New approach speeds up DNA sequence alignment.
problem Efficiently estimating alignment scores for large sets of reads.
method Rank-one crowdsourcing models and multi-armed bandit algorithm.
result Adaptive algorithm identifies pairs with large alignment scores.
Pairwise discriminators stabilize adversarial training by ensuring the generator's alignment is preserved.
problem Stability issues in adversarial training when using sub-optimal discriminators.
method Introducing a family of objectives using pairwise discriminators, ensuring the generator's alignment is preserved.
result Only the generator needs to converge, and the alignment is preserved with any discriminator.
A Markov Chain approach for aligning generative models from pairwise human preferences.
problem Aligning generative models from pairwise human preferences.
method Markov Chain from Human Feedback (MCHF)
result MCHF converges geometrically fast to the stationary distribution.
Pairwise ranking aligns subjective clinical evaluations with objective indicators.
problem Aligning subjective clinical evaluations with objective indicators for improved diagnosis.
method Pairwise ranking methods to align subjective evaluations with objective indicators.
result The resulting score improves classification accuracy and provides a nuanced severity assessment.
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples may bring in additional robustness to noise or local non-causal perturbations. Thi…
RCPO uses ranked choice modeling for better LLM alignment.
problem Pairwise preference optimization limits LLM alignment.
method Unified framework combining preference optimization and ranked choice modeling.
result RCPO outperforms competitive baselines in LLM alignment.
The paper explores game-theoretic alignment of LLMs with human preferences, finding limitations and conditions.
problem Aligning LLMs with human preferences using game theory.
method Systematic study of payoff choices in a two-player zero-sum game for desirable alignment properties.
result Impossibility of preference matching in game-theoretic LLM alignment under standard assumptions.
A new method reduces preference distortion in LLM alignment.
problem Vulnerability of traditional LLM alignment methods to human preference heterogeneity.
method Sign Estimator: A simple, provably consistent, and efficient estimator using binary classification loss.
result Substantially reduces preference distortion over a panel of simulated personas.
Develops a statistical framework to measure uncertainty in model rankings based on human preferences.
problem Uncertainty in model rankings based on human preferences due to mismatch between human and model preferences.
method Statistical framework using pairwise comparisons by humans and models to provide rank-sets for each model.
result Rank-sets constructed using only pairwise comparisons by strong models often do not cover the true ranking of human preferences.
RLHF performs well despite violating social choice theory axioms.
problem RLHF's empirical success contradicts social choice theory axioms.
method Showed RLHF satisfies pairwise majority and Condorcet consistency under mild assumptions, and introduced new alignment criteria.
result RLHF satisfies pairwise majority and Condorcet consistency under mild assumptions, explaining its practical success.
Unified framework for aligning LLMs from human feedback.
problem Lack of strong theoretical justification for RLHF and inability to compare methods.
method Reframed alignment as distribution learning from pairwise preferences, proposing three principled objectives.
result Proposed objectives achieve strong non-asymptotic convergence to target LM.
A new method estimates protein evolutionary fields and couplings from alignments.
problem Estimating evolutionary fields and couplings from protein sequence alignments.
method Boltzmann machine with parallel, persistent Markov chain Monte Carlo method.
result Improved precision in predicting contact residue pairs.
The alignment of a set of objects by means of transformations plays an important role in computer vision. Whilst the case for only two objects can be solved globally, when multiple objects are considered usually iterative methods are used. In practice the iterative methods perform well if the relative transformations b…
Paper introduces MSA for weakly supervised covariance alignment in MEG signals.
problem Limited labeled signals in target datasets for MEG applications.
method Mixing model Stiefel Adaptation (MSA) leveraging unlabeled data.
result MSA outperforms recent methods in brain-age regression with MEG signals.
Interpretable semantic textual similarity (iSTS) task adds a crucial explanatory layer to pairwise sentence similarity. We address various components of this task: chunk level semantic alignment along with assignment of similarity type and score for aligned chunks with a novel system presented in this paper. We propose…
The paper improves alignment methods for deep neural networks using geometric and spectral analysis.
problem Improving alignment methods for deep neural networks.
method Geometric and spectral analysis of residual Jacobian chains.
result Deterministic and margin-verified results on the transport of dominant singular subspaces across layers.
