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Nov 5

Taming generative video models for zero-shot optical flow extraction

Extracting optical flow from videos remains a core computer vision problem. Motivated by the success of large general-purpose models, we ask whether frozen self-supervised video models trained only for future frame prediction can be prompted, without fine-tuning, to output flow. Prior work reading out depth or illumination from video generators required fine-tuning, which is impractical for flow where labels are scarce and synthetic datasets suffer from a sim-to-real gap. Inspired by the Counterfactual World Model (CWM) paradigm, which can obtain point-wise correspondences by injecting a small tracer perturbation into a next-frame predictor and tracking its propagation, we extend this idea to generative video models. We explore several popular architectures and find that successful zero-shot flow extraction in this manner is aided by three model properties: (1) distributional prediction of future frames (avoiding blurry or noisy outputs); (2) factorized latents that treat each spatio-temporal patch independently; and (3) random-access decoding that can condition on any subset of future pixels. These properties are uniquely present in the recent Local Random Access Sequence (LRAS) architecture. Building on LRAS, we propose KL-tracing: a novel test-time procedure that injects a localized perturbation into the first frame, rolls out the model one step, and computes the Kullback-Leibler divergence between perturbed and unperturbed predictive distributions. Without any flow-specific fine-tuning, our method outperforms state-of-the-art models on real-world TAP-Vid DAVIS dataset (16.6% relative improvement for endpoint error) and synthetic TAP-Vid Kubric (4.7% relative improvement). Our results indicate that counterfactual prompting of controllable generative video models is a scalable and effective alternative to supervised or photometric-loss approaches for high-quality flow.

  • 11 authors
·
Jul 11 1

VideoAssembler: Identity-Consistent Video Generation with Reference Entities using Diffusion Model

Identity-consistent video generation seeks to synthesize videos that are guided by both textual prompts and reference images of entities. Current approaches typically utilize cross-attention layers to integrate the appearance of the entity, which predominantly captures semantic attributes, resulting in compromised fidelity of entities. Moreover, these methods necessitate iterative fine-tuning for each new entity encountered, thereby limiting their applicability. To address these challenges, we introduce VideoAssembler, a novel end-to-end framework for identity-consistent video generation that can conduct inference directly when encountering new entities. VideoAssembler is adept at producing videos that are not only flexible with respect to the input reference entities but also responsive to textual conditions. Additionally, by modulating the quantity of input images for the entity, VideoAssembler enables the execution of tasks ranging from image-to-video generation to sophisticated video editing. VideoAssembler comprises two principal components: the Reference Entity Pyramid (REP) encoder and the Entity-Prompt Attention Fusion (EPAF) module. The REP encoder is designed to infuse comprehensive appearance details into the denoising stages of the stable diffusion model. Concurrently, the EPAF module is utilized to integrate text-aligned features effectively. Furthermore, to mitigate the challenge of scarce data, we present a methodology for the preprocessing of training data. Our evaluation of the VideoAssembler framework on the UCF-101, MSR-VTT, and DAVIS datasets indicates that it achieves good performances in both quantitative and qualitative analyses (346.84 in FVD and 48.01 in IS on UCF-101). Our project page is at https://gulucaptain.github.io/videoassembler/.

  • 7 authors
·
Nov 28, 2023

Ctrl-Adapter: An Efficient and Versatile Framework for Adapting Diverse Controls to Any Diffusion Model

