Grounded Video Caption Generation

We propose a new task, dataset and model for grounded video caption generation. This task unifies captioning and object grounding in video, where the objects in the caption are grounded in the video via temporally consistent bounding boxes. We introduce the following contributions. First, we present a task definition and a manually annotated test dataset for this task, referred to as GROunded Video Caption Generation (GROC). Second, we introduce a large-scale automatic annotation method leveraging an existing model for grounded still image captioning together with an LLM for summarising frame-level captions into temporally consistent captions in video. Furthermore, we prompt the LLM to track by language -- classifying noun phrases from the frame-level captions into noun phrases of the video-level generated caption. We apply this approach to videos from the HowTo100M dataset, which results in a new large-scale training dataset, called HowToGround, with automatically annotated captions and spatio-temporally consistent bounding boxes with coherent natural language labels. Third, we introduce a new grounded video caption generation model, called VideoGround, and train the model on the new automatically annotated HowToGround dataset. Finally, results of our VideoGround model set the state of the art for the new task of grounded video caption generation. We perform extensive ablations and demonstrate the importance of key technical contributions of our model.

Training on test proteins improves fitness, structure, and function prediction

Data scarcity and distribution shifts often hinder the ability of machine learning models to generalize when applied to proteins and other biological data. Self-supervised pre-training on large datasets is a common method to enhance generalization. However, striving to perform well on all possible proteins can limit model's capacity to excel on any specific one, even though practitioners are often most interested in accurate predictions for the individual protein they study. To address this limitation, we propose an orthogonal approach to achieve generalization. Building on the prevalence of self-supervised pre-training, we introduce a method for self-supervised fine-tuning at test time, allowing models to adapt to the test protein of interest on the fly and without requiring any additional data. We study our test-time training (TTT) method through the lens of perplexity minimization and show that it consistently enhances generalization across different models, their scales, and datasets. Notably, our method leads to new state-of-the-art results on the standard benchmark for protein fitness prediction, improves protein structure prediction for challenging targets, and enhances function prediction accuracy.

MassSpecGym: A benchmark for the discovery and identification of molecules

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: \textit{de novo} molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at \url{https://github.com/pluskal-lab/MassSpecGym}.

Revealing data leakage in protein interaction benchmarks

In recent years, there has been remarkable progress in machine learning for protein-protein interactions. However, prior work has predominantly focused on improving learning algorithms, with less attention paid to evaluation strategies and data preparation. Here, we demonstrate that further development of machine learning methods may be hindered by the quality of existing train-test splits. Specifically, we find that commonly used splitting strategies for protein complexes, based on protein sequence or metadata similarity, introduce major data leakage. This may result in overoptimistic evaluation of generalization, as well as unfair benchmarking of the models, biased towards assessing their overfitting capacity rather than practical utility. To overcome the data leakage, we recommend constructing data splits based on 3D structural similarity of protein-protein interfaces and suggest corresponding algorithms. We believe that addressing the data leakage problem is critical for further progress in this research area.

POP-3D: Open-Vocabulary 3D Occupancy Prediction from Images

We describe an approach to predict open-vocabulary 3D semantic voxel occupancy map from input 2D images with the objective of enabling 3D grounding, segmentation and retrieval of free-form language queries. This is a challenging problem because of the 2D-3D ambiguity and the open-vocabulary nature of the target tasks, where obtaining annotated training data in 3D is difficult. The contributions of this work are three-fold. First, we design a new model architecture for open-vocabulary 3D semantic occupancy prediction. The architecture consists of a 2D-3D encoder together with occupancy prediction and 3D-language heads. The output is a dense voxel map of 3D grounded language embeddings enabling a range of open-vocabulary tasks. Second, we develop a tri-modal self-supervised learning algorithm that leverages three modalities: (i) images, (ii) language and (iii) LiDAR point clouds, and enables training the proposed architecture using a strong pre-trained vision-language model without the need for any 3D manual language annotations. Finally, we demonstrate quantitatively the strengths of the proposed model on several open-vocabulary tasks: Zero-shot 3D semantic segmentation using existing datasets; 3D grounding and retrieval of free-form language queries, using a small dataset that we propose as an extension of nuScenes. You can find the project page here https://vobecant.github.io/POP3D.

