Feature Alignment

Functional annotation of newly sequenced proteins remains a bottleneck in molecular biology: the number of sequences in public repositories grows far faster than the capacity for manual curation. Most computational approaches consider annotation as multi-label classification over a fixed ontology, which constrains predictions to a predefined label set. In this work we study the the protein annotation as a sequence-to-text generation problem. We fine-tune the 3B-parameter Ministral 3 base model with QLoRA (4-bit NF4 quantization with low-rank adapters) on sequence annotation pairs. We assess predictions with an LLM-as-expert protocol: a GPT model prompted as a senior molecular-biology curator scores organism identification as binary and function annotation quality. We conclude that QLoRA-fine-tuned compact LLMs can generate curator-style annotations with genuine biological value for a substantial subset of proteins. We also discuss future directions in data quality, model scaling, and evidence grounding that are needed to make the approach sufficiently reliable for practical use.

Gromov--Wasserstein optimal transport (GW-OT) extends classical optimal transport by introducing structure-aware transport cost. This is particularly relevant for spatial transcriptomics, where dynamical reconstruction should preserve tissue structure in addition to matching expression patterns. While static formulations have been widely used for such structure-aware alignment, a general dynamic formulation for reconstructing continuous trajectories is still missing. We introduce Travelling Pair Dynamical Alignment and Trajectory Estimation (TP-DATE), a theoretical and computational framework to generalize GW-OT dynamically in a simulation-free manner. We formulate a broad class of static and dynamic Quadratic-form OT (QOT) through path actions and prove the static dynamic equivalence. We further develop travelling-pair flow matching, which allows interacting conditional paths and marginalizes their interactions into a single vector field. On synthetic and real spatial transcriptomics data, TP-DATE better preserves spatial structure and improves continuous 3D dynamics reconstruction.

A document modeled as a discrete sequence of tokens can be thought of as being generated from a composition of texts from different domains; a README file, for example, moves between prose, code, and configuration. When such a document is corrupted and only frozen domain experts are available, restoring it requires deciding both what is missing and which expert to trust at each position, at test time and without region labels or a trained router. We introduce evidence-aligned local composition, which infers a soft, position-wise weighting over the experts from the marginal evidence of the corrupted observation under a given corruption model, estimating the evidence from the experts' own denoising losses and smoothing the weights across positions. Because the weighting is soft, it recovers a mixture when the true composition is mixed and concentrates on one expert when that suffices. Across a categorical simulator, byte-level experts, and experts fine-tuned from a $1.3$B discrete flow-matching model, the inferred weights track the true regions at $0.85$ field accuracy on naturally mixed scientific documents, and at $0.98$ on constructed mixtures whose regions are lexically disjoint. Restoration improves over a single global weight when the experts are genuinely distinct and reduces to it when they converge, tracking a measure of expert separation.

Computational RNA structure pipelines generate many candidate conformations for the same sequence. Reliable evaluation therefore requires more than recognising plausible geometry, it requires determining whether that geometry is compatible with the sequence. We introduce SIRGE, a sequence-informed geometric evaluator that conditions structural representations on nucleotide embeddings from a pretrained RNA language model. Early results show that SIRGE outperforms established evaluators in Kendall--$τ$ alignment, Top-1 selection, and Top-3 ranking. Controlled comparisons further show that sequence conditioning corrects errors made by an otherwise matched geometric model and improves target-level rank structure. These findings provide initial evidence that pretrained sequence representations supply ranking information that complements geometric reasoning.

Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

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.

Knowledge distillation effectively transfers reasoning capabilities from large language models to lightweight student models. To enable knowledge transfer across disparate model families, researchers increasingly explore cross-tokenizer distillation. However, cross-tokenizer distillation remains challenging due to vocabulary and sequence misalignment, while approximate vocabulary alignment can introduce additional noise into distillation. To address these challenges, we propose Anchor-Based Cross-Tokenizer Distillation with Residual Regularization (ACTD). ACTD bridges structural heterogeneity through vocabulary and sequence alignment, while mitigating alignment noise via a novel anchor loss with residual regularization. We further extend this framework to a multi-teacher setting. Evaluated across five reasoning benchmarks with three distinct teacher models, ACTD achieves state-of-the-art performance. Moreover, its multi-teacher extension outperforms the strongest single-teacher and multi-teacher baselines, further demonstrating the robustness of our method.

Automating alignment research may accelerate progress toward aligned AI, but whether it does is hard to measure. Luckily, many alignment failures, such as deception, sycophancy, and jailbreaks, are already measurable by public benchmarks. We study whether automated alignment researchers (AARs) can post-train to mitigate alignment failures by proposing training methods and data to simultaneously optimize multiple safety benchmarks, while largely preserving general capability. Across 10 alignment failures, the strongest AAR methods significantly reduce the targeted alignment failures and generalize to a held-out benchmark, multi-turn behavioral audits, and models up to 4.7x larger than the target model. As a human baseline, 28 experienced researchers receive up to eight hours to develop one-shot methods for the same benchmarks, but their methods underperform the best AAR methods. Using human ideas as the AARs' initial research direction does not improve performance, suggesting current AARs may not need guidance from experienced researchers. These results suggest that automating alignment research on well-characterized failures may be practical in the near term.

Reinforcement learning-based knowledge distillation has the potential to transfer complex reasoning from teacher to student models, yet it currently faces a critical dilemma: researchers must choose between sparse outcome-based rewards, which provide insufficient logical guidance, or expensive neural Process Reward Models (PRMs) for dense signals. We resolve this by introducing SPEAR (Symbolic Process Evaluation and Alignment Reward), a training-free and plug-and-play process reward method for sequence-level on-policy distillation. SPEAR projects natural-language reasoning traces into domain-adaptive symbolic milestones, providing an efficient proxy for process-level reasoning alignment. By utilizing the longest common subsequence (LCS) to align student explorations with teacher milestones, SPEAR provides a dense, order-aware reward signal that enforces logical consistency without the need for an external neural verifier. Our experiments across math, science, and commonsense reasoning tasks demonstrate that SPEAR effectively bridges the reasoning gap between student and teacher models via sequence-level distillation with efficient dense process rewards. Our code and data are available at: https://github.com/zhuochunli/SPEAR.

We study learning a mixture of $k$ Plackett-Luce models from multi-way ranking responses from annotators that may represent heterogeneous underlying preferences. This problem has many applications in AI alignment and preference optimization. Prior work has studied mixtures of Bradley-Terry models from pairwise comparisons. However, estimating a mixture of multi-way ranking models can become theoretically unidentifiable when $k$ exceeds $m/2$, where $m$ is the ranking length. We design an efficient algorithm to address this issue by first augmenting the rankings to a larger size (e.g., generating comparisons from a base model), followed by a gradient-based estimation to reduce inference cost (in the input embedding space). With this procedure in mind, we then fit a mixture of Plackett-Luce (PL) models via an expectation-maximization-style iteration, or MoPLEx in short. We conduct extensive experiments to verify this algorithm. First, we find that the gradient-based approximation estimates true probabilities with less than 5% error on models with up to 34 billion parameters. Second, MoPLEx improves clustering and ranking accuracy by an average of 43.7% and 15.2% over baselines using a single PL model or a mixture of Bradley-Terry models, on UltraFeedback and PERSONA datasets. These results demonstrate the effectiveness of MoPLEx for tackling multi-way rankings following heterogeneous preferences through measuring alignment via gradients.

