Yusong Wang

Shaoning Li, Mingyu Li, Yusong Wang et al.

Investigating conformational landscapes of proteins is a crucial way to understand their biological functions and properties. AlphaFlow stands out as a sequence-conditioned generative model that introduces flexibility into structure prediction models by fine-tuning AlphaFold under the flow-matching framework. Despite the advantages of efficient sampling afforded by flow-matching, AlphaFlow still requires multiple runs of AlphaFold to finally generate one single conformation. Due to the heavy consumption of AlphaFold, its applicability is limited in sampling larger set of protein ensembles or the longer chains within a constrained timeframe. In this work, we propose a feature-conditioned generative model called AlphaFlow-Lit to realize efficient protein ensembles generation. In contrast to the full fine-tuning on the entire structure, we focus solely on the light-weight structure module to reconstruct the conformation. AlphaFlow-Lit performs on-par with AlphaFlow and surpasses its distilled version without pretraining, all while achieving a significant sampling acceleration of around 47 times. The advancement in efficiency showcases the potential of AlphaFlow-Lit in enabling faster and more scalable generation of protein ensembles.

Dongyuan Li, Yusong Wang, Kotaro Funakoshi et al.

Multimodal emotion recognition aims to recognize emotions for each utterance of multiple modalities, which has received increasing attention for its application in human-machine interaction. Current graph-based methods fail to simultaneously depict global contextual features and local diverse uni-modal features in a dialogue. Furthermore, with the number of graph layers increasing, they easily fall into over-smoothing. In this paper, we propose a method for joint modality fusion and graph contrastive learning for multimodal emotion recognition (Joyful), where multimodality fusion, contrastive learning, and emotion recognition are jointly optimized. Specifically, we first design a new multimodal fusion mechanism that can provide deep interaction and fusion between the global contextual and uni-modal specific features. Then, we introduce a graph contrastive learning framework with inter-view and intra-view contrastive losses to learn more distinguishable representations for samples with different sentiments. Extensive experiments on three benchmark datasets indicate that Joyful achieved state-of-the-art (SOTA) performance compared to all baselines.

Yusong Wang, Shaoning Li, Zun Wang et al.

In the technical report, we provide our solution for OGB-LSC 2022 Graph Regression Task. The target of this task is to predict the quantum chemical property, HOMO-LUMO gap for a given molecule on PCQM4Mv2 dataset. In the competition, we designed two kinds of models: Transformer-M-ViSNet which is an geometry-enhanced graph neural network for fully connected molecular graphs and Pretrained-3D-ViSNet which is a pretrained ViSNet by distilling geomeotric information from optimized structures. With an ensemble of 22 models, ViSNet Team achieved the MAE of 0.0723 eV on the test-challenge set, dramatically reducing the error by 39.75% compared with the best method in the last year competition.

Dongyuan Li, Yusong Wang, Kotaro Funakoshi et al.

Speech emotion recognition (SER) has drawn increasing attention for its applications in human-machine interaction. However, existing SER methods ignore the information gap between the pre-training speech recognition task and the downstream SER task, leading to sub-optimal performance. Moreover, they require much time to fine-tune on each specific speech dataset, restricting their effectiveness in real-world scenes with large-scale noisy data. To address these issues, we propose an active learning (AL) based Fine-Tuning framework for SER that leverages task adaptation pre-training (TAPT) and AL methods to enhance performance and efficiency. Specifically, we first use TAPT to minimize the information gap between the pre-training and the downstream task. Then, AL methods are used to iteratively select a subset of the most informative and diverse samples for fine-tuning, reducing time consumption. Experiments demonstrate that using only 20\%pt. samples improves 8.45\%pt. accuracy and reduces 79\%pt. time consumption.

Dongyuan Li, Ying Zhang, Yusong Wang et al.

Speech emotion recognition (SER) has garnered increasing attention due to its wide range of applications in various fields, including human-machine interaction, virtual assistants, and mental health assistance. However, existing SER methods often overlook the information gap between the pre-training speech recognition task and the downstream SER task, resulting in sub-optimal performance. Moreover, current methods require much time for fine-tuning on each specific speech dataset, such as IEMOCAP, which limits their effectiveness in real-world scenarios with large-scale noisy data. To address these issues, we propose an active learning (AL)-based fine-tuning framework for SER, called \textsc{After}, that leverages task adaptation pre-training (TAPT) and AL methods to enhance performance and efficiency. Specifically, we first use TAPT to minimize the information gap between the pre-training speech recognition task and the downstream speech emotion recognition task. Then, AL methods are employed to iteratively select a subset of the most informative and diverse samples for fine-tuning, thereby reducing time consumption. Experiments demonstrate that our proposed method \textsc{After}, using only 20\% of samples, improves accuracy by 8.45\% and reduces time consumption by 79\%. The additional extension of \textsc{After} and ablation studies further confirm its effectiveness and applicability to various real-world scenarios. Our source code is available on Github for reproducibility. (https://github.com/Clearloveyuan/AFTER).

