arXiv subjects

Yan Zeng

Publications and source records attributed to Yan Zeng.

At least 55 records · Page 3Linked to original sources

arXiv2024

Propulsion Contribution from Individual Filament in Flagellar Bundle

Flagellated microorganisms overcome the low-Reynolds-number time reversibility by rotating helical flagella. For peritrichous bacteria, such as Escherichia coli, the randomly distributed flagellar filaments align along the same direction to form a bundle, facilitating complex locomotive strategies. To understand the process of flagella bundling, especially the propulsion force, we develop a multi-functional macroscopic experimental system and employ advanced numerical simulations for verification. Flagella arrangements and phase differences between helices are investigated, revealing the variation in propulsion contribution from the individual helix. Numerically, we build a time-dependent model to match the bundling process and study the influence of hydrodynamic interactions. Surprisingly, it is found that the total propulsion generated by a bundle of two filaments is constant at various phase differences between the helices. However, the difference between the propulsion from each helix is significantly affected by the phase difference, and only one of the helices is responsible for the total propulsion at a phase difference equals to pi. Through our experimental and computational results, we provide a new model considering the propulsion contribution of each filament to better understand microbial locomotion mechanisms, especially on the wobbling behavior of the cell. Our work also sheds light on the design and control of artificial microswimmers.

cond-mat.soft↗

arXiv2024

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.

stat.ME↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.CV↗

arXiv2024

Boximator: Generating Rich and Controllable Motions for Video Synthesis

Generating rich and controllable motion is a pivotal challenge in video synthesis. We propose Boximator, a new approach for fine-grained motion control. Boximator introduces two constraint types: hard box and soft box. Users select objects in the conditional frame using hard boxes and then use either type of boxes to roughly or rigorously define the object's position, shape, or motion path in future frames. Boximator functions as a plug-in for existing video diffusion models. Its training process preserves the base model's knowledge by freezing the original weights and training only the control module. To address training challenges, we introduce a novel self-tracking technique that greatly simplifies the learning of box-object correlations. Empirically, Boximator achieves state-of-the-art video quality (FVD) scores, improving on two base models, and further enhanced after incorporating box constraints. Its robust motion controllability is validated by drastic increases in the bounding box alignment metric. Human evaluation also shows that users favor Boximator generation results over the base model.

cs.CV↗

arXiv2023

Make Pixels Dance: High-Dynamic Video Generation

Creating high-dynamic videos such as motion-rich actions and sophisticated visual effects poses a significant challenge in the field of artificial intelligence. Unfortunately, current state-of-the-art video generation methods, primarily focusing on text-to-video generation, tend to produce video clips with minimal motions despite maintaining high fidelity. We argue that relying solely on text instructions is insufficient and suboptimal for video generation. In this paper, we introduce PixelDance, a novel approach based on diffusion models that incorporates image instructions for both the first and last frames in conjunction with text instructions for video generation. Comprehensive experimental results demonstrate that PixelDance trained with public data exhibits significantly better proficiency in synthesizing videos with complex scenes and intricate motions, setting a new standard for video generation.

cs.CV↗

arXiv2023

Toward Building General Foundation Models for Language, Vision, and Vision-Language Understanding Tasks

Foundation models or pre-trained models have substantially improved the performance of various language, vision, and vision-language understanding tasks. However, existing foundation models can only perform the best in one type of tasks, namely language, vision, or vision-language. It is still an open question whether it is possible to construct a foundation model performing the best for all the understanding tasks, which we call a general foundation model. In this paper, we propose a new general foundation model, X-FM (the X-Foundation Model). X-FM has one language encoder, one vision encoder, and one fusion encoder, as well as a new training method. The training method includes two new techniques for learning X-FM from text, image, and image-text pair data. One is to stop gradients from the vision-language training when learning the language encoder. The other is to leverage the vision-language training to guide the learning of the vision encoder. Extensive experiments on benchmark datasets show that X-FM can significantly outperform existing general foundation models and perform better than or comparable to existing foundation models specifically for language, vision, or vision-language understanding. Code and pre-trained models are released at https://github.com/zhangxinsong-nlp/XFM.