Group alignment adapts a language model to a demographic group to produce responses that reflect the group's opinions, values, and preferences. Sycophancy, a well-documented by-product of alignment, causes the model to over-agree with the user regardless of factual and objective information. However, existing group alignment methods and evaluations focus only on how closely the model matches the group's opinions, overlooking the induced change in sycophantic behaviour. To bridge this gap, we introduce \textbf{G}roup \textbf{A}lignment-induced \textbf{S}ycophancy (GAS) and systematically evaluate alignment across 3 methods, 4 models and 13 demographic groups, on both the intended gain in opinion alignment and the unintended shift in sycophancy. We find that gain and shift are non-uniform across groups: under an identical budget, some groups receive larger gains in opinion alignment than others, and the induced sycophancy shift forms a group-specific profile rather than a single-dimensional change. These results suggest that group alignment should be reported as a two-sided, multi-dimensional profile rather than a single fit score that accounts for per-group differences when adapting LLMs to diverse populations.

AlphaFold3-class structure predictors pair a representational trunk, which processes sequence and context, with a diffusion module, which generates atomic coordinates. How biological information changes as it crosses this architectural boundary remains poorly understood. We analyze per-residue activations from the Pairformer trunk and diffusion module of Boltz-1 using linear probes, sparse autoencoders (SAEs), and causal interventions. From the trunk, both geometry (secondary structure, disorder) and sequence chemistry (amino-acid identity, signal peptides, disulfide-bond annotations) are linearly decodable. In the diffusion module, the two diverge. Secondary structure transfers essentially unchanged, whereas sequence chemistry is strongly attenuated. We then test whether decodable directions can steer the model, intervening on the final trunk single representation that conditions the diffusion module. Helix and coil directions change predicted structure dose-dependently against matched-norm random controls, but a beta-strand direction that is highly predictive (F1 =0.82) produces no measurable increase in strand content: linear decodability does not imply causal influence at the site we tested. The same probes also score markedly lower against sparse SwissProt annotations than against dense DSSP labels, because unannotated residues that the model gets right are charged as false positives; such scores are therefore lower bounds. Finally, supervised probes outscore single SAE features wherever a label already exists. We release the trained trunk and diffusion SAEs, Boltz-1 per-residue activations, and the analysis code.

Understanding both expressed and evoked emotions is critical for multimodal large language models (MLLMs) to achieve comprehensive affect-aware interactions. However, existing benchmarks typically examine expressed and evoked emotions in isolation or are constrained to coarse-grained and incomplete affective characterizations. To bridge this gap, we introduce E$^3$mo-Bench, a scalable benchmark comprising $12{,}314$ question-answer pairs across $2{,}524$ videos with predefined affective perspectives. It evaluates evoked and expressed emotion understanding via $3$ complementary tasks: emotion perception, open-vocabulary recognition, and valence-arousal-dominance (VAD) assessment. To efficiently scale reliable continuous annotations, we propose Bayesian Pairwise Alignment, which aggregates sparse, low-burden pairwise judgments into anchor-referenced VAD estimates. Furthermore, we develop E$^3$mo-Score, a training-free agent that aggregates complementary judgments from a five-model committee to improve VAD estimation. Extensive experiments validate the effectiveness of our framework and expose a pronounced performance skew between evoked and expressed emotion paradigms. These findings, coupled with MLLMs' persistent deficits in fine-grained recognition and dimensional assessment, chart a clear course for advancing multimodal emotional intelligence.

Long speech separation typically employs a segment-separation-stitch paradigm where recordings are divided into short segments, processed independently, and stitched together. Its challenge lies in predicting cross-segment permutations. This paper proposes a training-free dynamic clustering approach for cross-segment permutation alignment using speaker embedding reference pools. The method predicts the permutation using the cosine similarity between current segment embeddings and the reference pools. The approach updates reference pools by retaining the most representative speaker embeddings based on their overall cosine similarity with existing references. As a plug-and-play post-processing module compatible with existing separation models, the proposed method demonstrates superior performance compared to existing methods on dense and sparse long speech scenarios, particularly in challenging sparse scenarios with extended utterance gaps, and further shows robustness to speaker count estimation errors in unknown speaker count scenarios.

Attention mechanisms have been widely utilized in modern deep learning, and many existing multi-omics models inherit their conventional use to allow unrestricted bidirectional interactions. However, the fundamental logic of life is directional. Existing designs often overlook the directionality suggested by the central dogma, potentially limiting transfer across heterogeneous cancers, downstream tasks, and incomplete modality settings. In this work, we present DoGMA, a central-dogma-guided foundation model for pan-cancer multi-omics analysis, arguing that robust transfer requires representations with domain-specific inductive bias. Concretely, we build it on a Transformer-MoE architecture where directed attention biases inter-omics communication toward central-dogma information flow. We further pretrain our model with masked hierarchical omics reconstruction to guide it toward learning central-dogma-consistent interactions. Across diverse downstream tasks, including cancer representation learning, survival prediction, and metastasis prediction, DoGMA consistently demonstrates strong predictive performance. Ablations and analyses further suggest that the performance gains arise from the synergy between central-dogma-guided directed attention and reconstruction-based pretraining, which together promote more biologically consistent cross-omics information exchange. Overall, DoGMA demonstrates that domain-specific inductive biases can improve the robustness and transferability of multi-omics foundation models, offering new insights into the design of attention mechanisms for multi-omics representation learning.

We present string2string Studio, an interactive in-browser platform for string-to-string analysis across natural language processing, computational biology, and the digital humanities. The system integrates six main modules (alignment, distance, similarity, search, generation metrics, and BLAST homology search), operating at character, word, token, line, and residue levels. Its C++-based algorithms compile to WebAssembly, so core operations run locally by default without any installation or data upload. The interface reports scores with their "evidence" (alignments, edit paths, metric matches, search hits, and homology traces), making methods inspectable, debuggable, and comparable on shared inputs. Internal benchmarks show speedups of up to 2,500x over the Python predecessor, faster global/local alignment than a general-purpose native C aligner, and exact agreement with independent references under declared settings. For homology search, the scoped client-side blastn path closely matches NCBI BLAST+ rankings and statistics under matched parameters. A curated showcase and Learn mode present canonical algorithms and metrics as reusable demonstrations. string2string Studio is open-source and freely available at string2string.org.

This study addresses the Variable Gapped Longest Common Subsequence Problem (VGLCSP), a variant of the classical longest common subsequence problem with additional gap constraints and applications in sequence alignment and time-series analysis. While the two-sequence version has been widely studied using dynamic programming, the generalized multi-sequence form is usually solved with beam search-based heuristics, whose hand-crafted designs often lack robustness. To overcome this limitation, we propose a learning-based approach for automatically designing more effective data-driven heuristics. The heuristics are represented by a neural network with predefined architecture, whose weights are optimized by a genetic algorithm within a neuro-evolutionary framework. The learning process alternates between weight optimization and evaluation within an iterative multi-source beam search procedure, a state-of-the-art method for the problem. Rather than constructing solutions directly, the neural network learns to guide the search process, producing a neuro-evolved heuristic. We further introduce an ensemble heuristic that combines the scores of learned and the best-performing hand-crafted heuristic. Integrated into the iterative multi-source beam search framework, the resulting hybrid approach outperforms existing methods on both synthetic benchmark instances and newly introduced real-world instances with data-driven gap constraints.

Language model-based text-to-speech (LM-based TTS) remains vulnerable to speech hallucinations that deviate from the target text. Existing mitigation mainly relies on architectural changes or additional training, while decoding-time control remains underexplored. We present a conditional information view that distinguishes text-derived alignment information from experience information supplied by acoustic context and learned speech regularities. We hypothesize that an important class of hallucinations begins when alignment support is insufficiently reflected in the selected token at a vulnerable transition. Using predictions from the same speech LM with and without text conditions, we propose Experience-Calibrated Contrastive Decoding (ECCD), a training-free method that strengthens alignment support while preserving useful experience information. ECCD preserves the original expert distribution, applies only positive alignment enhancement, and calibrates its strength using set-level experience compatibility. Across four models, ECCD reduces WER/CER by up to 55.6% in all SeedTTS-Eval settings and 24 of 25 multilingual CV3-Eval settings. A listening test yields a CMOS gain of $+0.644$ while retaining strong speaker similarity. Further analysis shows that alignment influence and decision-level gain vary within linguistic units and are lower at first-error boundaries than at matched correct boundaries. Overall, these extensive experiments and analyses identify conditional information control as a promising decoding-time direction for mitigating speech hallucination.

