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.

Meta-Personalizing Vision-Language Models to Find Named Instances in Video

Large-scale vision-language models (VLM) have shown impressive results for language-guided search applications. While these models allow category-level queries, they currently struggle with personalized searches for moments in a video where a specific object instance such as ``My dog Biscuit'' appears. We present the following three contributions to address this problem. First, we describe a method to meta-personalize a pre-trained VLM, i.e., learning how to learn to personalize a VLM at test time to search in video. Our method extends the VLM's token vocabulary by learning novel word embeddings specific to each instance. To capture only instance-specific features, we represent each instance embedding as a combination of shared and learned global category features. Second, we propose to learn such personalization without explicit human supervision. Our approach automatically identifies moments of named visual instances in video using transcripts and vision-language similarity in the VLM's embedding space. Finally, we introduce This-Is-My, a personal video instance retrieval benchmark. We evaluate our approach on This-Is-My and DeepFashion2 and show that we obtain a 15% relative improvement over the state of the art on the latter dataset.

Language-Guided Music Recommendation for Video via Prompt Analogies

We propose a method to recommend music for an input video while allowing a user to guide music selection with free-form natural language. A key challenge of this problem setting is that existing music video datasets provide the needed (video, music) training pairs, but lack text descriptions of the music. This work addresses this challenge with the following three contributions. First, we propose a text-synthesis approach that relies on an analogy-based prompting procedure to generate natural language music descriptions from a large-scale language model (BLOOM-176B) given pre-trained music tagger outputs and a small number of human text descriptions. Second, we use these synthesized music descriptions to train a new trimodal model, which fuses text and video input representations to query music samples. For training, we introduce a text dropout regularization mechanism which we show is critical to model performance. Our model design allows for the retrieved music audio to agree with the two input modalities by matching visual style depicted in the video and musical genre, mood, or instrumentation described in the natural language query. Third, to evaluate our approach, we collect a testing dataset for our problem by annotating a subset of 4k clips from the YT8M-MusicVideo dataset with natural language music descriptions which we make publicly available. We show that our approach can match or exceed the performance of prior methods on video-to-music retrieval while significantly improving retrieval accuracy when using text guidance.

Vid2Seq: Large-Scale Pretraining of a Visual Language Model for Dense Video Captioning

In this work, we introduce Vid2Seq, a multi-modal single-stage dense event captioning model pretrained on narrated videos which are readily-available at scale. The Vid2Seq architecture augments a language model with special time tokens, allowing it to seamlessly predict event boundaries and textual descriptions in the same output sequence. Such a unified model requires large-scale training data, which is not available in current annotated datasets. We show that it is possible to leverage unlabeled narrated videos for dense video captioning, by reformulating sentence boundaries of transcribed speech as pseudo event boundaries, and using the transcribed speech sentences as pseudo event captions. The resulting Vid2Seq model pretrained on the YT-Temporal-1B dataset improves the state of the art on a variety of dense video captioning benchmarks including YouCook2, ViTT and ActivityNet Captions. Vid2Seq also generalizes well to the tasks of video paragraph captioning and video clip captioning, and to few-shot settings. Our code is publicly available at https://antoyang.github.io/vid2seq.html.

MegaPose: 6D Pose Estimation of Novel Objects via Render & Compare

We introduce MegaPose, a method to estimate the 6D pose of novel objects, that is, objects unseen during training. At inference time, the method only assumes knowledge of (i) a region of interest displaying the object in the image and (ii) a CAD model of the observed object. The contributions of this work are threefold. First, we present a 6D pose refiner based on a render&compare strategy which can be applied to novel objects. The shape and coordinate system of the novel object are provided as inputs to the network by rendering multiple synthetic views of the object's CAD model. Second, we introduce a novel approach for coarse pose estimation which leverages a network trained to classify whether the pose error between a synthetic rendering and an observed image of the same object can be corrected by the refiner. Third, we introduce a large-scale synthetic dataset of photorealistic images of thousands of objects with diverse visual and shape properties and show that this diversity is crucial to obtain good generalization performance on novel objects. We train our approach on this large synthetic dataset and apply it without retraining to hundreds of novel objects in real images from several pose estimation benchmarks. Our approach achieves state-of-the-art performance on the ModelNet and YCB-Video datasets. An extensive evaluation on the 7 core datasets of the BOP challenge demonstrates that our approach achieves performance competitive with existing approaches that require access to the target objects during training. Code, dataset and trained models are available on the project page: https://megapose6d.github.io/.