ControlNets are widely used for adding spatial control in image generation with different conditions, such as depth maps, canny edges, and human poses. However, there are several challenges when leveraging the pretrained image ControlNets for controlled video generation. First, pretrained ControlNet cannot be directly plugged into new backbone models due to the mismatch of feature spaces, and the cost of training ControlNets for new backbones is a big burden. Second, ControlNet features for different frames might not effectively handle the temporal consistency. To address these challenges, we introduce Ctrl-Adapter, an efficient and versatile framework that adds diverse controls to any image/video diffusion models, by adapting pretrained ControlNets (and improving temporal alignment for videos). Ctrl-Adapter provides diverse capabilities including image control, video control, video control with sparse frames, multi-condition control, compatibility with different backbones, adaptation to unseen control conditions, and video editing. In Ctrl-Adapter, we train adapter layers that fuse pretrained ControlNet features to different image/video diffusion models, while keeping the parameters of the ControlNets and the diffusion models frozen. Ctrl-Adapter consists of temporal and spatial modules so that it can effectively handle the temporal consistency of videos. We also propose latent skipping and inverse timestep sampling for robust adaptation and sparse control. Moreover, Ctrl-Adapter enables control from multiple conditions by simply taking the (weighted) average of ControlNet outputs. With diverse image/video diffusion backbones (SDXL, Hotshot-XL, I2VGen-XL, and SVD), Ctrl-Adapter matches ControlNet for image control and outperforms all baselines for video control (achieving the SOTA accuracy on the DAVIS 2017 dataset) with significantly lower computational costs (less than 10 GPU hours).

  • 4 authors
·
Apr 15, 2024

Automatic Dataset Construction (ADC): Sample Collection, Data Curation, and Beyond

Large-scale data collection is essential for developing personalized training data, mitigating the shortage of training data, and fine-tuning specialized models. However, creating high-quality datasets quickly and accurately remains a challenge due to annotation errors, the substantial time and costs associated with human labor. To address these issues, we propose Automatic Dataset Construction (ADC), an innovative methodology that automates dataset creation with negligible cost and high efficiency. Taking the image classification task as a starting point, ADC leverages LLMs for the detailed class design and code generation to collect relevant samples via search engines, significantly reducing the need for manual annotation and speeding up the data generation process. Despite these advantages, ADC also encounters real-world challenges such as label errors (label noise) and imbalanced data distributions (label bias). We provide open-source software that incorporates existing methods for label error detection, robust learning under noisy and biased data, ensuring a higher-quality training data and more robust model training procedure. Furthermore, we design three benchmark datasets focused on label noise detection, label noise learning, and class-imbalanced learning. These datasets are vital because there are few existing datasets specifically for label noise detection, despite its importance. Finally, we evaluate the performance of existing popular methods on these datasets, thereby facilitating further research in the field.

  • 18 authors
·
Aug 21, 2024

PTMTorrent: A Dataset for Mining Open-source Pre-trained Model Packages

Due to the cost of developing and training deep learning models from scratch, machine learning engineers have begun to reuse pre-trained models (PTMs) and fine-tune them for downstream tasks. PTM registries known as "model hubs" support engineers in distributing and reusing deep learning models. PTM packages include pre-trained weights, documentation, model architectures, datasets, and metadata. Mining the information in PTM packages will enable the discovery of engineering phenomena and tools to support software engineers. However, accessing this information is difficult - there are many PTM registries, and both the registries and the individual packages may have rate limiting for accessing the data. We present an open-source dataset, PTMTorrent, to facilitate the evaluation and understanding of PTM packages. This paper describes the creation, structure, usage, and limitations of the dataset. The dataset includes a snapshot of 5 model hubs and a total of 15,913 PTM packages. These packages are represented in a uniform data schema for cross-hub mining. We describe prior uses of this data and suggest research opportunities for mining using our dataset. The PTMTorrent dataset (v1) is available at: https://app.globus.org/file-manager?origin_id=55e17a6e-9d8f-11ed-a2a2-8383522b48d9&origin_path=%2F~%2F. Our dataset generation tools are available on GitHub: https://doi.org/10.5281/zenodo.7570357.

