MERGE: Multi-faceted Hierarchical Graph-based GNN for Gene Expression Prediction from Whole Slide Histopathology Images

Recent advances in Spatial Transcriptomics (ST) pair histology images with spatially resolved gene expression profiles, enabling predictions of gene expression across different tissue locations based on image patches. This opens up new possibilities for enhancing whole slide image (WSI) prediction tasks with localized gene expression. However, existing methods fail to fully leverage the interactions between different tissue locations, which are crucial for accurate joint prediction. To address this, we introduce MERGE (Multi-faceted hiErarchical gRaph for Gene Expressions), which combines a multi-faceted hierarchical graph construction strategy with graph neural networks (GNN) to improve gene expression predictions from WSIs. By clustering tissue image patches based on both spatial and morphological features, and incorporating intra- and inter-cluster edges, our approach fosters interactions between distant tissue locations during GNN learning. As an additional contribution, we evaluate different data smoothing techniques that are necessary to mitigate artifacts in ST data, often caused by technical imperfections. We advocate for adopting gene-aware smoothing methods that are more biologically justified. Experimental results on gene expression prediction show that our GNN method outperforms state-of-the-art techniques across multiple metrics.

RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses challenges due to inherent spatial distortions and modality-specific variations. Existing methods largely rely on direct alignment, which often fails to capture complex cross-modal relationships. To address these limitations, we propose a novel framework that aligns gene and image features using a ranking-based alignment loss, preserving relative similarity across modalities and enabling robust multi-scale alignment. To further enhance the alignment's stability, we employ self-supervised knowledge distillation with a teacher-student network architecture, effectively mitigating disruptions from high dimensionality, sparsity, and noise in gene expression data. Extensive experiments on gene expression prediction and survival analysis demonstrate our framework's effectiveness, showing improved alignment and predictive performance over existing methods and establishing a robust tool for gene-guided image representation learning in digital pathology.

A Simple Yet Effective Corpus Construction Framework for Indonesian Grammatical Error Correction

Currently, the majority of research in grammatical error correction (GEC) is concentrated on universal languages, such as English and Chinese. Many low-resource languages lack accessible evaluation corpora. How to efficiently construct high-quality evaluation corpora for GEC in low-resource languages has become a significant challenge. To fill these gaps, in this paper, we present a framework for constructing GEC corpora. Specifically, we focus on Indonesian as our research language and construct an evaluation corpus for Indonesian GEC using the proposed framework, addressing the limitations of existing evaluation corpora in Indonesian. Furthermore, we investigate the feasibility of utilizing existing large language models (LLMs), such as GPT-3.5-Turbo and GPT-4, to streamline corpus annotation efforts in GEC tasks. The results demonstrate significant potential for enhancing the performance of LLMs in low-resource language settings. Our code and corpus can be obtained from https://github.com/GKLMIP/GEC-Construction-Framework.

Hard Negative Sample Mining for Whole Slide Image Classification

Weakly supervised whole slide image (WSI) classification is challenging due to the lack of patch-level labels and high computational costs. State-of-the-art methods use self-supervised patch-wise feature representations for multiple instance learning (MIL). Recently, methods have been proposed to fine-tune the feature representation on the downstream task using pseudo labeling, but mostly focusing on selecting high-quality positive patches. In this paper, we propose to mine hard negative samples during fine-tuning. This allows us to obtain better feature representations and reduce the training cost. Furthermore, we propose a novel patch-wise ranking loss in MIL to better exploit these hard negative samples. Experiments on two public datasets demonstrate the efficacy of these proposed ideas. Our codes are available at https://github.com/winston52/HNM-WSI

Convergence Analysis of Deep Residual Networks

Various powerful deep neural network architectures have made great contribution to the exciting successes of deep learning in the past two decades. Among them, deep Residual Networks (ResNets) are of particular importance because they demonstrated great usefulness in computer vision by winning the first place in many deep learning competitions. Also, ResNets were the first class of neural networks in the development history of deep learning that are really deep. It is of mathematical interest and practical meaning to understand the convergence of deep ResNets. We aim at characterizing the convergence of deep ResNets as the depth tends to infinity in terms of the parameters of the networks. Toward this purpose, we first give a matrix-vector description of general deep neural networks with shortcut connections and formulate an explicit expression for the networks by using the notions of activation domains and activation matrices. The convergence is then reduced to the convergence of two series involving infinite products of non-square matrices. By studying the two series, we establish a sufficient condition for pointwise convergence of ResNets. Our result is able to give justification for the design of ResNets. We also conduct experiments on benchmark machine learning data to verify our results.

