Daily Papers

Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous approaches leverage techniques such as flow or Schrödinger bridge matching to implicitly learn joint trajectories through data snapshots. However, many systems, including biomolecular systems and heterogeneous cell populations, undergo dynamic interactions that evolve over their trajectory and cannot be captured through static snapshots. To close this gap, we introduce Entangled Schrödinger Bridge Matching (EntangledSBM), a framework that learns the first- and second-order stochastic dynamics of interacting, multi-particle systems where the direction and magnitude of each particle's path depend dynamically on the paths of the other particles. We define the Entangled Schrödinger Bridge (EntangledSB) problem as solving a coupled system of bias forces that entangle particle velocities. We show that our framework accurately simulates heterogeneous cell populations under perturbations and rare transitions in high-dimensional biomolecular systems.

A comprehensive understanding of animal behavior ecology depends on scalable approaches to quantify and interpret complex, multidimensional behavioral patterns. Traditional field observations are often limited in scope, time-consuming, and labor-intensive, hindering the assessment of behavioral responses across landscapes. To address this, we present kabr-tools (Kenyan Animal Behavior Recognition Tools), an open-source package for automated multi-species behavioral monitoring. This framework integrates drone-based video with machine learning systems to extract behavioral, social, and spatial metrics from wildlife footage. Our pipeline leverages object detection, tracking, and behavioral classification systems to generate key metrics, including time budgets, behavioral transitions, social interactions, habitat associations, and group composition dynamics. Compared to ground-based methods, drone-based observations significantly improved behavioral granularity, reducing visibility loss by 15% and capturing more transitions with higher accuracy and continuity. We validate kabr-tools through three case studies, analyzing 969 behavioral sequences, surpassing the capacity of traditional methods for data capture and annotation. We found that, like Plains zebras, vigilance in Grevy's zebras decreases with herd size, but, unlike Plains zebras, habitat has a negligible impact. Plains and Grevy's zebras exhibit strong behavioral inertia, with rare transitions to alert behaviors and observed spatial segregation between Grevy's zebras, Plains zebras, and giraffes in mixed-species herds. By enabling automated behavioral monitoring at scale, kabr-tools offers a powerful tool for ecosystem-wide studies, advancing conservation, biodiversity research, and ecological monitoring.

HeH^+ was the first heteronuclear molecule to form in the metal-free Universe after the Big Bang. The molecule gained significant attention following its first circumstellar detection in the young and dense planetary nebula NGC 7027. We target some hydride ions associated with the noble gases (HeH^+, ArH^+, and NeH^+) to investigate their formation in harsh environments like the nova outburst region. We use a photoionization modeling (based on previously published best-fit physical parameters) of the moderately fast ONe type nova, QU Vulpeculae 1984, and the CO type novae, RS Ophiuchi and V1716 Scorpii. Our steady-state modeling reveals a convincing amount of HeH^+, especially in the dense clump of RS Ophiuchi and V1716 Scorpii. The calculated upper limit on the surface brightness of HeH^+ transitions suggests that the James Webb Space Telescope (JWST) could detect some of them, particularly in sources like RS Ophiuchi and V1716 Scorpii, which have similar physical and chemical conditions and evolution. It must be clearly noted that the sources studied are used as templates, and not as targets for observations. The detection of these lines could be useful for determining the physical conditions in similar types of systems and for validating our predictions based on new electron-impact ro-vibrational collisional data at temperatures of up to 20,000 K.

Training classifiers is difficult with severe class imbalance, but many rare events are the culmination of a sequence with much more common intermediate outcomes. For example, in online marketing a user first sees an ad, then may click on it, and finally may make a purchase; estimating the probability of purchases is difficult because of their rarity. We show both theoretically and through data experiments that the more abundant data in earlier steps may be leveraged to improve estimation of probabilities of rare events. We present PRESTO, a relaxation of the proportional odds model for ordinal regression. Instead of estimating weights for one separating hyperplane that is shifted by separate intercepts for each of the estimated Bayes decision boundaries between adjacent pairs of categorical responses, we estimate separate weights for each of these transitions. We impose an L1 penalty on the differences between weights for the same feature in adjacent weight vectors in order to shrink towards the proportional odds model. We prove that PRESTO consistently estimates the decision boundary weights under a sparsity assumption. Synthetic and real data experiments show that our method can estimate rare probabilities in this setting better than both logistic regression on the rare category, which fails to borrow strength from more abundant categories, and the proportional odds model, which is too inflexible.