Multi-Task Learning of Object State Changes from Uncurated Videos

We aim to learn to temporally localize object state changes and the corresponding state-modifying actions by observing people interacting with objects in long uncurated web videos. We introduce three principal contributions. First, we explore alternative multi-task network architectures and identify a model that enables efficient joint learning of multiple object states and actions such as pouring water and pouring coffee. Second, we design a multi-task self-supervised learning procedure that exploits different types of constraints between objects and state-modifying actions enabling end-to-end training of a model for temporal localization of object states and actions in videos from only noisy video-level supervision. Third, we report results on the large-scale ChangeIt and COIN datasets containing tens of thousands of long (un)curated web videos depicting various interactions such as hole drilling, cream whisking, or paper plane folding. We show that our multi-task model achieves a relative improvement of 40% over the prior single-task methods and significantly outperforms both image-based and video-based zero-shot models for this problem. We also test our method on long egocentric videos of the EPIC-KITCHENS and the Ego4D datasets in a zero-shot setup demonstrating the robustness of our learned model.

Benchmarking Learning Efficiency in Deep Reservoir Computing

It is common to evaluate the performance of a machine learning model by measuring its predictive power on a test dataset. This approach favors complicated models that can smoothly fit complex functions and generalize well from training data points. Although essential components of intelligence, speed and data efficiency of this learning process are rarely reported or compared between different candidate models. In this paper, we introduce a benchmark of increasingly difficult tasks together with a data efficiency metric to measure how quickly machine learning models learn from training data. We compare the learning speed of some established sequential supervised models, such as RNNs, LSTMs, or Transformers, with relatively less known alternative models based on reservoir computing. The proposed tasks require a wide range of computational primitives, such as memory or the ability to compute Boolean functions, to be effectively solved. Surprisingly, we observe that reservoir computing systems that rely on dynamically evolving feature maps learn faster than fully supervised methods trained with stochastic gradient optimization while achieving comparable accuracy scores. The code, benchmark, trained models, and results to reproduce our experiments are available at https://github.com/hugcis/benchmark_learning_efficiency/ .

Imitrob: Imitation Learning Dataset for Training and Evaluating 6D Object Pose Estimators

This paper introduces a dataset for training and evaluating methods for 6D pose estimation of hand-held tools in task demonstrations captured by a standard RGB camera. Despite the significant progress of 6D pose estimation methods, their performance is usually limited for heavily occluded objects, which is a common case in imitation learning where the object is typically partially occluded by the manipulating hand. Currently, there is a lack of datasets that would enable the development of robust 6D pose estimation methods for these conditions. To overcome this problem, we collect a new dataset (Imitrob) aimed at 6D pose estimation in imitation learning and other applications where a human holds a tool and performs a task. The dataset contains image sequences of three different tools and six manipulation tasks with two camera viewpoints, four human subjects, and left/right hand. Each image is accompanied by an accurate ground truth measurement of the 6D object pose, obtained by the HTC Vive motion tracking device. The use of the dataset is demonstrated by training and evaluating a recent 6D object pose estimation method (DOPE) in various setups. The dataset and code are publicly available at http://imitrob.ciirc.cvut.cz/imitrobdataset.php.

Differentiable Collision Detection: a Randomized Smoothing Approach

Collision detection appears as a canonical operation in a large range of robotics applications from robot control to simulation, including motion planning and estimation. While the seminal works on the topic date back to the 80s, it is only recently that the question of properly differentiating collision detection has emerged as a central issue, thanks notably to the ongoing and various efforts made by the scientific community around the topic of differentiable physics. Yet, very few solutions have been suggested so far, and only with a strong assumption on the nature of the shapes involved. In this work, we introduce a generic and efficient approach to compute the derivatives of collision detection for any pair of convex shapes, by notably leveraging randomized smoothing techniques which have shown to be particularly adapted to capture the derivatives of non-smooth problems. This approach is implemented in the HPP-FCL and Pinocchio ecosystems, and evaluated on classic datasets and problems of the robotics literature, demonstrating few micro-second timings to compute informative derivatives directly exploitable by many real robotic applications including differentiable simulation.