Variational autoencoders (VAEs) trained on multiple sequence alignments (MSAs) have emerged as powerful generative models for biological sequences, with applications ranging from disease variant prediction to functional RNA design. However, standard biological VAE training treats all sequences as exchangeable, ignoring the rich evolutionary structure that organizes homologous sequences from evolutionarily close to highly divergent. We propose Evolutionary Curriculum Learning (ECL), a training strategy that exploits this structure by progressively exposing the model to sequences of increasing evolutionary distance from sampled anchors, following a power-law expansion schedule. Applied to two architecturally distinct VAE models and two biological domains--protein variant effect prediction with EVE and RNA family sequence generation with RfamGen--ECL improves downstream task performance across five random seeds per configuration. Mean ClinVar classification AUROC rises from 0.981 to 0.989 for p53; for PTEN, ECL attains 1.000 in every seed whereas the baseline is unstable (mean 0.905, falling as low as 0.54). For RNA, ECL raises mean covariance-model bit scores on all three families tested and exceeds its seed-matched baseline in 12 of 15 training runs, though with only three families the effect cannot be established as significant at the family level. Ablation experiments show that progressively expanding the sampled sequences by evolutionary distance outperforms fixed-size neighborhood sampling in addition to uniform random sampling. Evolutionary distance is therefore a useful inductive bias for ordering the training curriculum in biological sequence modeling.

Vision-language pretraining learns rich medical image representations from radiology reports, but previous model variants commonly operate within a single shared embedding space, so concept-level structure and interpretability must be recovered post hoc, limiting model transparency and, hence, clinical utility. We introduce RadPRISM, which makes a clinician-defined radiology schema a designated stratification axis: an on-premise large language model extracts per-concept text spans from free-text reports, and each clinical concept is aligned in its own dedicated visual subspace, turning concept stratification into direct, top-level alignment supervision. Instantiated on chest radiographs with a 19-concept schema over $203{,}602$ examinations from an internal multi-year archive, RadPRISM improved internal dataset zero-shot classification from $0.717$ (95% CI, $0.710-0.723$) to $0.868$ (95% CI, $0.863-0.872$) macro AUROC over a matched global-alignment baseline, performed on par with the purpose-built CARZero reference in external zero-shot classification while substantially outperforming it (up to 4.3-fold) in pointing-game visual grounding. In addition, a radiologist reader study demonstrated concept-stratified retrieval ability ($0.78$ macro retrieval correctness rate within rank 3), surfacing disentangled descriptive findings that report-level retrieval and fixed-label vocabularies cannot express. RadPRISM yields discriminative, spatially faithful, natively concept-stratified representations shaped by and transparently inspectable by clinicians.

Deep learning based object detectors require trustworthiness beyond competitive detection performance, but deep neural networks are prone to overconfident predictions, assigning high confidence scores to predictions that are likely to be inaccurate. To improve the alignment between confidence scores and prediction accuracy, existing methods calibrate confidence scores based on box-level localization, such as precision or intersection over union with the ground truth bounding box. However, box-level localization reflects only a measure of agreement between the predicted box and the ground truth, resulting in calibrated confidence scores for box-level accuracy failing to capture the localization accuracy of coordinates of box. To tackle this issue, we propose a novel post-hoc calibration framework, rethinking detection calibration (ReDC), which provides reliable coordinate-level confidence scores, including directional information. The proposed framework defines coordinate-wise alignment and deviation direction between predictions and ground truth. Based on the alignment measure, confidence re-encoding produces reliable coordinate-level confidence scores, while directional displacement estimation predicts coordinate-wise deviation directions. Extensive experiments under in-domain and out-domain scenarios demonstrate that the proposed approach expresses the coordinate-wise localization of detected objects more precisely than existing methods. Furthermore, our method covers the representational scope of prior calibration approaches by aggregating coordinate-level confidence scores into box-level localization.

Multiple Sequence Alignments (MSAs) provide protein language models with explicit evolutionary context, but their large depth makes subsampling unavoidable under limited token budgets. Existing strategies, including random selection, identity-based filtering, and diversity-driven sampling, are effective heuristics, yet provide limited control over the evolutionary signals retained in the subset. In this work, we recast MSA subsampling as an explicit optimization problem, where key evolutionary measures, including query identity and diversity, are treated as controllable objectives. Building on this view, we introduce AP-REASONER, an Affinity-Propagation-based factor-graph approach. With evolution-aware unary factors, exemplar-consistency factors, and two control knobs, AP-REASONER performs factor-graph reasoning through message passing to infer a fixed-budget MSA subset. Experiments on long-range contact prediction and conformational ensemble prediction show that AP-REASONER outperforms baseline subsamplers on structure-sensitive downstream tasks and enables controllable recovery of alternative protein conformations. These results highlight the value of modeling MSA subsampling as a controllable optimization problem, where factor-graph reasoning offers an effective alternative to heuristic selection.

This paper studies the problem of stochastic variance reduction (SVR) for the maximum mean discrepancy (MMD) and correlation alignment (CORAL) loss functions. Although various offline SVR algorithms for these losses have been proposed, these are incompatible with online, distributed, or incremental learning settings. This paper presents Adaptive vaRiance Reduction via Online reWeighting (ARROW), the first online SVR algorithm for the MMD and CORAL for streamed data. The method maintains moving average references of the alignment statistics, and adaptively reweights incoming minibatches so that the minibatch and reference statistics are aligned. Further, we propose a relaxed reweighting scheme so that the ensuing weight-optimisation problem is tractable. In experiments and simulations, we show that ARROW performs competitively with offline algorithms in terms of runtime, degree of variance reduction achieved, and target domain accuracy.

Correlation alignment and the maximum mean discrepancy are two widely used distribution-matching frameworks for unsupervised domain adaptation (UDA). However, high variance in these losses has been shown to undermine their effectiveness in minibatch optimisation settings. Furthermore, the losses lack finite-sum structure, which renders them incompatible with classical stochastic variance reduction (SVR) methods. This paper proposes Paired Sampling for Domain Adaptation (PSDA), a novel SVR technique tailored to such objectives. PSDA pairs observations both within and across domains, to form quadruplets that are always sampled together during training. The pairings are designed to minimise expected gradient variance, and reduce to solving a set of linear assignment problems. Our simulations demonstrate reduced variance compared to related methods, and experiments on three domain shift datasets show improved target domain accuracy.

Visible-infrared (VIS-IR) alignment is a key pre-training task for robust multi-sensor perception. Most existing methods use uniform patch-wise contrastive learning, but this can be unreliable in VIS-IR data because imaging-physics differences make some spatially paired regions inherently less comparable, and aligning them with equal strength hinders representation learning and downstream transfer. In this paper, we revisit VIS-IR pre-training from a sampling perspective and propose Importance-Aware Sampling (IAS), which adjusts training emphasis based on patch reliability. Specifically, IAS (i) derives patch weights from infrared structural cues and uses them to reweight the contrastive objective; (ii) learns a soft importance mask with a lightweight sampler, optionally warm-started from the hand-crafted prior; and (iii) employs a patch curriculum learning strategy that gradually expands from high-reliability regions to harder patches. It is worth noting that IAS is plug-and-play and works with both patch-/correlation-level alignment (e.g., UNIV-style) and image-level contrastive baselines (e.g., ImageBind-style). Extensive experiments on multiple VIS-IR benchmarks demonstrate consistent improvements over strong baselines, including for IR semantic segmentation, IR object detection and VIS semantic segmentation and cross-modal retrieval task. Code will be released on https://github.com/KlayMa527/IAS.