Semi-supervised learning (SSL) tackles the label missing problem by enabling the effective usage of unlabeled data. While existing SSL methods focus on the traditional setting, a practical and challenging scenario called label Missing Not At Random (MNAR) is usually ignored. In MNAR, the labeled and unlabeled data fall into different class distributions resulting in biased label imputation, which deteriorates the performance of SSL models. In this work, class transition tracking based Pseudo-Rectifying Guidance (PRG) is devised for MNAR. We explore the class-level guidance information obtained by the Markov random walk, which is modeled on a dynamically created graph built over the class tracking matrix. PRG unifies the historical information of class distribution and class transitions caused by the pseudo-rectifying procedure to maintain the model's unbiased enthusiasm towards assigning pseudo-labels to all classes, so as the quality of pseudo-labels on both popular classes and rare classes in MNAR could be improved. Finally, we show the superior performance of PRG across a variety of MNAR scenarios, outperforming the latest SSL approaches combining bias removal solutions by a large margin. Code and model weights are available at https://github.com/NJUyued/PRG4SSL-MNAR.

In molecular dynamics (MD) simulations, rare events, such as protein folding, are typically studied by means of enhanced sampling techniques, most of which rely on the definition of a collective variable (CV) along which the acceleration occurs. Obtaining an expressive CV is crucial, but often hindered by the lack of information about the particular event, e.g., the transition from unfolded to folded conformation. We propose a simulation-free data augmentation strategy using physics-inspired metrics to generate geodesic interpolations resembling protein folding transitions, thereby improving sampling efficiency without true transition state samples. Leveraging interpolation progress parameters, we introduce a regression-based learning scheme for CV models, which outperforms classifier-based methods when transition state data is limited and noisy

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential to identify early warning signals that would allow researchers and managers to predict such events before they happen has therefore been an invaluable discovery that offers a way forward in spite of such seemingly unpredictable behavior. Research into early warning signals has demonstrated that it is possible to define and detect such early warning signals in advance of a transition in certain contexts. Here we describe the pattern emerging as research continues to explore just how far we can generalize these results. A core of examples emerges that shares three properties: the phenomenon of rapid regime shifts, a pattern of 'critical slowing down' that can be used to detect the approaching shift, and a mechanism of bifurcation driving the sudden change. As research has expanded beyond these core examples, it is becoming clear that not all systems that show regime shifts exhibit critical slowing down, or vice versa. Even when systems exhibit critical slowing down, statistical detection is a challenge. We review the literature that explores these edge cases and highlight the need for (a) new early warning behaviors that can be used in cases where rapid shifts do not exhibit critical slowing down, (b) the development of methods to identify which behavior might be an appropriate signal when encountering a novel system; bearing in mind that a positive indication for some systems is a negative indication in others, and (c) statistical methods that can distinguish between signatures of early warning behaviors and noise.

A fundamental dilemma in generative modeling persists: iterative diffusion models achieve outstanding fidelity, but at a significant computational cost, while efficient few-step alternatives are constrained by a hard quality ceiling. This conflict between generation steps and output quality arises from restrictive training objectives that focus exclusively on either infinitesimal dynamics (PF-ODEs) or direct endpoint prediction. We address this challenge by introducing an exact, continuous-time dynamics equation that analytically defines state transitions across any finite time interval. This leads to a novel generative paradigm, Transition Models (TiM), which adapt to arbitrary-step transitions, seamlessly traversing the generative trajectory from single leaps to fine-grained refinement with more steps. Despite having only 865M parameters, TiM achieves state-of-the-art performance, surpassing leading models such as SD3.5 (8B parameters) and FLUX.1 (12B parameters) across all evaluated step counts. Importantly, unlike previous few-step generators, TiM demonstrates monotonic quality improvement as the sampling budget increases. Additionally, when employing our native-resolution strategy, TiM delivers exceptional fidelity at resolutions up to 4096x4096.