A new slicing method reduces computational cost for cross-domain alignment.
problem High computational cost in solving Gromov-Wasserstein distance.
method Relation-Aware Projecting Direction (RAPD) and Relation-Aware Slicing Distribution (RASD).
result RASGW distance reduces computational cost and improves alignment accuracy.
Pair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have used one or two hidden states for each PHMM state type. However, few studies …
We show that the classification performance of graph convolutional networks (GCNs) is related to the alignment between features, graph, and ground truth, which we quantify using a subspace alignment measure (SAM) corresponding to the Frobenius norm of the matrix of pairwise chordal distances between three subspaces ass…
Representational similarity analysis (RSA) has been shown to be an effective framework to characterize brain-activity profiles and deep neural network activations as representational geometry by computing the pairwise distances of the response patterns as a representational dissimilarity matrix (RDM). However, how to p…
AOT aligns LLMs on distributional preferences via optimal transport.
problem Current LLM alignment techniques lack distributional level alignment.
method Alignment via Optimal Transport (AOT) aligns LLMs on unpaired preference data.
result AOT enables alignment by penalizing reward distribution violations.
A new method for aligning datasets without known correspondences.
problem Aligning datasets from different domains without labeled correspondences.
method Integrates MDS and Wasserstein Procrustes for joint optimization of embeddings and correspondences.
result Maps datasets to a common low-dimensional space without labeled correspondences.
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons …
We study unsupervised multilingual alignment, the problem of finding word-to-word translations between multiple languages without using any parallel data. One popular strategy is to reduce multilingual alignment to the much simplified bilingual setting, by picking one of the input languages as the pivot language that w…
Unified framework for higher-order network analysis.
problem Complex structure of space of networks.
method Measure-theoretic formalism, Gromov-Wasserstein distance, co-optimal transport distance.
result Unified theoretical treatment of generalized networks.
SARA uses similarity to learn rewards robustly and adaptively.
problem Robustness to labeler errors and adaptability to diverse feedback formats.
method Contrastive framework that learns latent representations and computes rewards as similarities.
result Strong performance on offline RL benchmarks and diverse applications.
New Gromov-Wasserstein metric controls rigidity and incorporates prior knowledge.
problem Inflexible Gromov-Wasserstein distance and lack of feature alignment.
method Augmented Gromov-Wasserstein distance with feature alignments and prior knowledge.
result Improved performance in single-cell multi-omic alignment and transfer learning.
We address the problem of image translation between domains or modalities for which no direct paired data is available (i.e. zero-pair translation). We propose mix and match networks, based on multiple encoders and decoders aligned in such a way that other encoder-decoder pairs can be composed at test time to perform u…
Constraint-based clustering algorithms exploit background knowledge to construct clusterings that are aligned with the interests of a particular user. This background knowledge is often obtained by allowing the clustering system to pose pairwise queries to the user: should these two elements be in the same cluster or n…
Foot-mounted inertial positioning (FMIP) can face problems of inertial drifts and unknown initial states in real applications, which renders the estimated trajectories inaccurate and not obtained in a well defined coordinate system for matching trajectories of different users. In this paper, an approach adopting receiv…
Paper investigates monotonicity issues in AI preference learning.
problem AI models may violate monotonicity when learning preferences.
method Investigates root causes of non-monotonicity in comparison-based preference learning.
result Proves local pairwise monotonicity under mild assumptions.
Various applications involve assigning discrete label values to a collection of objects based on some pairwise noisy data. Due to the discrete---and hence nonconvex---structure of the problem, computing the optimal assignment (e.g.~maximum likelihood assignment) becomes intractable at first sight. This paper makes prog…
This study explores how feature graphs enhance GNNs' performance in modeling interactions.
problem Improving GNNs' ability to model feature interactions effectively.
method Investigates feature graphs and their importance in GNNs, using experiments and theoretical support.
result Edges between interacting features are crucial for GNNs, while non-interaction edges can degrade performance.