Unified multimodal models (UMMs) aim to integrate visual understanding and generation within a single architecture, but architectural unification alone does not ensure semantic consistency. A model may describe the intended target correctly while generating an inconsistent edit. This exposes an understanding-generation alignment gap: linguistic and visual outputs live in different spaces, yet should be governed by the same target semantics. We study this gap in image editing, where an instruction defines a target state that can be both described and visually realized. Given a source image and an edit instruction, we compare a UMM's target caption with its edited image to test whether the two outputs converge on the same result. Our analysis shows that existing UMMs remain weakly aligned, especially for fine-grained entities, attributes, spatial relations, and local details, indicating that semantic unification is not achieved by architecture alone. To bridge this gap, we propose STBridge, a shared-target alignment framework that connects understanding and generation through a common target state. Here the target caption expresses the desired visual result, while the edited image realizes it visually, replacing separate task-specific paths with a shared information flow from target expression to target realization. STBridge follows an align-then-optimize strategy: supervised fine-tuning first establishes the shared-target channel, and sequential reinforcement learning further refines target-centered coordination. Across visual understanding, image generation, and image editing benchmarks, STBridge consistently improves over the initialization model. Alignment analysis confirms that STBridge narrows the gap between what the model describes and what it generates, demonstrating shared-target alignment as an effective post-training strategy for bridging understanding and generation in UMMs.

AlphaFold2's 93 million parameters, shaped by the evolutionary record of protein structure encoded in the Protein Data Bank and in sequence alignments, are conventionally treated only as machinery for converting sequence to structure. We propose they are also a scientific object that can be analyzed directly: a learned encoding of protein conformational organization that can be probed and characterized. By smoothing the Evoformer's weight tensors with a Gaussian convolution and scaling the result, we show that the trained model produces physically structured conformational landscapes. Under perturbation, ubiquitin's native contacts break in the order established by decades of folding experiments. For KaiB, five independently trained models agree that the alternative fold is not recovered under perturbation. For alpha-synuclein, five models produce five different but coherent landscapes, mapping where the training signal has determined the representation and where it has not. Matched-power noise controls confirm that random corruption of equal magnitude produces debris, not conformations. The model learned to predict static structures; the conformational organization visible under perturbation was not an explicit training target, suggesting it emerged as a byproduct of that objective. AlphaFold2's weights appear to encode structural constraints, shaped by evolutionary and structural training data, that extend beyond what unperturbed inference reveals. We call the approach of reading them neural spectroscopy, and Scaled Gaussian Convolution one such protocol.

Contrastive Language-Image Pre-training (CLIP) has been shown to have limitations in its fine-grained dense feature representation, due to its pre-training focusing on matching the whole image to a text description. Considering the large data and computational burden in pre-training a vision-language model from scratch, a series of works aim to enhance the fine-grained ability of CLIP through a fine-tuning scheme. However, existing works suffer from a variety of limitations: additional region annotations are usually required, which limits the semantic diversity due to the predefined categories and leads to a large effort to process the training data; and they usually sacrifice CLIP's original ability for global visual representation. To bypass these limitations, we propose SFF-CLIP (Self-annotated Fine-grained Fine-tuning for CLIP), which only uses image-text pairs as input to boost the fine-grained representation ability in the CLIP fine-tuning, while maintaining the global visual-semantic consistency. Concretely, a run-time region-phrase alignment scheme is designed, which obtains concept phrases from the input sentence, and aligns them with corresponding extracted region-based features using text-specific heat maps. Extensive experiments demonstrate that SFF-CLIP leads to significant performance improvements on fine-grained dense feature representation, as well as maintaining the performance of the original CLIP on image-level tasks. Code will be released later.

Evolved sequences can be used to infer the rules of evolution. Orally transmitted folk melodies are evolved sequences whose similarity to protein sequences (one-dimensional, drawn from a limited alphabet) invites application of bioinformatics methods to study cultural evolution. A major obstacle is that melodies encode rhythm, which breaks some assumptions of standard sequence-alignment algorithms. We develop a rhythm-aware alignment method and apply it to \num{40000} Irish dance tune variants, enabling the first large-scale automated melodic alignment. Four canonical bioinformatics analyses -- mutability, substitution matrices, positional conservation, and covariance -- reveal patterns distinct from those of molecular evolution, revealing the forces that shape each domain: biochemical and biophysical constraints for proteins; memory, motor, and social biases for melodies. Together the results show that bioinformatics provides a powerful framework -- conceptual as much as algorithmic -- for studying cultural evolution. Although the cultural transmission of music has been discussed for centuries, here we show how to analyze it at large scale.

Decoding brain activity is useful for characterizing brain processes and understanding the functional architecture underlying cognition. However, the inter-individual variability in brain response patterns limits the development of decoders that generalize across individuals. A solution to this challenge is functional alignment: aligning functional data across individuals before training population-level decoders. The core issue is to strike the balance between aligning functional features and preserving the anatomical structure, while maintaining computational efficiency. We introduce a new functional alignment method for fMRI, SpectralOT, that embeds cortical geometry into Laplace-Beltrami eigenmodes along functional data to regularize the alignment.

The lineage graph of open-weight language models is self-reported: Hugging Face's base_model metadata field is optional and unverified, and over 60% of Hub models document no parentage at all. Methods for detecting lineage from weights exist in the research literature, but each ships as paper code tied to one signal and one experiment; when a provenance dispute breaks, the analysis is redone by hand. This report describes modelDNA, a tool that fingerprints a model from roughly 100-300 MB of ranged HTTP reads (instead of a full 15 GB download for a 7B model), compares the fingerprint against a reference database of foundation models across four published signal families, and returns one of eight verdict classes with a calibrated probability, preferring honest abstention to confident error. On a benchmark of 15 real Hub models with org-documented parentage, judged against 8 candidate bases (13 positives, 107 hard negatives), the system achieves AUROC 1.0, zero false positives at its reporting threshold, and 13/13 correct top-1 parent attribution. The report's second contribution is merge decomposition. Every mainstream weight-merging method is (near-)linear per tensor, and fingerprint sample positions are deterministic functions of tensor identity, so a merged model's fingerprint is the same linear combination of its parents' fingerprints. Mixture weights can therefore be recovered from fingerprints alone by sum-to-one constrained least squares. Against merges with published mergekit configurations as ground truth, the method recovers a slerp merge's layer-interpolation curves at r = 0.999 and a dare_ties merge's mixture weights to within 0.011 of the published values, without downloading any weights beyond the fingerprints. All fingerprints, benchmarks, and the inferred lineage graph of 55 models are public and reproducible offline.

Network alignment identifies node correspondences across different networks and is a fundamental primitive in many data science applications, including social network analysis, fraud detection, and knowledge graph integration. However, state-of-the-art network alignment methods often achieve high accuracy by repeatedly constructing and updating dense matrices, sacrificing scalability in the process. To address this scalability limitation without compromising alignment accuracy, we present FastAlign, a scalable, sparsity-aware framework for optimal transport-based network alignment. Rather than introducing a new alignment model, FastAlign preserves the original OT formulation and reinterprets its computation as a set of recurring mixed sparse-dense operations. FastAlign combines sparsity-aware graph computation with domain-specific kernel fusion, including a custom SpMM kernel. Our results show that FastAlign achieves alignment quality comparable to state-of-the-art OT-based methods while substantially reducing end-to-end runtime up to 3.89x-9.45x on CPU and 2.24x-32.54x on GPU.