GenHowTo: Learning to Generate Actions and State Transformations from Instructional Videos

We address the task of generating temporally consistent and physically plausible images of actions and object state transformations. Given an input image and a text prompt describing the targeted transformation, our generated images preserve the environment and transform objects in the initial image. Our contributions are threefold. First, we leverage a large body of instructional videos and automatically mine a dataset of triplets of consecutive frames corresponding to initial object states, actions, and resulting object transformations. Second, equipped with this data, we develop and train a conditioned diffusion model dubbed GenHowTo. Third, we evaluate GenHowTo on a variety of objects and actions and show superior performance compared to existing methods. In particular, we introduce a quantitative evaluation where GenHowTo achieves 88% and 74% on seen and unseen interaction categories, respectively, outperforming prior work by a large margin.

Customizing Motion in Text-to-Video Diffusion Models

We introduce an approach for augmenting text-to-video generation models with customized motions, extending their capabilities beyond the motions depicted in the original training data. By leveraging a few video samples demonstrating specific movements as input, our method learns and generalizes the input motion patterns for diverse, text-specified scenarios. Our contributions are threefold. First, to achieve our results, we finetune an existing text-to-video model to learn a novel mapping between the depicted motion in the input examples to a new unique token. To avoid overfitting to the new custom motion, we introduce an approach for regularization over videos. Second, by leveraging the motion priors in a pretrained model, our method can produce novel videos featuring multiple people doing the custom motion, and can invoke the motion in combination with other motions. Furthermore, our approach extends to the multimodal customization of motion and appearance of individualized subjects, enabling the generation of videos featuring unique characters and distinct motions. Third, to validate our method, we introduce an approach for quantitatively evaluating the learned custom motion and perform a systematic ablation study. We show that our method significantly outperforms prior appearance-based customization approaches when extended to the motion customization task.

Visually Guided Model Predictive Robot Control via 6D Object Pose Localization and Tracking

The objective of this work is to enable manipulation tasks with respect to the 6D pose of a dynamically moving object using a camera mounted on a robot. Examples include maintaining a constant relative 6D pose of the robot arm with respect to the object, grasping the dynamically moving object, or co-manipulating the object together with a human. Fast and accurate 6D pose estimation is crucial to achieve smooth and stable robot control in such situations. The contributions of this work are three fold. First, we propose a new visual perception module that asynchronously combines accurate learning-based 6D object pose localizer and a high-rate model-based 6D pose tracker. The outcome is a low-latency accurate and temporally consistent 6D object pose estimation from the input video stream at up to 120 Hz. Second, we develop a visually guided robot arm controller that combines the new visual perception module with a torque-based model predictive control algorithm. Asynchronous combination of the visual and robot proprioception signals at their corresponding frequencies results in stable and robust 6D object pose guided robot arm control. Third, we experimentally validate the proposed approach on a challenging 6D pose estimation benchmark and demonstrate 6D object pose-guided control with dynamically moving objects on a real 7 DoF Franka Emika Panda robot.

Learning to design protein-protein interactions with enhanced generalization

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.

VidChapters-7M: Video Chapters at Scale

Segmenting long videos into chapters enables users to quickly navigate to the information of their interest. This important topic has been understudied due to the lack of publicly released datasets. To address this issue, we present VidChapters-7M, a dataset of 817K user-chaptered videos including 7M chapters in total. VidChapters-7M is automatically created from videos online in a scalable manner by scraping user-annotated chapters and hence without any additional manual annotation. We introduce the following three tasks based on this data. First, the video chapter generation task consists of temporally segmenting the video and generating a chapter title for each segment. To further dissect the problem, we also define two variants of this task: video chapter generation given ground-truth boundaries, which requires generating a chapter title given an annotated video segment, and video chapter grounding, which requires temporally localizing a chapter given its annotated title. We benchmark both simple baselines and state-of-the-art video-language models for these three tasks. We also show that pretraining on VidChapters-7M transfers well to dense video captioning tasks in both zero-shot and finetuning settings, largely improving the state of the art on the YouCook2 and ViTT benchmarks. Finally, our experiments reveal that downstream performance scales well with the size of the pretraining dataset. Our dataset, code, and models are publicly available at https://antoyang.github.io/vidchapters.html.