudo label for text-independent alignment (Chengdu-FC). Evaluation on an expert-annotated test set show that both methods significantly outperform Standard Mandarin baselines. Chengdu-MFA reduced average phone boundary differences by 31.8%, while Chengdu-FC achieved a 61.2% reduction. This work establishes a practical bootstrapping pipeline for developing accurate aligners for under-resourced varieties without labor- and time-intensive manual annotation.

Speech-to-text alignment means finding the temporal boundaries of each word in the audio. Some models provide such an alignment directly and others do not. Connectionist temporal classification (CTC) and transducer models have an alignment by construction, whereas attention-based encoder-decoders (AED) and speech large language models (LLMs) do not, and their word timings are usually read off the attention weights instead. All of these signals live on the encoder frame grid, which bounds their temporal precision. We study a generic gradient-based alignment that applies to any differentiable ASR model. We take the gradient of each teacher-forced token log probability with respect to the input, reduce it to a per-frame saliency, and decode the resulting matrix into word boundaries with a single dynamic-programming pass. The method needs no training, no model modification and no alignment heads, works across all model families including the speech LLMs, and aligns on the input grid rather than on the coarser encoder grid. We evaluate it on sixteen models from four families, on read (TIMIT) and spontaneous (Buckeye) speech, each against the model's own native or attention-based alignment. We find that the gradient yields a usable alignment for every model, that it is usually somewhat behind a strong native aligner but better where the native alignment is weak, as for the streaming models, and that its main disadvantage is the cost of one backward pass per token.

Aligner-Encoders are recently proposed seq2seq end-to-end ASR models that replace decoder attention by predicting the uth token directly from the u-th encoder position, so the encoder must learn the alignment internally without cross-attention or a transducer lattice. In practice, this alignment often forms abruptly in the upper layers, making training sensitive and brittle on long utterances. We propose InterAligner, which adds an intermediate Aligner objective so alignment can form progressively across depth, together with an intermediate CTC loss (InterCTC) to stabilize optimization. On LibriSpeech with a 17-layer Conformer, a final-only Aligner reaches 5.0/7.8 WER (test-clean/other). InterCTC improves to 3.4/6.0, and InterAligner further reduces WER to 3.1/5.6 with the largest gains on long utterances.

With 890,000 annual new cases globally, head and neck squamous cell carcinoma has one of the highest recurrence rates among solid malignancies. Although frozen section analysis is the standard of care for intraoperative margin assessment, accurately relocating detected positive margins on the resection bed remains challenging due to imprecise alignment between resected specimens and their resection bed, compounded by post-resection mucosal tissue shrinkage. We present a biomechanics-driven deformable registration framework that corrects post-resection tissue deformation to provide intraoperative guidance. Our approach registers 3D specimen meshes to intraoperative resection bed point clouds using a deformable registration approach based on regularized Kelvinlet basis functions. The registration matches surface point clouds, fiducial landmarks, and boundary contour constraints that directly penalize perpendicular distance-to-agreement between specimen and resection bed boundaries. Across nine specimens from skin, buccal mucosa, and tongue sites, the overall mean target registration error was $11.11 \pm 4.07$ mm using rigid registration, which decreased to $8.20 \pm 2.68$ mm (26.19% reduction) using deformable registration without contour constraint. The proposed contour-constrained deformable registration further reduced the error to $5.62 \pm 2.28$ mm, a 49.41% reduction relative to rigid registration. We observed the largest reduction in the most clinically challenging tongue specimens. We also performed a systematic two-stage parameter search to characterize the relative importance of surface alignment, fiducial correspondences, contour constraint, and strain energy regularization. This search revealed that contour weighting dominates registration accuracy for tissue types with large lateral deformation, while the algorithm operates over a broad range of parameter combinations.