  • 8 authors
·
Mar 15, 2023

PeaTMOSS: A Dataset and Initial Analysis of Pre-Trained Models in Open-Source Software

The development and training of deep learning models have become increasingly costly and complex. Consequently, software engineers are adopting pre-trained models (PTMs) for their downstream applications. The dynamics of the PTM supply chain remain largely unexplored, signaling a clear need for structured datasets that document not only the metadata but also the subsequent applications of these models. Without such data, the MSR community cannot comprehensively understand the impact of PTM adoption and reuse. This paper presents the PeaTMOSS dataset, which comprises metadata for 281,638 PTMs and detailed snapshots for all PTMs with over 50 monthly downloads (14,296 PTMs), along with 28,575 open-source software repositories from GitHub that utilize these models. Additionally, the dataset includes 44,337 mappings from 15,129 downstream GitHub repositories to the 2,530 PTMs they use. To enhance the dataset's comprehensiveness, we developed prompts for a large language model to automatically extract model metadata, including the model's training datasets, parameters, and evaluation metrics. Our analysis of this dataset provides the first summary statistics for the PTM supply chain, showing the trend of PTM development and common shortcomings of PTM package documentation. Our example application reveals inconsistencies in software licenses across PTMs and their dependent projects. PeaTMOSS lays the foundation for future research, offering rich opportunities to investigate the PTM supply chain. We outline mining opportunities on PTMs, their downstream usage, and cross-cutting questions.

  • 9 authors
·
Feb 1, 2024 1

MOSEv2: A More Challenging Dataset for Video Object Segmentation in Complex Scenes

Video object segmentation (VOS) aims to segment specified target objects throughout a video. Although state-of-the-art methods have achieved impressive performance (e.g., 90+% J&F) on existing benchmarks such as DAVIS and YouTube-VOS, these datasets primarily contain salient, dominant, and isolated objects, limiting their generalization to real-world scenarios. To advance VOS toward more realistic environments, coMplex video Object SEgmentation (MOSEv1) was introduced to facilitate VOS research in complex scenes. Building on the strengths and limitations of MOSEv1, we present MOSEv2, a significantly more challenging dataset designed to further advance VOS methods under real-world conditions. MOSEv2 consists of 5,024 videos and over 701,976 high-quality masks for 10,074 objects across 200 categories. Compared to its predecessor, MOSEv2 introduces significantly greater scene complexity, including more frequent object disappearance and reappearance, severe occlusions and crowding, smaller objects, as well as a range of new challenges such as adverse weather (e.g., rain, snow, fog), low-light scenes (e.g., nighttime, underwater), multi-shot sequences, camouflaged objects, non-physical targets (e.g., shadows, reflections), scenarios requiring external knowledge, etc. We benchmark 20 representative VOS methods under 5 different settings and observe consistent performance drops. For example, SAM2 drops from 76.4% on MOSEv1 to only 50.9% on MOSEv2. We further evaluate 9 video object tracking methods and find similar declines, demonstrating that MOSEv2 presents challenges across tasks. These results highlight that despite high accuracy on existing datasets, current VOS methods still struggle under real-world complexities. MOSEv2 is publicly available at https://MOSE.video.

GenIR: Generative Visual Feedback for Mental Image Retrieval

Vision-language models (VLMs) have shown strong performance on text-to-image retrieval benchmarks. However, bridging this success to real-world applications remains a challenge. In practice, human search behavior is rarely a one-shot action. Instead, it is often a multi-round process guided by clues in mind, that is, a mental image ranging from vague recollections to vivid mental representations of the target image. Motivated by this gap, we study the task of Mental Image Retrieval (MIR), which targets the realistic yet underexplored setting where users refine their search for a mentally envisioned image through multi-round interactions with an image search engine. Central to successful interactive retrieval is the capability of machines to provide users with clear, actionable feedback; however, existing methods rely on indirect or abstract verbal feedback, which can be ambiguous, misleading, or ineffective for users to refine the query. To overcome this, we propose GenIR, a generative multi-round retrieval paradigm leveraging diffusion-based image generation to explicitly reify the AI system's understanding at each round. These synthetic visual representations provide clear, interpretable feedback, enabling users to refine their queries intuitively and effectively. We further introduce a fully automated pipeline to generate a high-quality multi-round MIR dataset. Experimental results demonstrate that GenIR significantly outperforms existing interactive methods in the MIR scenario. This work establishes a new task with a dataset and an effective generative retrieval method, providing a foundation for future research in this direction.