Bispectral OT improves dataset comparison by preserving intrinsic coherence.
problem Ignoring intrinsic coherence in dataset comparisons using pairwise geometric distances.
method Introduces Bispectral Optimal Transport, a symmetry-aware extension of discrete OT.
result Transport plans computed with Bispectral OT achieve greater class preservation accuracy.
Unified framework for SSL methods linking contrastive and non-contrastive approaches.
problem Lack of theoretical foundations and design guidelines for SSL methods.
method Spectral manifold learning framework to unify SSL methods.
result Theoretical bridge between contrastive and non-contrastive methods.
Dynamic time warping (DTW) can be used to compute the similarity between two sequences of generally differing length. We propose a modification to DTW that performs individual and independent pairwise alignment of feature trajectories. The modified technique, termed feature trajectory dynamic time warping (FTDTW), is a…
Geometric stability predicts steerability and detects drift in language models.
problem Predicting steerability and detecting drift in language models.
method Supervised and unsupervised geometric stability measures.
result Supervised geometric stability predicts steerability with high accuracy and detects drift earlier.
iREPA shows spatial structure, not global semantic, drives generation performance in REPA.
problem Understanding what aspect of the target representation matters for generation.
method Empirical analysis of 27 vision encoders, two modifications to REPA.
result Spatial structure, not global semantic, drives generation performance.
RLHF uses human feedback to train AI models, posing statistical challenges.
problem Aligning AI models with human preferences using noisy, subjective feedback.
method Supervised fine-tuning, reward modeling, policy optimization, statistical ideas.
result Statistical methods for reward function learning and policy optimization.
New system constructs cell-type taxonomy across multiple samples.
problem Challenges in matching clusters from different datasets.
method Combines Optimal Transport with Relaxed Marginal Constraints (OT-RMC) for simultaneous alignment of clusters across multiple samples.
result Highly accurate annotation of cell types and sample-level feature extraction.
New method improves consistency in preference learning for neural networks.
problem Inconsistent surrogate losses in preference learning for neural networks.
method Formulated a margin-shifted ranking framework and introduced Structure-Aware H-consistency. result Proved superior consistency guarantees for capacity-bounded models using heavy-tailed surrogates.
A new method embeds distributions in a common space for optimal transport comparison.
problem Comparing distributions in different metric spaces.
method Sub-embedding robust Wasserstein (SERW) distance.
result SERW mimics GW distance properties and provides a cost relation.
Paper solves robust multi-dimensional scaling with accelerated projections.
problem Localize point locations from noisy pairwise distances.
method Alternating projections with tangent space acceleration.
result Linear convergence of reconstructed points to original points.
Proposes supervised method for whole DAG causal structure learning.
problem Learning causal directions from data, especially for whole DAG structure.
method Supervised learning approach using permutation equivariant models.
result Promising results compared to previous approaches on synthetic and real data.
Parametric spatial transformation models have been successfully applied to image registration tasks. In such models, the transformation of interest is parameterized by a fixed set of basis functions as for example B-splines. Each basis function is located on a fixed regular grid position among the image domain, because…
The paper addresses calibration in label ranking, a structured prediction task.
problem Calibration in label ranking is not well understood and often poorly calibrated.
method Formalized calibration for label ranking, developed a hierarchy of notions, and empirically evaluated models.
result Popular label ranking models are often poorly calibrated, with differences between sub-ranking and top-k metrics.
A new method for analyzing latent space models without reference configurations.
problem Posterior summaries of latent coordinates in Euclidean latent space models are not canonical due to likelihood invariance.
method Quotient-based posterior analysis using the centered Gram map.
result Intrinsic posterior summaries of mean structure and uncertainty can be computed directly from posterior samples.
Global pairwise network alignment (GPNA) aims to find a one-to-one node mapping between two networks that identifies conserved network regions. GPNA algorithms optimize node conservation (NC) and edge conservation (EC). NC quantifies topological similarity between nodes. Graphlet-based degree vectors (GDVs) are a state…