cs.CV↗

arXiv2023

CryoFormer: Continuous Heterogeneous Cryo-EM Reconstruction using Transformer-based Neural Representations

Cryo-electron microscopy (cryo-EM) allows for the high-resolution reconstruction of 3D structures of proteins and other biomolecules. Successful reconstruction of both shape and movement greatly helps understand the fundamental processes of life. However, it is still challenging to reconstruct the continuous motions of 3D structures from hundreds of thousands of noisy and randomly oriented 2D cryo-EM images. Recent advancements use Fourier domain coordinate-based neural networks to continuously model 3D conformations, yet they often struggle to capture local flexible regions accurately. We propose CryoFormer, a new approach for continuous heterogeneous cryo-EM reconstruction. Our approach leverages an implicit feature volume directly in the real domain as the 3D representation. We further introduce a novel query-based deformation transformer decoder to improve the reconstruction quality. Our approach is capable of refining pre-computed pose estimations and locating flexible regions. In experiments, our method outperforms current approaches on three public datasets (1 synthetic and 2 experimental) and a new synthetic dataset of PEDV spike protein. The code and new synthetic dataset will be released for better reproducibility of our results. Project page: https://cryoformer.github.io.

cs.CV↗

arXiv2023

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

cs.CV↗

arXiv2023

Selective formation of metastable polymorphs in solid-state synthesis

Metastable polymorphs often result from the interplay between thermodynamics and kinetics. Despite advances in predictive synthesis for solution-based techniques, there remains a lack of methods to design solid-state reactions targeting metastable materials. Here, we introduce a theoretical framework to predict and control polymorph selectivity in solid-state reactions. This framework presents reaction energy as a rarely used handle for polymorph selection, which influences the role of surface energy in promoting the nucleation of metastable phases. Through in situ characterization and density functional theory calculations on two distinct synthesis pathways targeting LiTiOPO4, we demonstrate how precursor selection and its effect on reaction energy can effectively be used to control which polymorph is obtained from solid-state synthesis. A general approach is outlined to quantify the conditions under which metastable polymorphs are experimentally accessible. With comparison to historical data, this approach suggests that using appropriate precursors could enable the synthesis of many novel materials through selective polymorph nucleation.

cond-mat.mtrl-sci↗

arXiv2023

X$^2$-VLM: All-In-One Pre-trained Model For Vision-Language Tasks

Vision language pre-training aims to learn alignments between vision and language from a large amount of data. Most existing methods only learn image-text alignments. Some others utilize pre-trained object detectors to leverage vision language alignments at the object level. In this paper, we propose to learn multi-grained vision language alignments by a unified pre-training framework that learns multi-grained aligning and multi-grained localization simultaneously. Based on it, we present X$^2$-VLM, an all-in-one model with a flexible modular architecture, in which we further unify image-text pre-training and video-text pre-training in one model. X$^2$-VLM is able to learn unlimited visual concepts associated with diverse text descriptions. Experiment results show that X$^2$-VLM performs the best on base and large scale for both image-text and video-text tasks, making a good trade-off between performance and model scale. Moreover, we show that the modular design of X$^2$-VLM results in high transferability for it to be utilized in any language or domain. For example, by simply replacing the text encoder with XLM-R, X$^2$-VLM outperforms state-of-the-art multilingual multi-modal pre-trained models without any multilingual pre-training. The code and pre-trained models are available at https://github.com/zengyan-97/X2-VLM.

cs.CV↗

arXiv2023

What Matters in Training a GPT4-Style Language Model with Multimodal Inputs?