The Montreal Forced Aligner (MFA) was released in 2016 and has since become the most widely used tool for forced alignment in research and industry. In the decade since, MFA has undergone substantial development, including expanded coverage across more languages and dialects using larger open-source datasets, harmonized IPA dictionaries, model adaptation, cross-language phone remapping, and support utilities. This paper documents MFA 3.0's developments since version 1.0 and evaluates MFA's performance across English, Japanese, and Korean, benchmarked against classic and neural forced aligners. MFA 3.0 achieves state-of-the-art or near state-of-the-art performance across all four benchmark datasets with mean boundary errors below 15 ms. Adaptation and cross-language remapping are effective for languages outside MFA's training distribution, and pronunciation probability modeling and phonological rules provide gains in specific conditions.

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

One-step image editing is important for making text-guided editing fast, practical, and easy to deploy, but its underlying mechanism is still not fully understood. We revisit ChordEdit through reproduction, ablation, and simplification. Our analysis shows that a) the chord window $δ$ largely acts as an effective timestep shift from $t$ to $t - δ$; b) chord transport acts on high-noise images and mainly performs low-frequency semantic editing; and c) proximal alignment acts on low-noise images and complements it by adding high-frequency target details. In this view, ChordEdit naturally decomposes editing into a coarse low-frequency transport stage and a fine high-frequency alignment stage. These findings suggest a path toward prompt-conditioned dynamic timestep selection for adaptive image editing. All code and results can be found at \href{https://github.com/Harvard-AI-and-Robotics-Lab/ChordEdit-Reproduction}{link}.

Renewable energy is essential for meeting future energy demands; however, solar energy generation, which occurs only during daylight hours often does not align with household consumption patterns. Appliances such as cookers, washing machines, and dryers are typically operated according to user preferred schedules rather than solar energy availability, creating a scheduling optimization problem. The objective is to determine optimal appliance start times to maximize renewable energy utilization while minimizing user inconvenience and adhering to system constraints. This paper presents a metaheuristic approach using Iterated Local Search (ILS) and Simulated Annealing (SA) to optimize appliance start times, while considering appliance operating durations, power consumption, inverter limit, battery state of charge constraints, and solar generation forecasts. Unlike most existing work, the scheduling is extended beyond a single day to accommodate unfinished tasks from previous days (spillover), ensuring operational continuity and enabling sequential operation across multiple days. Experimental results show that the sequential multi-day scheduling framework effectively manages system constraints while ensuring user convenience under exclusive solar generation. These findings also open opportunities for future research on multi-objective trade-offs between investment in equipment of various sizes, return on that investment, and user satisfaction.

Word-level cross-lingual alignment is central to annotation projection, translation auditing, and cross-lingual faithfulness estimation, yet existing neural aligners are rarely adapted to specialized domains. In this paper, we introduce ClinicalAligner26AM, a large-context multilingual aligner model for biomedical and clinical text initialized from ClinicalEncoder26AM. Our training recipe is inspired by AWESoME Align. We build our soft alignment target by sharpening with Sinkhorn-Knop optimal transport a cost matrix established for parallel clinical texts and conversations through the fusion of sentence-level, phrase-level, and token-level signals. We distill this sharpened alignment matrix directly into our student aligner, by encouraging its naive cosine-based token similarity scores to match this target. At inference time, we project source-span scores through the learned token alignment matrix and decode the longest valid high-scoring span in the target text, optionally supported by MultiClinNER predictions summarized in Appendix B. We evaluate CA26AM on the MultiClinCorpus shared task, which projects Spanish clinical entity annotations into six target languages. Our two submitted systems ranked respectively first and second across all languages and entity types, with character-weighted F1 scores above 0.95 in nearly all settings.

Multimodal neuroimaging fusion of functional MRI (fMRI) and diffusion tensor imaging (DTI) provides complementary information for cognitive impairment analysis, but remains challenged by heterogeneous feature spaces and misaligned representations. We propose \textit{NeuroAlign}, a hierarchical framework for structured multimodal fusion. It introduces (1) \textit{Dual-Modal Hierarchical Alignment} (DMHA), which models multi-scale dynamic connectivity and aligns dynamic-static and functional-structural embeddings; and (2) \textit{Dual-Domain Hierarchical Interaction} (DDHI), which enables fine-grained modulation and global interaction between connectivity- and region-level features. To support feature-level inspection, we design \textit{Synergistic Activation Mapping} (SAM), a gradient-free, marker-oriented attribution method for DFC, SFC, ALFF, and FA. Evaluated on GUTCM, ADNI, and OASIS under five-fold validation, NeuroAlign achieves competitive MCI/SCD detection and preliminary cross-dataset transferability. Attribution analyses reveal modality-specific and partially consistent brain patterns, providing model-derived evidence for multimodal representation analysis.

