DRACO: A Denoising-Reconstruction Autoencoder for Cryo-EM

Foundation models in computer vision have demonstrated exceptional performance in zero-shot and few-shot tasks by extracting multi-purpose features from large-scale datasets through self-supervised pre-training methods. However, these models often overlook the severe corruption in cryogenic electron microscopy (cryo-EM) images by high-level noises. We introduce DRACO, a Denoising-Reconstruction Autoencoder for CryO-EM, inspired by the Noise2Noise (N2N) approach. By processing cryo-EM movies into odd and even images and treating them as independent noisy observations, we apply a denoising-reconstruction hybrid training scheme. We mask both images to create denoising and reconstruction tasks. For DRACO's pre-training, the quality of the dataset is essential, we hence build a high-quality, diverse dataset from an uncurated public database, including over 270,000 movies or micrographs. After pre-training, DRACO naturally serves as a generalizable cryo-EM image denoiser and a foundation model for various cryo-EM downstream tasks. DRACO demonstrates the best performance in denoising, micrograph curation, and particle picking tasks compared to state-of-the-art baselines. We will release the code, pre-trained models, and the curated dataset to stimulate further research.

Identification and Estimation of the Bi-Directional MR with Some Invalid Instruments

We consider the challenging problem of estimating causal effects from purely observational data in the bi-directional Mendelian randomization (MR), where some invalid instruments, as well as unmeasured confounding, usually exist. To address this problem, most existing methods attempt to find proper valid instrumental variables (IVs) for the target causal effect by expert knowledge or by assuming that the causal model is a one-directional MR model. As such, in this paper, we first theoretically investigate the identification of the bi-directional MR from observational data. In particular, we provide necessary and sufficient conditions under which valid IV sets are correctly identified such that the bi-directional MR model is identifiable, including the causal directions of a pair of phenotypes (i.e., the treatment and outcome). Moreover, based on the identification theory, we develop a cluster fusion-like method to discover valid IV sets and estimate the causal effects of interest. We theoretically demonstrate the correctness of the proposed algorithm. Experimental results show the effectiveness of our method for estimating causal effects in bi-directional MR.

An Improved Method for Personalizing Diffusion Models

Diffusion models have demonstrated impressive image generation capabilities. Personalized approaches, such as textual inversion and Dreambooth, enhance model individualization using specific images. These methods enable generating images of specific objects based on diverse textual contexts. Our proposed approach aims to retain the model's original knowledge during new information integration, resulting in superior outcomes while necessitating less training time compared to Dreambooth and textual inversion.

Training-free Camera Control for Video Generation

We propose a training-free and robust solution to offer camera movement control for off-the-shelf video diffusion models. Unlike previous work, our method does not require any supervised finetuning on camera-annotated datasets or self-supervised training via data augmentation. Instead, it can be plugged and played with most pretrained video diffusion models and generate camera controllable videos with a single image or text prompt as input. The inspiration of our work comes from the layout prior that intermediate latents hold towards generated results, thus rearranging noisy pixels in them will make output content reallocated as well. As camera move could also be seen as a kind of pixel rearrangement caused by perspective change, videos could be reorganized following specific camera motion if their noisy latents change accordingly. Established on this, we propose our method CamTrol, which enables robust camera control for video diffusion models. It is achieved by a two-stage process. First, we model image layout rearrangement through explicit camera movement in 3D point cloud space. Second, we generate videos with camera motion using layout prior of noisy latents formed by a series of rearranged images. Extensive experiments have demonstrated the robustness our method holds in controlling camera motion of generated videos. Furthermore, we show that our method can produce impressive results in generating 3D rotation videos with dynamic content. Project page at https://lifedecoder.github.io/CamTrol/.

Local Causal Structure Learning in the Presence of Latent Variables

Discovering causal relationships from observational data, particularly in the presence of latent variables, poses a challenging problem. While current local structure learning methods have proven effective and efficient when the focus lies solely on the local relationships of a target variable, they operate under the assumption of causal sufficiency. This assumption implies that all the common causes of the measured variables are observed, leaving no room for latent variables. Such a premise can be easily violated in various real-world applications, resulting in inaccurate structures that may adversely impact downstream tasks. In light of this, our paper delves into the primary investigation of locally identifying potential parents and children of a target from observational data that may include latent variables. Specifically, we harness the causal information from m-separation and V-structures to derive theoretical consistency results, effectively bridging the gap between global and local structure learning. Together with the newly developed stop rules, we present a principled method for determining whether a variable is a direct cause or effect of a target. Further, we theoretically demonstrate the correctness of our approach under the standard causal Markov and faithfulness conditions, with infinite samples. Experimental results on both synthetic and real-world data validate the effectiveness and efficiency of our approach.