Recent advancements in Large Language Models (LLMs) such as GPT4 have displayed exceptional multi-modal capabilities in following open-ended instructions given images. However, the performance of these models heavily relies on design choices such as network structures, training data, and training strategies, and these choices have not been extensively discussed in the literature, making it difficult to quantify progress in this field. To address this issue, this paper presents a systematic and comprehensive study, quantitatively and qualitatively, on training such models. We implement over 20 variants with controlled settings. Concretely, for network structures, we compare different LLM backbones and model designs. For training data, we investigate the impact of data and sampling strategies. For instructions, we explore the influence of diversified prompts on the instruction-following ability of the trained models. For benchmarks, we contribute the first, to our best knowledge, comprehensive evaluation set including both image and video tasks through crowd-sourcing. Based on our findings, we present Lynx, which performs the most accurate multi-modal understanding while keeping the best multi-modal generation ability compared to existing open-sourced GPT4-style models.

cs.CV↗

arXiv2023

Cross-View Language Modeling: Towards Unified Cross-Lingual Cross-Modal Pre-training

In this paper, we introduce Cross-View Language Modeling, a simple and effective pre-training framework that unifies cross-lingual and cross-modal pre-training with shared architectures and objectives. Our approach is motivated by a key observation that cross-lingual and cross-modal pre-training share the same goal of aligning two different views of the same object into a common semantic space. To this end, the cross-view language modeling framework considers both multi-modal data (i.e., image-caption pairs) and multi-lingual data (i.e., parallel sentence pairs) as two different views of the same object, and trains the model to align the two views by maximizing the mutual information between them with conditional masked language modeling and contrastive learning. We pre-train CCLM, a Cross-lingual Cross-modal Language Model, with the cross-view language modeling framework. Empirical results on IGLUE, a multi-lingual multi-modal benchmark, and two multi-lingual image-text retrieval datasets show that while conceptually simpler, CCLM significantly outperforms the prior state-of-the-art with an average absolute improvement of over 10%. Moreover, CCLM is the first multi-lingual multi-modal pre-trained model that surpasses the translate-test performance of representative English vision-language models by zero-shot cross-lingual transfer.

cs.CL↗

arXiv2023

A Survey on Causal Reinforcement Learning

While Reinforcement Learning (RL) achieves tremendous success in sequential decision-making problems of many domains, it still faces key challenges of data inefficiency and the lack of interpretability. Interestingly, many researchers have leveraged insights from the causality literature recently, bringing forth flourishing works to unify the merits of causality and address well the challenges from RL. As such, it is of great necessity and significance to collate these Causal Reinforcement Learning (CRL) works, offer a review of CRL methods, and investigate the potential functionality from causality toward RL. In particular, we divide existing CRL approaches into two categories according to whether their causality-based information is given in advance or not. We further analyze each category in terms of the formalization of different models, ranging from the Markov Decision Process (MDP), Partially Observed Markov Decision Process (POMDP), Multi-Arm Bandits (MAB), and Dynamic Treatment Regime (DTR). Moreover, we summarize the evaluation matrices and open sources while we discuss emerging applications, along with promising prospects for the future development of CRL.

cs.AI↗

arXiv2023

Autonomous decision making for solid-state synthesis of inorganic materials

To aid in the automation of inorganic materials synthesis, we introduce an algorithm (ARROWS3) that guides the selection of precursors used in solid-state reactions. Given a target phase, ARROWS3 iteratively proposes experiments and learns from their outcomes to identify an optimal set of precursors that leads to maximal yield of that target. Initial experiments are selected based on thermochemical data collected from first principles calculations, which enable the identification of precursors exhibiting large thermodynamic force to form the desired target. Should the initial experiments fail, their associated reaction paths are determined by sampling a range of synthesis temperatures and identifying their products. ARROWS3 then uses this information to pinpoint which intermediate reactions consume most of the available free energy associated with the starting materials. In subsequent experimental iterations, precursors are selected to avoid such unfavorable reactions and therefore maintain a strong driving force to form the target. We validate this approach on three experimental datasets containing results from more than 200 distinct synthesis procedures. When compared to several black-box optimization algorithms, ARROWS3 identifies the most effective set of precursors for each target while requiring substantially fewer experimental iterations. These findings highlight the importance of using domain knowledge in the design of optimization algorithms for materials synthesis, which are critical for the development of fully autonomous research platforms.