Recovering high-quality video from sparse event streams is a challenging task. Regression methods often blur textures, while existing generative models struggle with long-term stability. We propose LongE2V, a novel approach that leverages pre-trained video diffusion priors to jointly handle event-based video reconstruction, prediction, and frame interpolation. By fine-tuning a foundational video model, our approach achieves high data efficiency and superior perceptual quality. We introduce Autoregressive Unrolling and Adaptive Context Switching to mitigate temporal drift in extremely long sequences. We also propose Reencoding Alignment with Cross Residual Correction to ensure precise bidirectional consistency during frame interpolation. Furthermore, Event Voxel Density Augmentation ensures robustness across varying sensor resolutions. Extensive experiments on real-world benchmarks demonstrate that LongE2V outperforms state-of-the-art methods across all three tasks, exhibiting exceptional temporal coherence and zero-shot generalization. Project page: https://cdfan0627.github.io/LongE2V-page/

Most cooperative Vision-Language Navigation (VLN) methods assume unlimited communication, not considering real-world applications where bandwidth is restricted and information efficiency is critical. We introduce \textbf{bandwidth-constrained cooperative VLN} and propose \textbf{hindsight gating}: a lightweight supervised gate that labels communication-critical steps post-hoc from navigation failures, avoiding the high variance of REINFORCE. Contrary to the intuition that agents should communicate when uncertain, we observe a consistent counter-intuitive pattern: trained gates fire predominantly in early episode steps and more often when agents are confident, across all budget levels ($B \in \{1,3,5\}$). We explain this through \textbf{recurrent hidden-state alignment}: early communication injects grounded trajectory representations that persist and compound through subsequent Gated Recurrent Unit (GRU) updates, achieving $+0.072$ cumulative alignment gain with $B{=}3$ transmissions, approaching unconstrained communication ($+0.078$) at 260% greater alignment efficiency than random gating ($+0.020$) and 320% greater efficiency than entropy-based gating ($+0.017$). Our results establish a new communication regime for bandwidth-limited embodied agents: synchronise representations early, navigate independently later. Our codebase is available at: https://github.com/AravG13/bandwidth-constrained-cooperative-vln

Referring expression comprehension (REC) aims to localize the object in an image described by natural language. In Weakly supervised REC (WREC), existing approaches primarily operate on anchor-level visual representations. Even when enriched with auxiliary cues, relational interactions remain implicitly encoded within individual anchor features. The resulting visual representation remains flat and unary-only, limiting its ability to align with the structured nature of language. In this work, we propose a Structured Visual Compositional Representation (SVCR) learning framework for WREC. Rather than implicitly encoding relations within unary anchors, the proposed SVCR explicitly models both unary object embeddings and pairwise relational embeddings, forming a structured visual representation space. We further introduce a compositional alignment mechanism that matches unary and pairwise visual representations with their corresponding textual embeddings in a unified manner, enabling compositional visual-textual matching under weak supervision. Extensive experiments on RefCOCO, RefCOCO+, and RefCOCOg show that the proposed SVCR achieves state-of-the-art performance. These results demonstrate the effectiveness of explicit structured visual representations and visual-textual alignment for WREC.

Large language models (LLMs) are increasingly deployed in question answering (QA) systems, yet they may generate hallucinated or misaligned responses without reliable confidence estimates. Uncertainty quantification (UQ) offers a natural basis for selective answering, where a system answers only when its prediction is deemed reliable and abstains otherwise. However, existing uncertainty scores for LLMs are often heuristic: a threshold chosen on such scores does not, by itself, provide statistical guarantees on the error rate among accepted answers. We propose CIC, a confidence-interval-based calibration framework that converts arbitrary uncertainty scores into risk-controlled selective answering rules. Given a held-out calibration set, CIC evaluates each generated response using an application-specific alignment criterion and associates it with an uncertainty score and a binary error label. For each candidate uncertainty threshold, CIC estimates the acceptance-conditioned error rate and constructs a high-probability upper confidence bound using either Hoeffding-style or Clopper-Pearson confidence intervals. It then selects the largest threshold whose upper bound is below a user-specified risk level $α$, thereby maximizing the answering rate subject to a finite-sample reliability constraint. Under exchangeability, CIC guarantees with probability at least $1-δ$ that the selected threshold, if non-null, controls the error rate among accepted answers at level $α$. We evaluate CIC on both closed-ended and open-ended QA benchmarks across seven LLMs and multiple uncertainty estimators. Experimental results show that CIC consistently achieves valid risk control while retaining strong answering efficiency, providing a practical and statistically grounded mechanism for deploying LLMs in reliability-sensitive QA workflows.

Codon harmonization aims to adapt the coding sequences for heterologous expression while preserving the native-like patterns of frequent and rare codons that may influence local translation dynamics and co-translational protein folding. However, widely used harmonization metrics, such as $\%$MinMax, are defined on discrete codon sequences and are, therefore, not readily compatible with gradient-based neural codon design. Here, we introduce Smooth $\%$MinMax, denoted as $\%{\rm MinMax}_{(s)}$, a differentiable relaxation of the conventional hard $\%$MinMax metric, denoted as $\%{\rm MinMax}_{(h)}$. $\%{\rm MinMax}_{(s)}$ replaces the discrete codon-usage values with probability-weighted synonymous-codon usage values and replaces the hard $\%$Max/$\%$Min branch with a sigmoid-gated interpolation. This formulation preserves the signed interpretation of $\%{\rm MinMax}_{(h)}$, while enabling optimization with respect to the synonymous-codon probabilities and learnable parameters. In human-to-Escherichia coli codon harmonization experiments, $\%{\rm MinMax}_{(s)}$ closely approximates $\%{\rm MinMax}_{(h)}$ and supports gradient-based profile matching in synonymous-codon probability space. These results suggest $\%{\rm MinMax}_{(s)}$ as a practical bridge between profile-based codon harmonization and neural synonymous-sequence design.

Fast estimation of the size of the largest overlap between tables enables blocking and query-by-table retrieval in large table repositories. The first and the state-of-the-art estimator Armadillo improves efficiency by embedding each table independently and approximating overlap ratio via embedding similarity. However, accurate estimation in heterogeneous repositories remains limited by three challenges: (C1) overlap depends on row-column structure, i.e., each matched cell must preserve both its row and column membership under a joint alignment of the two tables, but existing encodings leave this structure to be inferred indirectly; (C2) independent encoding provides no explicit channel for inter-table alignment signals, biasing prediction toward global similarity; (C3) naive value encodings overfit to corpus-specific distributions, causing cross-domain degradation. Hence, we propose ALORE, a scalable and domain-robust overlap ratio estimator built on three principles: (P1) explicitly represent row-column structure; (P2) expose inter-table alignment signals during training without expensive alignment search; (P3) reduce sensitivity to corpus-specific value distributions. ALORE instantiates these principles with a Two-View Row-Column Hypergraph encoder, alignment-guided objectives with inexpensive interaction signals, and a domain-robust value mapping. Experiments on multiple datasets spanning diverse domains and scales, including a large real-world corpus beyond prior benchmarks, show that ALORE outperforms the state of the art. ALORE reduces MAE by up to 55% overall and 69% in zero-shot transfer, while achieving up to 89x speedup. We further validate its effectiveness for query-by-table retrieval.

Aligning generative 3D reconstructions with partial monocular observations is a critical but under-explored challenge in computer vision. This task is inherently ill-posed due to severe asymmetries between noisy, sparse monocular inputs and dense generative priors, whose scale ambiguity and geometric hallucinations, combined with the lack of initial overlap, render traditional registration pipelines ineffective. To resolve these issues, we propose a training-free and interpretable geometric alignment framework that grounds generative 3D priors via a 3D similarity transformation (Sim(3)), which can recover accurate metric scale and pose. Specifically, we introduce an explicit scale factor to resolve metric ambiguity and employ a coarse-to-fine alignment strategy, leveraging geometry-aware descriptors for robust initialization and a decoupled closed-form solver for precision refinement. In addition, we introduce a Hallucination Filtering operation to effectively suppress outliers caused by hallucinated geometry. To evaluate alignment performance under these extreme conditions, we introduce GenPMOAlign--Where2Place, a rigorous benchmark specifically designed for Generative-to-Partial Monocular Observational Alignment. Experiments demonstrate that our method achieves stable and accurate registration, substantially outperforming both classical geometric pipelines and state-of-the-art learning-based baselines. Code and the benchmark will be publicly released.