We investigate whether in-context examples, widely used in decoder-only language models (LLMs), can improve embedding model performance in retrieval tasks. Unlike in LLMs, naively prepending in-context examples (query-document pairs) to the target query at inference time does not work out of the box. We introduce a simple approach to enable retrievers to use in-context examples. Our approach, RARe, finetunes a pre-trained model with in-context examples whose query is semantically similar to the target query. This can be applied to adapt various base architectures (i.e., decoder-only language models, retriever models) and consistently achieves performance gains of up to +2.72% nDCG across various open-domain retrieval datasets (BeIR, RAR-b). In particular, we find RARe exhibits stronger out-of-domain generalization compared to models using queries without in-context examples, similar to what is seen for in-context learning in LLMs. We further provide analysis on the design choices of in-context example augmentation and lay the foundation for future work in this space.

Direct speech translation (ST) models often struggle with rare words. Incorrect translation of these words can have severe consequences, impacting translation quality and user trust. While rare word translation is inherently challenging for neural models due to sparse learning signals, real-world scenarios often allow access to translations of past recordings on similar topics. To leverage these valuable resources, we propose a retrieval-and-demonstration approach to enhance rare word translation accuracy in direct ST models. First, we adapt existing ST models to incorporate retrieved examples for rare word translation, which allows the model to benefit from prepended examples, similar to in-context learning. We then develop a cross-modal (speech-to-speech, speech-to-text, text-to-text) retriever to locate suitable examples. We demonstrate that standard ST models can be effectively adapted to leverage examples for rare word translation, improving rare word translation accuracy over the baseline by 17.6% with gold examples and 8.5% with retrieved examples. Moreover, our speech-to-speech retrieval approach outperforms other modalities and exhibits higher robustness to unseen speakers. Our code is publicly available (https://github.com/SiqiLii/Retrieve-and-Demonstration-ST).

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls, or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model based approach in order to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favorable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different data sets, and suggest that uncertainty quantification become a more central part of early warning predictions.

Deep generative models are proficient in generating realistic data but struggle with producing rare samples in low density regions due to their scarcity of training datasets and the mode collapse problem. While recent methods aim to improve the fidelity of generated samples, they often reduce diversity and coverage by ignoring rare and novel samples. This study proposes a novel approach for generating diverse rare samples from high-resolution image datasets with pretrained GANs. Our method employs gradient-based optimization of latent vectors within a multi-objective framework and utilizes normalizing flows for density estimation on the feature space. This enables the generation of diverse rare images, with controllable parameters for rarity, diversity, and similarity to a reference image. We demonstrate the effectiveness of our approach both qualitatively and quantitatively across various datasets and GANs without retraining or fine-tuning the pretrained GANs.

Transition videos play a crucial role in media production, enhancing the flow and coherence of visual narratives. Traditional methods like morphing often lack artistic appeal and require specialized skills, limiting their effectiveness. Recent advances in diffusion model-based video generation offer new possibilities for creating transitions but face challenges such as poor inter-frame relationship modeling and abrupt content changes. We propose a novel training-free Transition Video Generation (TVG) approach using video-level diffusion models that addresses these limitations without additional training. Our method leverages Gaussian Process Regression (GPR) to model latent representations, ensuring smooth and dynamic transitions between frames. Additionally, we introduce interpolation-based conditional controls and a Frequency-aware Bidirectional Fusion (FBiF) architecture to enhance temporal control and transition reliability. Evaluations of benchmark datasets and custom image pairs demonstrate the effectiveness of our approach in generating high-quality smooth transition videos. The code are provided in https://sobeymil.github.io/tvg.com.

Smaller-scale Vision-Langauge Models (VLMs) often claim to perform on par with larger models in general-domain visual grounding and question-answering benchmarks while offering advantages in computational efficiency and storage. However, their ability to handle rare objects, which fall into the long tail of data distributions, is less understood. To rigorously evaluate this aspect, we introduce the "Uncontextualized Uncommon Objects" (UOUO) benchmark. This benchmark focuses on systematically testing VLMs with both large and small parameter counts on rare and specialized objects. Our comprehensive analysis reveals that while smaller VLMs maintain competitive performance on common datasets, they significantly underperform on tasks involving uncommon objects. We also propose an advanced, scalable pipeline for data collection and cleaning, ensuring the UOUO benchmark provides high-quality, challenging instances. These findings highlight the need to consider long-tail distributions when assessing the true capabilities of VLMs.

