Jiaxi Wang

Shuxin Zheng, Jiyan He, Chang Liu et al. · microsoft-research

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather determined from the equilibrium distribution of structures. Traditional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. In this paper, we introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system, such as a chemical graph or a protein sequence. This framework enables efficient generation of diverse conformations and provides estimations of state densities. We demonstrate the performance of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst-adsorbate sampling, and property-guided structure generation. DiG presents a significant advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in molecular science.

Jiaxi Wang, Ji Wu, Lei Huang

Batch Normalization (BN) is a core and prevalent technique in accelerating the training of deep neural networks and improving the generalization on Computer Vision (CV) tasks. However, it fails to defend its position in Natural Language Processing (NLP), which is dominated by Layer Normalization (LN). In this paper, we are trying to answer why BN usually performs worse than LN in NLP tasks with Transformer models. We find that the inconsistency between training and inference of BN is the leading cause that results in the failure of BN in NLP. We define Training Inference Discrepancy (TID) to quantitatively measure this inconsistency and reveal that TID can indicate BN's performance, supported by extensive experiments, including image classification, neural machine translation, language modeling, sequence labeling, and text classification tasks. We find that BN can obtain much better test performance than LN when TID keeps small through training. To suppress the explosion of TID, we propose Regularized BN (RBN) that adds a simple regularization term to narrow the gap between batch statistics and population statistics of BN. RBN improves the performance of BN consistently and outperforms or is on par with LN on 17 out of 20 settings, involving ten datasets and two common variants of Transformer Our code is available at https://github.com/wjxts/RegularizedBN.

Xun Zhu, Fanbin Mo, Zheng Zhang et al.

The emergence of medical generalist foundation models has revolutionized conventional task-specific model development paradigms, aiming to better handle multiple tasks through joint training on large-scale medical datasets. However, recent advances prioritize simple data scaling or architectural component enhancement, while neglecting to re-examine multi-task learning from a data-centric perspective. Critically, simply aggregating existing data resources leads to decentralized image-task alignment, which fails to cultivate comprehensive image understanding or align with clinical needs for multi-dimensional image interpretation. In this paper, we introduce the image-centric multi-annotation X-ray dataset (IMAX), the first attempt to enhance the multi-task learning capabilities of medical multi-modal large language models (MLLMs) from the data construction level. To be specific, IMAX is featured from the following attributes: 1) High-quality data curation. A comprehensive collection of more than 354K entries applicable to seven different medical tasks. 2) Image-centric dense annotation. Each X-ray image is associated with an average of 4.10 tasks and 7.46 training entries, ensuring multi-task representation richness per image. Compared to the general decentralized multi-annotation X-ray dataset (DMAX), IMAX consistently demonstrates significant multi-task average performance gains ranging from 3.20% to 21.05% across seven open-source state-of-the-art medical MLLMs. Moreover, we investigate differences in statistical patterns exhibited by IMAX and DMAX training processes, exploring potential correlations between optimization dynamics and multi-task performance. Finally, leveraging the core concept of IMAX data construction, we propose an optimized DMAX-based training strategy to alleviate the dilemma of obtaining high-quality IMAX data in practical scenarios.

Jiaxi Wang, Wenhui Hu, Xueyang Liu et al.

Visual grounding aims to align visual information of specific regions of images with corresponding natural language expressions. Current visual grounding methods leverage pre-trained visual and language backbones independently to obtain visual features and linguistic features. Although these two types of features are then fused through elaborately designed networks, the heterogeneity of the features renders them unsuitable for multi-modal reasoning. This problem arises from the domain gap between the single-modal pre-training backbones used in current visual grounding methods, which can hardly be bridged by the traditional end-to-end training method. To alleviate this, our work proposes an Empowering Pre-trained Model for Visual Grounding (EpmVG) framework, which distills a multimodal pre-trained model to guide the visual grounding task. EpmVG relies on a novel cross-modal distillation mechanism that can effectively introduce the consistency information of images and texts from the pre-trained model, reducing the domain gap in the backbone networks, and thereby improving the performance of the model in the visual grounding task. Extensive experiments have been conducted on five conventionally used datasets, and the results demonstrate that our method achieves better performance than state-of-the-art methods.

Jiaxi Wang, Yaosen Min, Xun Zhu et al.

Polymers, composed of repeating structural units called monomers, are fundamental materials in daily life and industry. Accurate property prediction for polymers is essential for their design, development, and application. However, existing modeling approaches, which typically represent polymers by the constituent monomers, struggle to capture the whole properties of polymer, since the properties change during the polymerization process. In this study, we propose a Multimodal Infinite Polymer Sequence (MIPS) pre-training framework, which represents polymers as infinite sequences of monomers and integrates both topological and spatial information for comprehensive modeling. From the topological perspective, we generalize message passing mechanism (MPM) and graph attention mechanism (GAM) to infinite polymer sequences. For MPM, we demonstrate that applying MPM to infinite polymer sequences is equivalent to applying MPM on the induced star-linking graph of monomers. For GAM, we propose to further replace global graph attention with localized graph attention (LGA). Moreover, we show the robustness of the "star linking" strategy through Repeat and Shift Invariance Test (RSIT). Despite its robustness, "star linking" strategy exhibits limitations when monomer side chains contain ring structures, a common characteristic of polymers, as it fails the Weisfeiler-Lehman~(WL) test. To overcome this issue, we propose backbone embedding to enhance the capability of MPM and LGA on infinite polymer sequences. From the spatial perspective, we extract 3D descriptors of repeating monomers to capture spatial information. Finally, we design a cross-modal fusion mechanism to unify the topological and spatial information. Experimental validation across eight diverse polymer property prediction tasks reveals that MIPS achieves state-of-the-art performance.

Jiaxi Wang, Karel Mundnich, Allison T. Knoll et al.

Mice vocalize in the ultrasonic range during social interactions. These vocalizations are used in neuroscience and clinical studies to tap into complex behaviors and states. The analysis of these ultrasonic vocalizations (USVs) has been traditionally a manual process, which is prone to errors and human bias, and is not scalable to large scale analysis. We propose a new method to automatically create a dictionary of USVs based on a two-step spectral clustering approach, where we split the set of USVs into inlier and outlier data sets. This approach is motivated by the known degrading performance of sparse subspace clustering with outliers. We apply spectral clustering to the inlier data set and later find the clusters for the outliers. We propose quantitative and qualitative performance measures to evaluate our method in this setting, where there is no ground truth. Our approach outperforms two baselines based on k-means and spectral clustering in all of the proposed performance measures, showing greater distances between clusters and more variability between clusters.