arXiv subjects

Tianle Ma

Publications and source records attributed to Tianle Ma.

7 recordsLinked to original sources

arXiv2026

Experimentally-validated multi-slice simulation of electron diffraction patterns

High-Resolution Electron Backscatter Diffraction (HR-EBSD) has advanced rapidly in recent years, significantly improving elastic strain measurements and dislocation density evaluation with submicron spatial resolution. To achieve better accuracy in the measurements, high-quality dynamical simulation patterns are required to be matched with experimental ones. Currently, the most widely used pattern simulation method, the Bloch Wave method (BW), can accurately predict the positions and brightness of Kikuchi poles and bands, but is intrinsically limited to perfect crystal structures. Another simulation scheme, the multi-slice method (MS), follows the evolution of electron waves as they travel through the sample. MS is advantageous in simulating various defect structures with more diffraction details. Yet, it is mainly considered for theoretical developments and has not been compared to experimental data. This paper optimizes the MS method by abandoning the high-energy hypothesis and utilizing higher-order Taylor expansions to approach the forward-only Schrodinger equation. Experimental EBSD patterns of polycrystal Al-Mg alloys are used to challenge MS simulations as a reference for indexation. It is demonstrated that the 5th-order expansion of MS, referred to as MS5, achieves a good balance between computational cost and pattern precision. A tailored isotropic distortion correction model and standard stereographic triangle reconstruction enhance the precision of MS5 to be comparable with BW. To the best of our knowledge, this study provides the first comparison of MS EBSD simulations with experimental data. It opens new possibilities for EBSD characterization, such as reproducing diffraction patterns of crystals with various defects.

cond-mat.mtrl-sci↗

arXiv2024

A Two-Phase Visualization System for Continuous Human-AI Collaboration in Sequelae Analysis and Modeling

In healthcare, AI techniques are widely used for tasks like risk assessment and anomaly detection. Despite AI's potential as a valuable assistant, its role in complex medical data analysis often oversimplifies human-AI collaboration dynamics. To address this, we collaborated with a local hospital, engaging six physicians and one data scientist in a formative study. From this collaboration, we propose a framework integrating two-phase interactive visualization systems: one for Human-Led, AI-Assisted Retrospective Analysis and another for AI-Mediated, Human-Reviewed Iterative Modeling. This framework aims to enhance understanding and discussion around effective human-AI collaboration in healthcare.

cs.HC↗

arXiv2019

Incorporating Biological Knowledge with Factor Graph Neural Network for Interpretable Deep Learning

While deep learning has achieved great success in many fields, one common criticism about deep learning is its lack of interpretability. In most cases, the hidden units in a deep neural network do not have a clear semantic meaning or correspond to any physical entities. However, model interpretability and explainability are crucial in many biomedical applications. To address this challenge, we developed the Factor Graph Neural Network model that is interpretable and predictable by combining probabilistic graphical models with deep learning. We directly encode biological knowledge such as Gene Ontology as a factor graph into the model architecture, making the model transparent and interpretable. Furthermore, we devised an attention mechanism that can capture multi-scale hierarchical interactions among biological entities such as genes and Gene Ontology terms. With parameter sharing mechanism, the unrolled Factor Graph Neural Network model can be trained with stochastic depth and generalize well. We applied our model to two cancer genomic datasets to predict target clinical variables and achieved better results than other traditional machine learning and deep learning models. Our model can also be used for gene set enrichment analysis and selecting Gene Ontology terms that are important to target clinical variables.

q-bio.GN↗

arXiv2018

Multi-view Factorization AutoEncoder with Network Constraints for Multi-omic Integrative Analysis

Multi-omic data provides multiple views of the same patients. Integrative analysis of multi-omic data is crucial to elucidate the molecular underpinning of disease etiology. However, multi-omic data has the "big p, small N" problem (the number of features is large, but the number of samples is small), it is challenging to train a complicated machine learning model from the multi-omic data alone and make it generalize well. Here we propose a framework termed Multi-view Factorization AutoEncoder with network constraints to integrate multi-omic data with domain knowledge (biological interactions networks). Our framework employs deep representation learning to learn feature embeddings and patient embeddings simultaneously, enabling us to integrate feature interaction network and patient view similarity network constraints into the training objective. The whole framework is end-to-end differentiable. We applied our approach to the TCGA Pan-cancer dataset and achieved satisfactory results to predict disease progression-free interval (PFI) and patient overall survival (OS) events. Code will be made publicly available.

cs.LG↗

arXiv2018

AffinityNet: semi-supervised few-shot learning for disease type prediction

While deep learning has achieved great success in computer vision and many other fields, currently it does not work very well on patient genomic data with the "big p, small N" problem (i.e., a relatively small number of samples with high-dimensional features). In order to make deep learning work with a small amount of training data, we have to design new models that facilitate few-shot learning. Here we present the Affinity Network Model (AffinityNet), a data efficient deep learning model that can learn from a limited number of training examples and generalize well. The backbone of the AffinityNet model consists of stacked k-Nearest-Neighbor (kNN) attention pooling layers. The kNN attention pooling layer is a generalization of the Graph Attention Model (GAM), and can be applied to not only graphs but also any set of objects regardless of whether a graph is given or not. As a new deep learning module, kNN attention pooling layers can be plugged into any neural network model just like convolutional layers. As a simple special case of kNN attention pooling layer, feature attention layer can directly select important features that are useful for classification tasks. Experiments on both synthetic data and cancer genomic data from TCGA projects show that our AffinityNet model has better generalization power than conventional neural network models with little training data. The code is freely available at https://github.com/BeautyOfWeb/AffinityNet .

cs.LG↗

arXiv2018

Affinity Network Fusion and Semi-supervised Learning for Cancer Patient Clustering

Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate multi-omic data are more advantageous to those using only one data type for patient clustering and disease subtype discovery. However, it is challenging to integrate multi-omic data as they are heterogeneous and noisy. In this paper, we present Affinity Network Fusion (ANF) to integrate multi-omic data for patient clustering. ANF first constructs patient affinity networks for each omic data type, and then calculates a fused network for spectral clustering. We applied ANF to a processed harmonized cancer dataset downloaded from GDC data portal consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Moreover, we developed a semi-supervised model combining ANF and neural network for few-shot learning. In several cases, the model can achieve greater than 90% acccuracy on test set with training less than 1% of the data. This demonstrates the power of ANF in learning a good representation of patients, and shows the great potential of semi-supervised learning in cancer patient clustering.

q-bio.QM↗

arXiv2017

Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering

Clustering cancer patients into subgroups and identifying cancer subtypes is an important task in cancer genomics. Clustering based on comprehensive multi-omic molecular profiling can often achieve better results than those using a single data type, since each omic data type (representing one view of patients) may contain complementary information. However, it is challenging to integrate heterogeneous omic data types directly. Based on one popular method -- Similarity Network Fusion (SNF), we presented Affinity Network Fusion (ANF) in this paper, an "upgrade" of SNF with several advantages. Similar to SNF, ANF treats each omic data type as one view of patients and learns a fused affinity (transition) matrix for clustering. We applied ANF to a carefully processed harmonized cancer dataset downloaded from GDC data portals consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Our experimental results also demonstrated the power of feature selection and transformation combined with using ANF in patient clustering. Moreover, eigengap analysis suggests that the learned affinity matrices of four cancer types using our proposed framework may have successfully captured patient group structure and can be used for discovering unknown cancer subtypes.

q-bio.GN↗