Yusong Wang, Chuang Yang, Jiawei Wang et al.

Human mobility generation aims to synthesize plausible trajectory data, which is widely used in urban system research. While Large Language Model-based methods excel at generating routine trajectories, they struggle to capture deviated mobility during large-scale societal events. This limitation stems from two critical gaps: (1) the absence of event-annotated mobility datasets for design and evaluation, and (2) the inability of current frameworks to reconcile competitions between users' habitual patterns and event-imposed constraints when making trajectory decisions. This work addresses these gaps with a twofold contribution. First, we construct the first event-annotated mobility dataset covering three major events: Typhoon Hagibis, COVID-19, and the Tokyo 2021 Olympics. Second, we propose ELLMob, a self-aligned LLM framework that first extracts competing rationales between habitual patterns and event constraints, based on Fuzzy-Trace Theory, and then iteratively aligns them to generate trajectories that are both habitually grounded and event-responsive. Extensive experiments show that ELLMob wins state-of-the-art baselines across all events, demonstrating its effectiveness. Our codes and datasets are available at https://github.com/deepkashiwa20/ELLMob.

Yusong Wang, Jialun Shen, Zhihao Wu et al.

Graph Neural Networks (GNNs) have been widely adopted for Protein Representation Learning (PRL), as residue interaction networks can be naturally represented as graphs. Current GNN-based PRL methods typically rely on single-perspective graph construction strategies, which capture partial properties of residue interactions, resulting in incomplete protein representations. To address this limitation, we propose MMPG, a framework that constructs protein graphs from multiple perspectives and adaptively fuses them via Mixture of Experts (MoE) for PRL. MMPG constructs graphs from physical, chemical, and geometric perspectives to characterize different properties of residue interactions. To capture both perspective-specific features and their synergies, we develop an MoE module, which dynamically routes perspectives to specialized experts, where experts learn intrinsic features and cross-perspective interactions. We quantitatively verify that MoE automatically specializes experts in modeling distinct levels of interaction from individual representations, to pairwise inter-perspective synergies, and ultimately to a global consensus across all perspectives. Through integrating this multi-level information, MMPG produces superior protein representations and achieves advanced performance on four different downstream protein tasks.

Yicheng Xu, Yuxin Chen, Jiahao Nie et al.

Continual learning (CL) with Vision-Language Models (VLMs) has overcome the constraints of traditional CL, which only focuses on previously encountered classes. During the CL of VLMs, we need not only to prevent the catastrophic forgetting on incrementally learned knowledge but also to preserve the zero-shot ability of VLMs. However, existing methods require additional reference datasets to maintain such zero-shot ability and rely on domain-identity hints to classify images across different domains. In this study, we propose Regression-based Analytic Incremental Learning (RAIL), which utilizes a recursive ridge regression-based adapter to learn from a sequence of domains in a non-forgetting manner and decouple the cross-domain correlations by projecting features to a higher-dimensional space. Cooperating with a training-free fusion module, RAIL absolutely preserves the VLM's zero-shot ability on unseen domains without any reference data. Additionally, we introduce Cross-domain Task-Agnostic Incremental Learning (X-TAIL) setting. In this setting, a CL learner is required to incrementally learn from multiple domains and classify test images from both seen and unseen domains without any domain-identity hint. We theoretically prove RAIL's absolute memorization on incrementally learned domains. Experiment results affirm RAIL's state-of-the-art performance in both X-TAIL and existing Multi-domain Task-Incremental Learning settings. The code is released at https://github.com/linghan1997/Regression-based-Analytic-Incremental-Learning.

Shaoning Li, Yusong Wang, Mingyu Li et al.

Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency, emerging enhanced sampling approaches like coarse-graining (CG) and generative models have been employed. In this work, we propose a \underline{Frame-to-Frame} generative model with guided \underline{Flow}-matching (F$3$low) for enhanced sampling, which (a) extends the domain of CG modeling to the SE(3) Riemannian manifold; (b) retreating CGMD simulations as autoregressively sampling guided by the former frame via flow-matching models; (c) targets the protein backbone, offering improved insights into secondary structure formation and intricate folding pathways. Compared to previous methods, F$3$low allows for broader exploration of conformational space. The ability to rapidly generate diverse conformations via force-free generative paradigm on SE(3) paves the way toward efficient enhanced sampling methods.

Siyuan Liu, Yusong Wang, Tong Wang et al.

The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based approaches achieved better performance than molecular docking, existing models often neglect certain aspects of the intermolecular information, hindering the performance of prediction. We recognize this problem and propose a novel approach named Intermolecular Graph Transformer (IGT) that employs a dedicated attention mechanism to model intermolecular information with a three-way Transformer-based architecture. IGT outperforms state-of-the-art approaches by 9.1% and 20.5% over the second best for binding activity and binding pose prediction respectively, and shows superior generalization ability to unseen receptor proteins. Furthermore, IGT exhibits promising drug screening ability against SARS-CoV-2 by identifying 83.1% active drugs that have been validated by wet-lab experiments with near-native predicted binding poses.