Large-scale text-to-image foundation models have achieved remarkable visual realism, yet generating human images with correct anatomical structures remains challenging. Existing approaches enforce anatomical constraints through part-specific modules or localized loss weighting during supervised fine-tuning on high-quality human photos, but such datasets are limited and often provide ambiguous optimization signals due to confounding factors such as lighting, pose, and background. Preference-based alignment offers an alternative, but standard Direct Preference Optimization (DPO) treats all pixels equally and therefore fails to exploit the localized nature of anatomical artifacts. To address this, we propose the framework of Alignment via Synthetic Anatomical Preference (ASAP), which constructs controlled preference pairs through a localized degradation mechanism applied to high-fidelity human images. This mechanism performs a controlled experiment on images by introducing explicit anatomical errors in targeted regions while preserving the remaining content. With this mechanism, we create the Human Anatomical Preference (HAP) dataset with over 10K curated pairs for effective anatomical alignment of text-to-image human image generative models. To better leverage the locality of these controlled preference pairs, we introduce a localized and margin-bounded variant of DPO that prioritizes optimization in targeted anatomical regions while enforcing a finite preference margin to prevent over-optimization and preserve global semantics. We further introduce HAF-Bench, a benchmark for systematic evaluation of anatomical fidelity. Extensive experiments demonstrate that ASAP consistently reduces anatomical errors across multiple foundation models while maintaining overall image quality.

This paper investigates the critical role of eigenalignments between the kernel matrix and learning targets in achieving robust generalization in learning problems. We establish a direct connection between generalization performance in kernel methods and the estimation of eigenvectors and eigenvalues of matrices, offering a more intuitive understanding compared to prior work with minimal assumptions. We also show that, since the prediction task in KRR is essentially the weighted sum of eigenvectors/singular vectors, by analyzing how much error can be caused by perturbations to the kernel matrix, we can then derive a bound on this generalization error using the estimation stability of matrix eigenvalues and eigenvectors. Compared with previous work, our analysis concentrates on finite-sample settings and on the generalization error arising from having a suboptimal finite training set. Our findings reveal that in kernel methods, as long as the kernel is of high rank, the near-zero reconstruction error can be trivially obtained, implying that the reconstruction error will have limited predictive power for generalization. Finally, we establish a generalization bound from an eigenvalues/eigenvectors estimation perspective, showing that strong generalization requires increasing eigenvector alignment, eigenvalue magnitude, or gaps between consecutive eigenvalues.

Scalable embodied intelligence is constrained by the scarcity of diverse, long-horizon robotic manipulation data. Existing video world models in this domain are limited to synthesizing short clips of simple actions and often rely on manually defined trajectories. To this end, we introduce MIND-V, a cognitive hierarchical world model designed to synthesize physically plausible and logically coherent videos of long-horizon robotic manipulation. Inspired by cognitive science, MIND-V bridges high-level reasoning with pixel-level synthesis through three core components: a Semantic Reasoning Hub (SRH) that leverages a pre-trained vision-language model for task planning; a Behavioral Semantic Bridge (BSB) that translates abstract instructions into domain-invariant representations; and a Motor Video Generator (MVG) for conditional video rendering. MIND-V employs Staged Visual Future Rollouts, a test-time optimization strategy to enhance long-horizon robustness. To enforce adherence to physical laws, we introduce a GRPO reinforcement learning post-training phase guided by a novel Physical Foresight Coherence (PFC) reward. PFC leverages the V-JEPA2 world model as a physics referee to penalize implausible dynamics in the latent feature space. Experiments confirm MIND-V's SOTA performance in long-horizon simulation and its significant value for policy learning, introducing a scalable and fully autonomous framework for embodied data synthesis.