Recently video generation has achieved substantial progress with realistic results. Nevertheless, existing AI-generated videos are usually very short clips ("shot-level") depicting a single scene. To deliver a coherent long video ("story-level"), it is desirable to have creative transition and prediction effects across different clips. This paper presents a short-to-long video diffusion model, SEINE, that focuses on generative transition and prediction. The goal is to generate high-quality long videos with smooth and creative transitions between scenes and varying lengths of shot-level videos. Specifically, we propose a random-mask video diffusion model to automatically generate transitions based on textual descriptions. By providing the images of different scenes as inputs, combined with text-based control, our model generates transition videos that ensure coherence and visual quality. Furthermore, the model can be readily extended to various tasks such as image-to-video animation and autoregressive video prediction. To conduct a comprehensive evaluation of this new generative task, we propose three assessing criteria for smooth and creative transition: temporal consistency, semantic similarity, and video-text semantic alignment. Extensive experiments validate the effectiveness of our approach over existing methods for generative transition and prediction, enabling the creation of story-level long videos. Project page: https://vchitect.github.io/SEINE-project/ .

We study the problem of detecting the correlation between two Gaussian databases XinR^{ntimes d} and Y^{ntimes d}, each composed of n users with d features. This problem is relevant in the analysis of social media, computational biology, etc. We formulate this as a hypothesis testing problem: under the null hypothesis, these two databases are statistically independent. Under the alternative, however, there exists an unknown permutation sigma over the set of n users (or, row permutation), such that X is rho-correlated with Y^sigma, a permuted version of Y. We determine sharp thresholds at which optimal testing exhibits a phase transition, depending on the asymptotic regime of n and d. Specifically, we prove that if rho^2dto0, as dtoinfty, then weak detection (performing slightly better than random guessing) is statistically impossible, irrespectively of the value of n. This compliments the performance of a simple test that thresholds the sum all entries of X^TY. Furthermore, when d is fixed, we prove that strong detection (vanishing error probability) is impossible for any rho<rho^star, where rho^star is an explicit function of d, while weak detection is again impossible as long as rho^2dto0. These results close significant gaps in current recent related studies.

Leveraging text, images, structure maps, or motion trajectories as conditional guidance, diffusion models have achieved great success in automated and high-quality video generation. However, generating smooth and rational transition videos given the first and last video frames as well as descriptive text prompts is far underexplored. We present VTG, a Versatile Transition video Generation framework that can generate smooth, high-fidelity, and semantically coherent video transitions. VTG introduces interpolation-based initialization that helps preserve object identity and handle abrupt content changes effectively. In addition, it incorporates dual-directional motion fine-tuning and representation alignment regularization to mitigate the limitations of pre-trained image-to-video diffusion models in motion smoothness and generation fidelity, respectively. To evaluate VTG and facilitate future studies on unified transition generation, we collected TransitBench, a comprehensive benchmark for transition generation covering two representative transition tasks: concept blending and scene transition. Extensive experiments show that VTG achieves superior transition performance consistently across all four tasks.

While transformer-based systems have enabled greater accuracies with fewer training examples, data acquisition obstacles still persist for rare-class tasks -- when the class label is very infrequent (e.g. < 5% of samples). Active learning has in general been proposed to alleviate such challenges, but choice of selection strategy, the criteria by which rare-class examples are chosen, has not been systematically evaluated. Further, transformers enable iterative transfer-learning approaches. We propose and investigate transfer- and active learning solutions to the rare class problem of dissonance detection through utilizing models trained on closely related tasks and the evaluation of acquisition strategies, including a proposed probability-of-rare-class (PRC) approach. We perform these experiments for a specific rare class problem: collecting language samples of cognitive dissonance from social media. We find that PRC is a simple and effective strategy to guide annotations and ultimately improve model accuracy while transfer-learning in a specific order can improve the cold-start performance of the learner but does not benefit iterations of active learning.