  • 5 authors
·
Jun 6

MasakhaNEWS: News Topic Classification for African languages

African languages are severely under-represented in NLP research due to lack of datasets covering several NLP tasks. While there are individual language specific datasets that are being expanded to different tasks, only a handful of NLP tasks (e.g. named entity recognition and machine translation) have standardized benchmark datasets covering several geographical and typologically-diverse African languages. In this paper, we develop MasakhaNEWS -- a new benchmark dataset for news topic classification covering 16 languages widely spoken in Africa. We provide an evaluation of baseline models by training classical machine learning models and fine-tuning several language models. Furthermore, we explore several alternatives to full fine-tuning of language models that are better suited for zero-shot and few-shot learning such as cross-lingual parameter-efficient fine-tuning (like MAD-X), pattern exploiting training (PET), prompting language models (like ChatGPT), and prompt-free sentence transformer fine-tuning (SetFit and Cohere Embedding API). Our evaluation in zero-shot setting shows the potential of prompting ChatGPT for news topic classification in low-resource African languages, achieving an average performance of 70 F1 points without leveraging additional supervision like MAD-X. In few-shot setting, we show that with as little as 10 examples per label, we achieved more than 90\% (i.e. 86.0 F1 points) of the performance of full supervised training (92.6 F1 points) leveraging the PET approach.

  • 65 authors
·
Apr 19, 2023

COPILOT: Human-Environment Collision Prediction and Localization from Egocentric Videos

The ability to forecast human-environment collisions from egocentric observations is vital to enable collision avoidance in applications such as VR, AR, and wearable assistive robotics. In this work, we introduce the challenging problem of predicting collisions in diverse environments from multi-view egocentric videos captured from body-mounted cameras. Solving this problem requires a generalizable perception system that can classify which human body joints will collide and estimate a collision region heatmap to localize collisions in the environment. To achieve this, we propose a transformer-based model called COPILOT to perform collision prediction and localization simultaneously, which accumulates information across multi-view inputs through a novel 4D space-time-viewpoint attention mechanism. To train our model and enable future research on this task, we develop a synthetic data generation framework that produces egocentric videos of virtual humans moving and colliding within diverse 3D environments. This framework is then used to establish a large-scale dataset consisting of 8.6M egocentric RGBD frames. Extensive experiments show that COPILOT generalizes to unseen synthetic as well as real-world scenes. We further demonstrate COPILOT outputs are useful for downstream collision avoidance through simple closed-loop control. Please visit our project webpage at https://sites.google.com/stanford.edu/copilot.

  • 7 authors
·
Oct 4, 2022

MACPruning: Dynamic Operation Pruning to Mitigate Side-Channel DNN Model Extraction

As deep learning gains popularity, edge IoT devices have seen proliferating deployment of pre-trained Deep Neural Network (DNN) models. These DNNs represent valuable intellectual property and face significant confidentiality threats from side-channel analysis (SCA), particularly non-invasive Differential Electromagnetic (EM) Analysis (DEMA), which retrieves individual model parameters from EM traces collected during model inference. Traditional SCA mitigation methods, such as masking and shuffling, can still be applied to DNN inference, but will incur significant performance degradation due to the large volume of operations and parameters. Based on the insight that DNN models have high redundancy and are robust to input variation, we introduce MACPruning, a novel lightweight defense against DEMA-based parameter extraction attacks, exploiting specific characteristics of DNN execution. The design principle of MACPruning is to randomly deactivate input pixels and prune the operations (typically multiply-accumulate-MAC) on those pixels. The technique removes certain leakages and overall redistributes weight-dependent EM leakages temporally, and thus effectively mitigates DEMA. To maintain DNN performance, we propose an importance-aware pixel map that preserves critical input pixels, keeping randomness in the defense while minimizing its impact on DNN performance due to operation pruning. We conduct a comprehensive security analysis of MACPruning on various datasets for DNNs on edge devices. Our evaluations demonstrate that MACPruning effectively reduces EM leakages with minimal impact on the model accuracy and negligible computational overhead.