Dynamic Time Warping (DTW) is a cornerstone for time series classification, but its reliance on Euclidean distances fails to capture latent cross-channel correlations in complex multivariate data. We propose a hybrid Quantum Dynamic Time Warping (qDTW) architecture, replacing the classical distance metric with the parameterized geometry of a quantum Hilbert space. Through structural ablation on benchmarks up to $C=8$ spatial dimensions, we establish fundamental topological rules for quantum sequence alignment. We introduce a Unified Pre-Embedding Adjoint Ansatz that decouples trainable entanglement from classical data, eliminating the severe phase-scrambling and information bottlenecks inherent to traditional measurements. We demonstrate this decoupled architecture allows untrained quantum kernels to act as highly expressive baselines, while parameterized training effectively untangles deeply overlapping hyper-dimensional data. Furthermore, we identify a strict spatial-temporal expressivity tradeoff: temporal depth (data re-uploading) is necessary for dimensionally restricted univariate circuits, but applying it to wide multi-qubit registers triggers chaotic frequency-spectrum explosions and representation collapse. By navigating these topological hazards, our multivariate quantum architecture outperforms classical baselines, setting a new standard for integrating parameterized quantum circuits with dynamic programming

Training-free source selection for LLM families with shared vocabularies arises in scientific string domains such as SMILES, protein, and genomic sequences, where candidate corpora share a tokenizer but differ in prediction targets. This creates an activation-dark regime: representation-similarity metrics can be uninformative without assumptions about label-conditioned error geometry, while classical update-geometry metrics are computationally prohibitive at vocabulary scale. We show that, in a shared-output head setting, representation metrics (e.g., CKA) are non-identifiable for transfer; models can share identical representations yet have orthogonal head updates. The key identity is that head Fisher alignment is exactly a cosine between kernel mean embeddings in the joint activation-error space, exposing activation, error, and coupling factors rather than requiring a materialized Fisher matrix. FisherSketch estimates this cosine directly in a single streaming pass, making K=128,256 head Fisher alignment practical with a 16 KB task signature (m=4096) and a 192 KB per-task streaming state, small enough to store next to a model hash, but encoding transfer-relevant update structure. Beyond source selection, the same signatures and marginals provide a diagnostic instrument for studying whether LLM task similarity is driven by activations, errors, or their coupling; shared-parameter and internal-layer validations, together with Llama-3.1-8B verbalizer-shift experiments, show that FisherSketch remains informative when activation similarity cannot distinguish tasks.

The Unigram tokenizer uses an elegant representation which makes it straightforward to edit vocabularies, but its training is comparatively heavy and complex. We introduce MinGram (Minimalist Unigram), which keeps the token-list representation but simplifies training using a BPE-derived seed vocabulary, Hard EM on a minimum-token path, and a single flat score-pruning step. This removes the suffix array, the forward-backward pass, and the iterative prune loop, leaving a procedure that requires little beyond tokenizer inference itself. By making token count the primary objective and using a Unigram score only as a tiebreak, MinGram keeps the compression of pure token-count methods while retaining much of the morphological alignment and downstream quality of probabilistic ones. Across six languages, MinGram compresses better than both BPE and standard Unigram, and a compression-oriented variant matches the strongest token-count compressors while retaining substantially higher morphological alignment. In controlled downstream language-model training, Unigram-family tokenizers, with MinGram among the best, consistently beat BPE in bits-per-byte.

Learning discrete speech representations that preserve similarity across variable-length utterances is central to query-by-example spoken term detection (QbE-STD). While wav2tok introduced CTC-based sequence alignment to enforce token consistency, its tightly coupled clustering and alignment training recipe limits scalability. We propose wav2tok 2.0, a scalable alignment-aware speech tokenizer built on the BEST-STD backbone. wav2tok 2.0 employs staged training, first learning discriminative, speaker-invariant representations via contrastive learning and vector quantization, and then enforcing pairwise token consistency using a CTC alignment loss and a novel DTW-aligned framewise prediction objective with adaptive weighting. Experiments show that wav2tok 2.0 consistently outperforms BEST-STD and general-purpose tokenizers on QbE-STD while remaining efficient and scalable.

Reinforcement learning has improved the reasoning ability of large language models, but applying outcome-only rewards to video multimodal large language models (Video-MLLMs) provides limited guidance on which visual evidence should support the answer. Inspired by multisensory integration, where consistent cues can enhance the salience and reliability of perceptual estimates, we introduce Consensus Frame GRPO (CF-GRPO), a temporal-annotation-free process-level reward framework for evidence-aware video reasoning. CF-GRPO constructs a consensus frame prior from intrinsic video cues, including temporal coverage, scene-transition cues, and query-conditioned visual relevance. It then computes a model-side frame-use score from visual and response representations and optimizes their agreement through the Consensus Frame Reward (CFR). With salience-aware sparse aggregation and distribution sharpening, CFR provides a high-contrast reward signal without requiring human temporal annotations. Experiments show that VideoCFR achieves competitive performance across complex video reasoning benchmarks and improves several metrics over representative Video-MLLM and RL baselines, while the consensus prior provides an interpretable view of the evidence frames emphasized during training. The implementation is available at https://github.com/1Pansy/VideoCFR.

We study the graph alignment problem for correlated Gaussian Orthogonal Ensemble (GOE) matrices, where the goal is to recover a hidden vertex permutation given two correlated symmetric Gaussian matrices $(A, B)$ with correlation $1/\sqrt{1+σ^2}$. While the maximum likelihood estimator is information-theoretically optimal, its computation, which reduces to a quadratic assignment problem, is intractable. Motivated by this, we analyze convex relaxations based on minimizing $\|AX - XB\|_F$ over the set of doubly stochastic matrices and the unit hypercube. We show that when the correlation parameter satisfies $σ= o(n^{-1/2}/\log^4 n)$, the solution of either relaxation $(X^\star)$ concentrates around the ground-truth permutation matrix $(Π^\star)$, i.e., $\|X^\star-Π^\star\|_F^2 = o(n)$, implying recovery of all but a vanishing fraction of vertices after simple post-processing. Combined with existing lower bounds, our results precisely characterize that $\|X^\star-Π^\star\|_F^2$ transitions from $o(n)$ for $σ= \tilde{o}(n^{-1/2})$ to $Ω(n)$ for $σ= \tildeΩ(n^{-1/2})$. In doing so, our analysis significantly tightens prior results and extends them beyond doubly stochastic relaxations.

Typical video object-centric learning (VOCL) approaches employ slot-based frameworks that rely on reconstruction-driven encoder-decoder architectures, where learning is mediated by two spatial maps: attention maps from the encoder and object maps from the decoder. As these two distinct maps exhibit different properties, a recent dense alignment strategy attempted to reconcile this discrepancy by enforcing agreement across all spatio-temporal patches via contrastive learning. However, this indiscriminate alignment inadvertently propagates the inherent weaknesses of each module, such as noisy encoder predictions and blurred decoder boundaries. Moreover, computing dense similarities across all pairs incurs a computational cost quadratic in the total number of spatio-temporal patches, severely limiting scalability. Motivated by this, we propose Selective Synergistic Learning (SSync). Instead of exhaustive patch-to-patch alignment, SSync prevents error propagation by selectively distilling only the most reliable cues: leveraging the encoder strictly for boundary refinement and the decoder for interior denoising. This is realized via a pseudo-labeling with linear complexity, eliminating the need for quadratic spatial comparisons. Also, to prevent the reinforcement of architectural biases like slot redundancy, we introduce a transitive pseudo-label merging that consolidates overlapping slots based on spatio-temporal activation consistency. Extensive studies demonstrate that SSync improves decomposition quality and serves as a versatile, plug-and-play module while also exhibiting exceptional robustness to slot configurations. Code is available at github.com/wjun0830/SSync.