cond-mat.mtrl-sci↗

arXiv2023

eTag: Class-Incremental Learning with Embedding Distillation and Task-Oriented Generation

Class-Incremental Learning (CIL) aims to solve the neural networks' catastrophic forgetting problem, which refers to the fact that once the network updates on a new task, its performance on previously-learned tasks drops dramatically. Most successful CIL methods incrementally train a feature extractor with the aid of stored exemplars, or estimate the feature distribution with the stored prototypes. However, the stored exemplars would violate the data privacy concerns, while the stored prototypes might not reasonably be consistent with a proper feature distribution, hindering the exploration of real-world CIL applications. In this paper, we propose a method of \textit{e}mbedding distillation and \textit{Ta}sk-oriented \textit{g}eneration (\textit{eTag}) for CIL, which requires neither the exemplar nor the prototype. Instead, eTag achieves a data-free manner to train the neural networks incrementally. To prevent the feature extractor from forgetting, eTag distills the embeddings of the network's intermediate blocks. Additionally, eTag enables a generative network to produce suitable features, fitting the needs of the top incremental classifier. Experimental results confirmed that our proposed eTag considerably outperforms the state-of-the-art methods on CIFAR-100 and ImageNet-sub\footnote{Our code is available in the Supplementary Materials.

cs.CV↗

arXiv2022

EfficientVLM: Fast and Accurate Vision-Language Models via Knowledge Distillation and Modal-adaptive Pruning

Pre-trained vision-language models (VLMs) have achieved impressive results in a range of vision-language tasks. However, popular VLMs usually consist of hundreds of millions of parameters which brings challenges for fine-tuning and deployment in real-world applications due to space, memory, and latency constraints. In this work, we introduce a distilling then pruning framework to compress large vision-language models into smaller, faster, and more accurate ones. We first shrink the size of a pre-trained large VLM and apply knowledge distillation in the vision-language pre-training stage to obtain a task-agnostic compact VLM. Then we propose a modal-adaptive pruning algorithm to automatically infer the importance of vision and language modalities for different downstream tasks and adaptively remove redundant structures and neurons in different encoders with controllable target sparsity. We apply our framework to train EfficientVLM, a fast and accurate vision-language model consisting of 6 vision layers, 3 text layers, and 3 cross-modal fusion layers, accounting for only 93 million parameters in total, which is 44.3% of the teacher model. EfficientVLM retains 98.4% performance of the teacher model and accelerates its inference speed by 2.2x. EfficientVLM achieves a large absolute improvement over previous SoTA efficient VLMs of similar sizes by a large margin on various vision-language tasks, including VQAv2 (+4.9%), NLVR2 (+5.6%), ITR (R@1 on TR +17.2%, on IR + 15.6% ) and COCO caption generation (CIDEr +6.5), demonstrating a large potential on training lightweight VLMs.

cs.CL↗

arXiv2022

Multi-Grained Vision Language Pre-Training: Aligning Texts with Visual Concepts

Most existing methods in vision language pre-training rely on object-centric features extracted through object detection and make fine-grained alignments between the extracted features and texts. It is challenging for these methods to learn relations among multiple objects. To this end, we propose a new method called X-VLM to perform `multi-grained vision language pre-training.' The key to learning multi-grained alignments is to locate visual concepts in the image given the associated texts, and in the meantime align the texts with the visual concepts, where the alignments are in multi-granularity. Experimental results show that X-VLM effectively leverages the learned multi-grained alignments to many downstream vision language tasks and consistently outperforms state-of-the-art methods.

cs.CL↗