  • 5 authors
·
Feb 20

CLIMB: Curriculum Learning for Infant-inspired Model Building

We describe our team's contribution to the STRICT-SMALL track of the BabyLM Challenge. The challenge requires training a language model from scratch using only a relatively small training dataset of ten million words. We experiment with three variants of cognitively-motivated curriculum learning and analyze their effect on the performance of the model on linguistic evaluation tasks. In the vocabulary curriculum, we analyze methods for constraining the vocabulary in the early stages of training to simulate cognitively more plausible learning curves. In the data curriculum experiments, we vary the order of the training instances based on i) infant-inspired expectations and ii) the learning behavior of the model. In the objective curriculum, we explore different variations of combining the conventional masked language modeling task with a more coarse-grained word class prediction task to reinforce linguistic generalization capabilities. Our results did not yield consistent improvements over our own non-curriculum learning baseline across a range of linguistic benchmarks; however, we do find marginal gains on select tasks. Our analysis highlights key takeaways for specific combinations of tasks and settings which benefit from our proposed curricula. We moreover determine that careful selection of model architecture, and training hyper-parameters yield substantial improvements over the default baselines provided by the BabyLM challenge.

  • 7 authors
·
Nov 15, 2023

INDUS: Effective and Efficient Language Models for Scientific Applications

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

  • 34 authors
·
May 17, 2024 1

Causal evidence for the primordiality of colours in trans-Neptunian objects

The origins of the colours of Trans-Neptunian Objects (TNOs) represent a crucial unresolved question, central to understanding the history of our Solar System. Recent observational surveys revealed correlations between the eccentricity and inclination of TNOs, and their colours. This rekindled the long-standing debate on whether these colours reflect the conditions of TNO formation or their subsequent evolution. We address this question using a model-agnostic, data-driven approach that unanimously converges to a common causal graph from the analysis of two different datasets, each from two different conditional independence test methods. For evaluation, we demonstrate how our model is consistent with the currently-accepted paradigms of TNOs' dynamical histories, without involving any orbital modelling or physics-based assumptions. Our causal model (with no knowledge of the existence of Neptune) predicts the need for an unknown confounding variable, consistent with Neptune's effects. The model predicts that the colour of TNOs is the root cause of their inclination distribution, rather than the other way around. This strongly suggests that the colours of TNOs reflect an underlying dynamical property, most likely their formation location. Our model excludes formation scenarios that invoke substantial colour modification by subsequent evolution. We conclude that the colours of TNOs are predominantly primordial.

  • 6 authors
·
Aug 13

Soft-NMS -- Improving Object Detection With One Line of Code

Non-maximum suppression is an integral part of the object detection pipeline. First, it sorts all detection boxes on the basis of their scores. The detection box M with the maximum score is selected and all other detection boxes with a significant overlap (using a pre-defined threshold) with M are suppressed. This process is recursively applied on the remaining boxes. As per the design of the algorithm, if an object lies within the predefined overlap threshold, it leads to a miss. To this end, we propose Soft-NMS, an algorithm which decays the detection scores of all other objects as a continuous function of their overlap with M. Hence, no object is eliminated in this process. Soft-NMS obtains consistent improvements for the coco-style mAP metric on standard datasets like PASCAL VOC 2007 (1.7% for both R-FCN and Faster-RCNN) and MS-COCO (1.3% for R-FCN and 1.1% for Faster-RCNN) by just changing the NMS algorithm without any additional hyper-parameters. Using Deformable-RFCN, Soft-NMS improves state-of-the-art in object detection from 39.8% to 40.9% with a single model. Further, the computational complexity of Soft-NMS is the same as traditional NMS and hence it can be efficiently implemented. Since Soft-NMS does not require any extra training and is simple to implement, it can be easily integrated into any object detection pipeline. Code for Soft-NMS is publicly available on GitHub (http://bit.ly/2nJLNMu).