Reward models are a key component of reinforcement learning from human feedback (RLHF), aligning language models toward both helpful and harmless behaviour. However, the internal mechanisms underlying these objectives and their conflicts remain poorly understood. We study alignment tension in reward models trained under helpfulness-only, harmlessness-only, and mixed-objective settings. We find that mixed-objective models often underperform single-objective models, indicating interference between objectives. Using activation-based methods, we identify neurons associated with each objective and study their functional roles via targeted ablations. We find that these neurons causally support their corresponding objectives while often negatively affecting the opposing one. We find that a substantial proportion of neurons are shared between helpfulness and harmlessness, and that these shared neurons exert a disproportionate influence on model behaviour, contributing to alignment tension. Additionally, our results provide insights and mechanistic interpretation into how alignment objectives are represented in reward models and why multi-objective alignment remains challenging, motivating future work on disentangled and controllable alignment methods.

Reward models for text-to-video (T2V) generation guide post-training but often fail at fine-grained semantic alignment. We trace this to two structural weaknesses in existing reasoning-based reward models: they do not systematically verify every condition described in the prompt, and the visual evidence supporting each judgment remains implicit in their free-form reasoning. We propose SG-PVR, a video reward model that addresses these limitations through plan-and-verify reasoning grounded in spatio-temporal scene graphs. The verification plan decomposes the prompt into atomic claims, ensuring every requirement is checked. The spatio-temporal scene graph, encoding entities, attributes, and temporally-grounded relations, is extracted from the video and maintained as a persistent structured visual reference throughout reasoning. Each claim is verified against both the video and the scene graph, anchoring judgments in explicit visual evidence. SG-PVR achieves strong performance on semantic alignment, including fine-grained temporal semantics. As a test-time reranker, it further enhances compositional alignment in T2V generation.

Precise rover localization is a prerequisite for autonomous lunar exploration, yet the absence of Global Navigation Satellite System (GNSS) signals and the cumulative drift of local localization methods severely constrain long-range missions. Cross-view localization provides a promising drift-free global solution by matching rover-view and satellite-view imagery. However, the lunar environment poses unique challenges for correspondence alignment, including inter-entity entanglement, inter-viewpoint divergence, and simulation-to-real domain shift. To address these challenges, we propose Warped Alignment of Reprojected Graphs (WARG), a framework that leverages unified graph learning and reprojected graph matching for robust cross-view alignment. Pretrained on the synthetic LuSNAR dataset, WARG achieves an average test error of 0.32 m and demonstrates robust zero-shot generalization to the synthetic lunar south pole region with an error of 3.63 m. More importantly, when validated on real-world data from the YuTu-2 rover, WARG achieves a localization error of 1.68 m within a 100 m x 100 m search area, corresponding to nearly one-pixel precision in low-resolution satellite imagery with a spatial resolution of 1.40 m/pixel. Beyond accuracy, WARG is computationally efficient, containing only 1.56M parameters, corresponding to 16.12% of previous lightweight models, and operating at 5.49 Hz on an NVIDIA RTX A6000 GPU, approaching GNSS-level update frequency. Finally, we observe that WARG naturally develops low-level spatial awareness, including semantic segmentation and structural reasoning, through cross-view localization learning, highlighting its potential as a promising paradigm for spatial intelligence with minimal annotation cost. The source code is available at https://github.com/maochen-casia/warg.

Multimodal $ΔΔG$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations. Existing approaches address these limitations primarily through additional architectural components, leaving optimization-level intervention comparatively underexplored. We introduce a constraint-aware optimization framework combining Balanced Mean Squared Error, a Siamese anti-symmetric regularizer, and a novel OOD-margin consistency loss on the per-position feature representation, requiring no architectural changes to the SPURS backbone. Across eleven benchmarks and three random seeds, the framework improves Spearman correlation on S669 from 0.486 to 0.540 ($σ=0.002$ across seeds), matching the published SPURS baseline (0.50) without architectural modification, and on S461 from 0.653 to 0.711, with consistent smaller gains on five additional OOD datasets. A controlled diagnostic on Ssym reveals that anti-symmetric training does not eliminate systematic forward-reverse bias, indicating that gains arise through implicit regularization rather than exact thermodynamic constraint enforcement.

Performance estimation under distribution shift aims to predict how a model behaves on an unlabeled test set whose distribution differs from the training data, a scenario that requires reliable indicators that can faithfully reflect model behavior without ground-truth labels. Existing approaches rely solely on the outputs of the given model whose biases are amplified once the distribution shifts, weakening the correlation with the true performance. Motivated by this limitation, we propose Fused Reference Alignment Prediction (FRAP), which leverages the complementary strengths of an external foundation model and the base model to construct a more reliable surrogate of the ground-truth labels. FRAP aligns the prediction distribution of the foundation model with that of the base model by applying temperature-scaled calibration that minimizes their divergence. The aligned predictions are fused through confidence-based weighting into a refined reference distribution that integrates robustness from the foundation model and domain-specific expertise from the base model, and performance estimation is obtained by measuring how closely the base model predictions agree with this reference. Extensive experiments across diverse datasets and architectures show that FRAP provides consistent and substantial improvements over representative performance-estimation methods under distribution shift.

We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines $p$-adic numbers with topological data analysis. Each DNA sequence is encoded along two complementary axes: a $p$-adic distance on $k$-mer prefixes, which captures hierarchical positional structure, and a compositional $L_1$ distance on $k$-mer frequencies, which captures local sequence content. The two distances jointly parameterise a bi-filtered Vietoris--Rips complex, and per-sequence topological summaries from this bi-filtration serve as features for standard machine learning classifiers. We establish theoretical guarantees for the construction: stability under metric perturbations and invariance to the choice of prime, alongside a result that explains why a single $p$-adic axis is topologically uninformative and why the bi-filtration recovers nontrivial homology. On twelve genomic benchmarks ($28$ to $500$ sequences, $3$ to $7$ classes), pVR outperforms four established alignment-free baselines on three of six low-sample datasets, with gains of up to $21$ percentage points; it underperforms only on a SARS-CoV-2 variant benchmark whose point-mutation divergence violates the hierarchical assumption, and all methods saturate in the large-sample regime. pVR also outperforms zero-shot frozen embeddings from the 500M-parameter Nucleotide Transformer v2 by $6.7$ to $11.4$ percentage points on three low-sample benchmarks. The pVR codebase is publicly available at https://github.com/MAHI-Group/pVR.

Quantizing deep neural networks is essential for efficient inference on resource-constrained devices. However, most existing methods are designed for single-domain and class-balanced data, leaving practical settings with domain shifts or severe class imbalance underexplored. We address these challenges with Efficient Multi-Domain Alignment Quantization (EmaQ), which aligns domain distributions through a CDF-based projection and uses sensitivity-aware weight aggregation to stabilize multi-domain quantization. We further extend EmaQ to EmaQ-LT for long-tailed quantization by introducing class-conditioned variance scaling and confidence-based logit adjustment to mitigate majority-class overconfidence. Theoretical analyses establish convergence guarantees and motivate the proposed sensitivity and scaling mechanisms. Experiments on standard, multi-domain (Office-31, Digits), and long-tailed (SynDigits-LT, CIFAR-10-LT, CIFAR-100-LT) benchmarks show that EmaQ and EmaQ-LT achieve strong low-bit performance under domain shift and class imbalance.