HetHub: A Heterogeneous distributed hybrid training system for large-scale models

The development of large-scale models relies on a vast number of computing resources. For example, the GPT-4 model (1.8 trillion parameters) requires 25000 A100 GPUs for its training. It is a challenge to build a large-scale cluster with a type of GPU-accelerator. Using multiple types of GPU-accelerators to construct a cluster is an effective way to solve the problem of insufficient homogeneous GPU-accelerators. However, the existing distributed training systems for large-scale models only support homogeneous GPU-accelerators, not heterogeneous GPU-accelerators. To address the problem, this paper proposes a distributed training system with hybrid parallelism support on heterogeneous GPU-accelerators for large-scale models. It introduces a distributed unified communicator to realize the communication between heterogeneous GPU-accelerators, a distributed performance predictor, and an automatic hybrid parallel module to develop and train models efficiently with heterogeneous GPU-accelerators. Compared to the distributed training system with homogeneous GPU-accelerators, our system can support six different combinations of heterogeneous GPU-accelerators and the optimal performance of heterogeneous GPU-accelerators has achieved at least 90% of the theoretical upper bound performance of homogeneous GPU-accelerators.

AlabOS: A Python-based Reconfigurable Workflow Management Framework for Autonomous Laboratories

The recent advent of autonomous laboratories, coupled with algorithms for high-throughput screening and active learning, promises to accelerate materials discovery and innovation. As these autonomous systems grow in complexity, the demand for robust and efficient workflow management software becomes increasingly critical. In this paper, we introduce AlabOS, a general-purpose software framework for orchestrating experiments and managing resources, with an emphasis on automated laboratories for materials synthesis and characterization. We demonstrate the implementation of AlabOS in a prototype autonomous materials laboratory. AlabOS features a reconfigurable experiment workflow model, enabling the simultaneous execution of varied workflows composed of modular tasks. Therefore, AlabOS is well-suited to handle the rapidly changing experimental protocols defining the progress of self-driving laboratory development for materials research.

Policy Learning for Balancing Short-Term and Long-Term Rewards

Empirical researchers and decision-makers spanning various domains frequently seek profound insights into the long-term impacts of interventions. While the significance of long-term outcomes is undeniable, an overemphasis on them may inadvertently overshadow short-term gains. Motivated by this, this paper formalizes a new framework for learning the optimal policy that effectively balances both long-term and short-term rewards, where some long-term outcomes are allowed to be missing. In particular, we first present the identifiability of both rewards under mild assumptions. Next, we deduce the semiparametric efficiency bounds, along with the consistency and asymptotic normality of their estimators. We also reveal that short-term outcomes, if associated, contribute to improving the estimator of the long-term reward. Based on the proposed estimators, we develop a principled policy learning approach and further derive the convergence rates of regret and estimation errors associated with the learned policy. Extensive experiments are conducted to validate the effectiveness of the proposed method, demonstrating its practical applicability.

Exemplar-Free Class Incremental Learning via Incremental Representation

Exemplar-Free Class Incremental Learning (efCIL) aims to continuously incorporate the knowledge from new classes while retaining previously learned information, without storing any old-class exemplars (i.e., samples). For this purpose, various efCIL methods have been proposed over the past few years, generally with elaborately constructed old pseudo-features, increasing the difficulty of model development and interpretation. In contrast, we propose a \textbf{simple Incremental Representation (IR) framework} for efCIL without constructing old pseudo-features. IR utilizes dataset augmentation to cover a suitable feature space and prevents the model from forgetting by using a single L2 space maintenance loss. We discard the transient classifier trained on each one of the sequence tasks and instead replace it with a 1-near-neighbor classifier for inference, ensuring the representation is incrementally updated during CIL. Extensive experiments demonstrate that our proposed IR achieves comparable performance while significantly preventing the model from forgetting on CIFAR100, TinyImageNet, and ImageNetSubset datasets.

ACE : Off-Policy Actor-Critic with Causality-Aware Entropy Regularization

The varying significance of distinct primitive behaviors during the policy learning process has been overlooked by prior model-free RL algorithms. Leveraging this insight, we explore the causal relationship between different action dimensions and rewards to evaluate the significance of various primitive behaviors during training. We introduce a causality-aware entropy term that effectively identifies and prioritizes actions with high potential impacts for efficient exploration. Furthermore, to prevent excessive focus on specific primitive behaviors, we analyze the gradient dormancy phenomenon and introduce a dormancy-guided reset mechanism to further enhance the efficacy of our method. Our proposed algorithm, ACE: Off-policy Actor-critic with Causality-aware Entropy regularization, demonstrates a substantial performance advantage across 29 diverse continuous control tasks spanning 7 domains compared to model-free RL baselines, which underscores the effectiveness, versatility, and efficient sample efficiency of our approach. Benchmark results and videos are available at https://ace-rl.github.io/.