  • 4 authors
·
Apr 14, 2017

Causal Discovery in Astrophysics: Unraveling Supermassive Black Hole and Galaxy Coevolution

Correlation does not imply causation, but patterns of statistical association between variables can be exploited to infer a causal structure (even with purely observational data) with the burgeoning field of causal discovery. As a purely observational science, astrophysics has much to gain by exploiting these new methods. The supermassive black hole (SMBH)--galaxy interaction has long been constrained by observed scaling relations, that is low-scatter correlations between variables such as SMBH mass and the central velocity dispersion of stars in a host galaxy's bulge. This study, using advanced causal discovery techniques and an up-to-date dataset, reveals a causal link between galaxy properties and dynamically-measured SMBH masses. We apply a score-based Bayesian framework to compute the exact conditional probabilities of every causal structure that could possibly describe our galaxy sample. With the exact posterior distribution, we determine the most likely causal structures and notice a probable causal reversal when separating galaxies by morphology. In elliptical galaxies, bulge properties (built from major mergers) tend to influence SMBH growth, while in spiral galaxies, SMBHs are seen to affect host galaxy properties, potentially through feedback in gas-rich environments. For spiral galaxies, SMBHs progressively quench star formation, whereas in elliptical galaxies, quenching is complete, and the causal connection has reversed. Our findings support theoretical models of hierarchical assembly of galaxies and active galactic nuclei feedback regulating galaxy evolution. Our study suggests the potentiality for further exploration of causal links in astrophysical and cosmological scaling relations, as well as any other observational science.

  • 12 authors
·
Oct 1, 2024

DESI 2024 V: Full-Shape Galaxy Clustering from Galaxies and Quasars

We present the measurements and cosmological implications of the galaxy two-point clustering using over 4.7 million unique galaxy and quasar redshifts in the range 0.1<z<2.1 divided into six redshift bins over a sim 7,500 square degree footprint, from the first year of observations with the Dark Energy Spectroscopic Instrument (DESI Data Release 1). By fitting the full power spectrum, we extend previous DESI DR1 baryon acoustic oscillation (BAO) measurements to include redshift-space distortions and signals from the matter-radiation equality scale. For the first time, this Full-Shape analysis is blinded at the catalogue-level to avoid confirmation bias and the systematic errors are accounted for at the two-point clustering level, which automatically propagates them into any cosmological parameter. When analysing the data in terms of compressed model-agnostic variables, we obtain a combined precision of 4.7\% on the amplitude of the redshift space distortion signal reaching similar precision with just one year of DESI data than with 20 years of observation from previous generation surveys. We analyse the data to directly constrain the cosmological parameters within the LambdaCDM model using perturbation theory and combine this information with the reconstructed DESI DR1 galaxy BAO. Using a Big Bang Nucleosynthesis Gaussian prior on the baryon density parameter, and a Gaussian prior on the spectral index, we constrain the matter density is Omega_m=0.296pm 0.010 and the Hubble constant H_0=(68.63 pm 0.79)[{rm km, s^{-1}Mpc^{-1}}]. Additionally, we measure the amplitude of clustering sigma_8=0.841 pm 0.034. The DESI DR1 results are in agreement with the LambdaCDM model based on general relativity with parameters consistent with those from Planck. The cosmological interpretation of these results in combination with external datasets are presented in a companion paper.