The choice between cross-attention and concatenation for multimodal fusion remains governed by practitioner intuition rather than principled understanding. In this paper, we demonstrate that feature alignment quality, not data scale alone, is the primary determinant of which fusion strategy excels. Through controlled experiments on Flickr8k using two feature extraction backbones (ResNet18 and CLIP ViT-B/32), we show that concatenation outperforms cross-attention by 4.1-5.1 percentage points across all tested scales (2048-16384 samples) when features are pre-aligned by a vision-language pretraining objective. We provide a theoretical explanation grounded in sample complexity analysis: concatenation requires O(d_v + d_t) samples to learn its fusion projection, while cross-attention requires O(d_v * d_t) samples to learn bilinear attention weights, over 256 times as many for 512-dimensional CLIP features. When features are already aligned, the approximation error gap between the two methods vanishes, and concatenation's sample efficiency dominates at all practical dataset sizes. An alignment degradation study confirms a monotonic trend: as feature alignment degrades, concatenation's advantage grows from 1.3% to 2.8%. These findings provide a principled decision framework for fusion method selection in multimodal systems, with direct implications for the design of Multimodal Large Language Models.

Adversarial Training (AT) is a leading defense against adversarial examples but often suffers from Catastrophic Overfitting (CO) in efficient single-step variants, where robustness to multi-step attacks collapses despite high single-step performance. We address this failure mode with two contributions. First, we formalize Epsilon Overfitting (EO), a perspective in which fixed perturbation magnitudes and directions exacerbate CO, and show that introducing perturbation variability significantly improves robust generalization across different architectures and datasets. Second, we propose PertAlign (Perturbation Alignment), a theoretically grounded, computationally negligible metric that predicts CO onset by measuring gradient alignment across attack stages. Leveraging these insights, we introduce SORA, an adaptive step-size AT method that dynamically adjusts perturbations based on loss surface geometry. SORA consistently prevents CO, achieves state-of-the-art robustness and clean accuracy, and generalizes across datasets and architectures using a single fixed set of hyperparameters, which is essential for applicability in fast AT. Extensive experiments on diverse datasets and architectures show that SORA matches or surpasses the robustness of prior methods while delivering higher clean accuracy and superior efficiency. Code is available at https://github.com/SecondOrderAT/SORA.

Pairwise preference data is widely used in language-model evaluation and alignment, often for model ranking, reward modeling, or preference optimization. This note formulates a more basic measurement question: given a reference distribution of pairwise preferences, what model-level quantity is estimated when we test whether a model ranks preferred responses above rejected responses? We define pairwise reference alignment as an ordinal observable induced by a model scoring function. Given a reference pair distribution $P_{\mathrm{pair}}$ over triples $(x,y^+,y^-)$, and a scalar model score $S_M(x,y)$, we define the alignment observable as the probability that the model-induced ordering agrees with the reference preference ordering. We further define a centered order-parameter-like statistic and discuss a margin-based extension. The resulting quantities admit simple finite-sample estimators and concentration bounds under independent sampling assumptions. This note does not introduce a new benchmark. It provides a conceptual and statistical formulation for pairwise reference alignment, clarifies the role of the reference pair distribution, and distinguishes the general ordinal observable from scoring choices such as normalized log-probability or energy-based scores. We also provide an initial empirical study on Qwen2.5 models and RewardBench, where the proposed statistics increase with model size and instruction tuning and vary across reference-pair subsets as predicted by the formulation.

Multimodal alignment of histopathology encoders with transcriptomic and genomic data has been shown to significantly improve performance in downstream diagnostic tasks. Hematological cytology is unique in that visual single-cell evaluation is often paired with cytogenetics and molecular genetics for blood cancer diagnosis. In this study, we present a framework to align single white blood cell images with chromosomal aberrations (karyotype) and somatic mutations from targeted gene panels. Our training strategy follows a two-stage approach: (i) self-supervised, vision-only pretraining of a transformer aggregator using an iBOT head on a cohort of over 1500 patients, and (ii) genetic alignment via supervised contrastive loss on acute myeloid leukemia patients. Our genetically aligned patient encoder improves hematological diagnostic tasks, outperforming slide-level histopathology foundation models. Additionally, the model provides off-the-shelf retrieval capabilities for diseases and genetic alterations. Incorporating genetic data into patient encoders increases the quality of patient representations, providing a framework that aligns with clinical diagnostic workflows and paves the way for future multimodal hematology-specific AI. The code and model weights are available at https://github.com/marrlab/GenBloom.

In the context of resource-constrained environments such as embedded systems, adapting reduced-size foundation models to downstream tasks has become increasingly popular. This has recently motivated the emerging setting of task-specific distillation, where a larger and a smaller version of the same foundation model are both adapted to the same downstream task, with the goal of transferring knowledge from the former to the latter. Recent work has demonstrated the benefits of using a larger version of the same foundation model to assist the adaptation of a smaller one. Typically, the larger model (teacher) is first adapted via fine-tuning or linear probing before its knowledge is distilled into the smaller model (student). While fine-tuning the teacher often increases its performance, recent work showed that probing it leads to better knowledge distillation to the student. Our findings show that this is mainly due to a mis-alignment in feature representation between the teacher and the student which occurs during the teacher's fine-tuning. Inspired by existing efforts to preserve previously learned knowledge, we first propose leveraging low-rank adaptation, resulting in better feature alignment and therefore better knowledge transfer. Drawing from this insight, we further enhance the feature alignment through a parameter-sharing strategy of the adapters between the two encoders during joint training. Our proposed method, SLAD, shows better feature alignment between the teacher and student, which results in increased performance for not only the student but also the teacher model, while being 2x faster to train than fine-tuning. Through extensive experiments on multiple classification and segmentation datasets, we demonstrate the improved accuracy and transfer efficiency of our method, achieving state-of-the-art performance in the task-specific distillation framework.

Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose sensitivity. Protein language models provide context-aware representations that could improve alignment sensitivity in this regime. However, prior protein embedding-based retrieval pipelines often pool these representations into a single vector, potentially obscuring local motifs, domains, or conserved residues that reveal remote homology. We introduce ProtoCol, a model which represents proteins as sets of residue embeddings and uses ColBERT-style late interaction to test whether residue-level comparison improves homolog retrieval. ProtoCol encodes proteins independently, keeps candidate representations pre-computable, and scores candidates with MaxSim over residue embeddings. On SCOPe superfamily and Pfam clan benchmarks, ProtoCol outperforms sequence-composition, alignment-based, pooled PLM, and trained single-vector baselines, supporting late interaction as an effective retrieval layer for remote homology search.

In recent years, thanks to advances in automatic music transcription (AMT), several large-scale datasets of automatically transcribed piano solo music have been released. While these datasets undoubtedly offer extensive material for performance studies, they vary substantially in quality. In the case of classical music, performances often differ not only in expressive aspects such as tempo, but also in their structural interpretation of the score (including repeat patterns and edition-specific variants). To meaningfully use large-scale transcribed datasets for performance research, transcriptions of the same piece must be grouped according to their underlying structural realisation to support valid comparison. We address this by applying sequence-to-sequence alignment followed by hierarchical clustering: we create pairwise alignments for all pairs of transcriptions of a given piece, and use the alignment cost and (dis)similarity of performed sequence lengths to resolve structural mismatches as features for grouping. We propose this approach as a first step towards automatically evaluating large-scale transcribed datasets that lack ground-truth score and/or audio, shifting the evaluation criterion from truth-based accuracy to musical coherence and plausibility. We demonstrate our score-agnostic approach on around 1,500 transcriptions of 88 compositions from a recently published large-scale transcribed piano performance dataset.