Xinyi Xu

Kelly Payette, Hongwei Li, Priscille de Dumast et al.

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

Xinyi Xu, Zhengyang Wang, Cheng Deng et al.

Grouping has been commonly used in deep metric learning for computing diverse features. However, current methods are prone to overfitting and lack interpretability. In this work, we propose an improved and interpretable grouping method to be integrated flexibly with any metric learning framework. Our method is based on the attention mechanism with a learnable query for each group. The query is fully trainable and can capture group-specific information when combined with the diversity loss. An appealing property of our method is that it naturally lends itself interpretability. The attention scores between the learnable query and each spatial position can be interpreted as the importance of that position. We formally show that our proposed grouping method is invariant to spatial permutations of features. When used as a module in convolutional neural networks, our method leads to translational invariance. We conduct comprehensive experiments to evaluate our method. Our quantitative results indicate that the proposed method outperforms prior methods consistently and significantly across different datasets, evaluation metrics, base models, and loss functions. For the first time to the best of our knowledge, our interpretation results clearly demonstrate that the proposed method enables the learning of distinct and diverse features across groups. The code is available on https://github.com/XinyiXuXD/DGML-master.

Zijian Zhou, Xiaoqiang Lin, Xinyi Xu et al.

In-context learning (ICL) allows transformer-based language models that are pre-trained on general text to quickly learn a specific task with a few "task demonstrations" without updating their parameters, significantly boosting their flexibility and generality. ICL possesses many distinct characteristics from conventional machine learning, thereby requiring new approaches to interpret this learning paradigm. Taking the viewpoint of recent works showing that transformers learn in context by formulating an internal optimizer, we propose an influence function-based attribution technique, DETAIL, that addresses the specific characteristics of ICL. We empirically verify the effectiveness of our approach for demonstration attribution while being computationally efficient. Leveraging the results, we then show how DETAIL can help improve model performance in real-world scenarios through demonstration reordering and curation. Finally, we experimentally prove the wide applicability of DETAIL by showing our attribution scores obtained on white-box models are transferable to black-box models in improving model performance.

Zijian Zhou, Xinyi Xu, Daniela Rus et al.

For gradient-based machine learning (ML) methods commonly adopted in practice such as stochastic gradient descent, the de facto differential privacy (DP) technique is perturbing the gradients with random Gaussian noise. Data valuation attributes the ML performance to the training data and is widely used in privacy-aware applications that require enforcing DP such as data pricing, collaborative ML, and federated learning (FL). Can existing data valuation methods still be used when DP is enforced via gradient perturbations? We show that the answer is no with the default approach of injecting i.i.d.~random noise to the gradients because the estimation uncertainty of the data value estimation paradoxically linearly scales with more estimation budget, producing estimates almost like random guesses. To address this issue, we propose to instead inject carefully correlated noise to provably remove the linear scaling of estimation uncertainty w.r.t.~the budget. We also empirically demonstrate that our method gives better data value estimates on various ML tasks and is applicable to use cases including dataset valuation and~FL.

Xiaoliang Luo, Xinyi Xu, Michael Ramscar et al.

Can autoregressive large language models (LLMs) learn consistent probability distributions when trained on sequences in different token orders? We prove formally that for any well-defined probability distribution, sequence perplexity is invariant under any factorization, including forward, backward, or arbitrary permutations. This result establishes a rigorous theoretical foundation for studying how LLMs learn from data and defines principled protocols for empirical evaluation. Applying these protocols, we show that prior studies examining ordering effects suffer from critical methodological flaws. We retrain GPT-2 models across forward, backward, and arbitrary permuted orders on scientific text. We find systematic deviations from theoretical invariance across all orderings with arbitrary permutations strongly deviating from both forward and backward models, which largely (but not completely) agreed with one another. Deviations were traceable to differences in self-attention, reflecting positional and locality biases in processing. Our theoretical and empirical results provide novel avenues for understanding positional biases in LLMs and suggest methods for detecting when LLMs' probability distributions are inconsistent and therefore untrustworthy.

Zhao Xu, Yaochen Xie, Youzhi Luo et al.

Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to computing ground-state 3D molecular geometries from 2D graphs is lacking. Here, we propose a novel deep learning framework to predict 3D geometries from molecular graphs. To this end, we develop an equilibrium message passing neural network (EMPNN) to better capture ground-state geometries from molecular graphs. To provide a testbed for 3D molecular geometry analysis, we develop a benchmark that includes a large-scale molecular geometry dataset, data splits, and evaluation protocols. Experimental results show that EMPNN can efficiently predict more accurate ground-state 3D geometries than RDKit and other deep learning methods. Results also show that the proposed framework outperforms self-supervised learning methods on property prediction tasks.

Sebastian Shenghong Tay, Xinyi Xu, Chuan Sheng Foo et al.

This paper presents a novel collaborative generative modeling (CGM) framework that incentivizes collaboration among self-interested parties to contribute data to a pool for training a generative model (e.g., GAN), from which synthetic data are drawn and distributed to the parties as rewards commensurate to their contributions. Distributing synthetic data as rewards (instead of trained models or money) offers task- and model-agnostic benefits for downstream learning tasks and is less likely to violate data privacy regulation. To realize the framework, we firstly propose a data valuation function using maximum mean discrepancy (MMD) that values data based on its quantity and quality in terms of its closeness to the true data distribution and provide theoretical results guiding the kernel choice in our MMD-based data valuation function. Then, we formulate the reward scheme as a linear optimization problem that when solved, guarantees certain incentives such as fairness in the CGM framework. We devise a weighted sampling algorithm for generating synthetic data to be distributed to each party as reward such that the value of its data and the synthetic data combined matches its assigned reward value by the reward scheme. We empirically show using simulated and real-world datasets that the parties' synthetic data rewards are commensurate to their contributions.

Xinyi Xu, Cheng Deng, Yaochen Xie et al.

We study self-supervised learning on graphs using contrastive methods. A general scheme of prior methods is to optimize two-view representations of input graphs. In many studies, a single graph-level representation is computed as one of the contrastive objectives, capturing limited characteristics of graphs. We argue that contrasting graphs in multiple subspaces enables graph encoders to capture more abundant characteristics. To this end, we propose a group contrastive learning framework in this work. Our framework embeds the given graph into multiple subspaces, of which each representation is prompted to encode specific characteristics of graphs. To learn diverse and informative representations, we develop principled objectives that enable us to capture the relations among both intra-space and inter-space representations in groups. Under the proposed framework, we further develop an attention-based representor function to compute representations that capture different substructures of a given graph. Built upon our framework, we extend two current methods into GroupCL and GroupIG, equipped with the proposed objective. Comprehensive experimental results show our framework achieves a promising boost in performance on a variety of datasets. In addition, our qualitative results show that features generated from our representor successfully capture various specific characteristics of graphs.