  • 198 authors
·
Nov 18, 2024

Learning Support and Trivial Prototypes for Interpretable Image Classification

Prototypical part network (ProtoPNet) methods have been designed to achieve interpretable classification by associating predictions with a set of training prototypes, which we refer to as trivial prototypes because they are trained to lie far from the classification boundary in the feature space. Note that it is possible to make an analogy between ProtoPNet and support vector machine (SVM) given that the classification from both methods relies on computing similarity with a set of training points (i.e., trivial prototypes in ProtoPNet, and support vectors in SVM). However, while trivial prototypes are located far from the classification boundary, support vectors are located close to this boundary, and we argue that this discrepancy with the well-established SVM theory can result in ProtoPNet models with inferior classification accuracy. In this paper, we aim to improve the classification of ProtoPNet with a new method to learn support prototypes that lie near the classification boundary in the feature space, as suggested by the SVM theory. In addition, we target the improvement of classification results with a new model, named ST-ProtoPNet, which exploits our support prototypes and the trivial prototypes to provide more effective classification. Experimental results on CUB-200-2011, Stanford Cars, and Stanford Dogs datasets demonstrate that ST-ProtoPNet achieves state-of-the-art classification accuracy and interpretability results. We also show that the proposed support prototypes tend to be better localised in the object of interest rather than in the background region.

  • 8 authors
·
Jan 8, 2023

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

  • 9 authors
·
Jun 20, 2022

RGB-Only Supervised Camera Parameter Optimization in Dynamic Scenes

Although COLMAP has long remained the predominant method for camera parameter optimization in static scenes, it is constrained by its lengthy runtime and reliance on ground truth (GT) motion masks for application to dynamic scenes. Many efforts attempted to improve it by incorporating more priors as supervision such as GT focal length, motion masks, 3D point clouds, camera poses, and metric depth, which, however, are typically unavailable in casually captured RGB videos. In this paper, we propose a novel method for more accurate and efficient camera parameter optimization in dynamic scenes solely supervised by a single RGB video. Our method consists of three key components: (1) Patch-wise Tracking Filters, to establish robust and maximally sparse hinge-like relations across the RGB video. (2) Outlier-aware Joint Optimization, for efficient camera parameter optimization by adaptive down-weighting of moving outliers, without reliance on motion priors. (3) A Two-stage Optimization Strategy, to enhance stability and optimization speed by a trade-off between the Softplus limits and convex minima in losses. We visually and numerically evaluate our camera estimates. To further validate accuracy, we feed the camera estimates into a 4D reconstruction method and assess the resulting 3D scenes, and rendered 2D RGB and depth maps. We perform experiments on 4 real-world datasets (NeRF-DS, DAVIS, iPhone, and TUM-dynamics) and 1 synthetic dataset (MPI-Sintel), demonstrating that our method estimates camera parameters more efficiently and accurately with a single RGB video as the only supervision.

  • 3 authors
·
Sep 18 2

Exploring Temporally-Aware Features for Point Tracking

Point tracking in videos is a fundamental task with applications in robotics, video editing, and more. While many vision tasks benefit from pre-trained feature backbones to improve generalizability, point tracking has primarily relied on simpler backbones trained from scratch on synthetic data, which may limit robustness in real-world scenarios. Additionally, point tracking requires temporal awareness to ensure coherence across frames, but using temporally-aware features is still underexplored. Most current methods often employ a two-stage process: an initial coarse prediction followed by a refinement stage to inject temporal information and correct errors from the coarse stage. These approach, however, is computationally expensive and potentially redundant if the feature backbone itself captures sufficient temporal information. In this work, we introduce Chrono, a feature backbone specifically designed for point tracking with built-in temporal awareness. Leveraging pre-trained representations from self-supervised learner DINOv2 and enhanced with a temporal adapter, Chrono effectively captures long-term temporal context, enabling precise prediction even without the refinement stage. Experimental results demonstrate that Chrono achieves state-of-the-art performance in a refiner-free setting on the TAP-Vid-DAVIS and TAP-Vid-Kinetics datasets, among common feature backbones used in point tracking as well as DINOv2, with exceptional efficiency. Project page: https://cvlab-kaist.github.io/Chrono/

  • 6 authors
·
Jan 21