Convergence of Deep Neural Networks with General Activation Functions and Pooling

Deep neural networks, as a powerful system to represent high dimensional complex functions, play a key role in deep learning. Convergence of deep neural networks is a fundamental issue in building the mathematical foundation for deep learning. We investigated the convergence of deep ReLU networks and deep convolutional neural networks in two recent researches (arXiv:2107.12530, 2109.13542). Only the Rectified Linear Unit (ReLU) activation was studied therein, and the important pooling strategy was not considered. In this current work, we study the convergence of deep neural networks as the depth tends to infinity for two other important activation functions: the leaky ReLU and the sigmoid function. Pooling will also be studied. As a result, we prove that the sufficient condition established in arXiv:2107.12530, 2109.13542 is still sufficient for the leaky ReLU networks. For contractive activation functions such as the sigmoid function, we establish a weaker sufficient condition for uniform convergence of deep neural networks.

Exploring Multi-dimensional Data via Subset Embedding

Multi-dimensional data exploration is a classic research topic in visualization. Most existing approaches are designed for identifying record patterns in dimensional space or subspace. In this paper, we propose a visual analytics approach to exploring subset patterns. The core of the approach is a subset embedding network (SEN) that represents a group of subsets as uniformly-formatted embeddings. We implement the SEN as multiple subnets with separate loss functions. The design enables to handle arbitrary subsets and capture the similarity of subsets on single features, thus achieving accurate pattern exploration, which in most cases is searching for subsets having similar values on few features. Moreover, each subnet is a fully-connected neural network with one hidden layer. The simple structure brings high training efficiency. We integrate the SEN into a visualization system that achieves a 3-step workflow. Specifically, analysts (1) partition the given dataset into subsets, (2) select portions in a projected latent space created using the SEN, and (3) determine the existence of patterns within selected subsets. Generally, the system combines visualizations, interactions, automatic methods, and quantitative measures to balance the exploration flexibility and operation efficiency, and improve the interpretability and faithfulness of the identified patterns. Case studies and quantitative experiments on multiple open datasets demonstrate the general applicability and effectiveness of our approach.

Information-Theoretic Bounds and Approximations in Neural Population Coding

While Shannon's mutual information has widespread applications in many disciplines, for practical applications it is often difficult to calculate its value accurately for high-dimensional variables because of the curse of dimensionality. This paper is focused on effective approximation methods for evaluating mutual information in the context of neural population coding. For large but finite neural populations, we derive several information-theoretic asymptotic bounds and approximation formulas that remain valid in high-dimensional spaces. We prove that optimizing the population density distribution based on these approximation formulas is a convex optimization problem which allows efficient numerical solutions. Numerical simulation results confirmed that our asymptotic formulas were highly accurate for approximating mutual information for large neural populations. In special cases, the approximation formulas are exactly equal to the true mutual information. We also discuss techniques of variable transformation and dimensionality reduction to facilitate computation of the approximations.

An Information-Theoretic Framework for Fast and Robust Unsupervised Learning via Neural Population Infomax

A framework is presented for unsupervised learning of representations based on infomax principle for large-scale neural populations. We use an asymptotic approximation to the Shannon's mutual information for a large neural population to demonstrate that a good initial approximation to the global information-theoretic optimum can be obtained by a hierarchical infomax method. Starting from the initial solution, an efficient algorithm based on gradient descent of the final objective function is proposed to learn representations from the input datasets, and the method works for complete, overcomplete, and undercomplete bases. As confirmed by numerical experiments, our method is robust and highly efficient for extracting salient features from input datasets. Compared with the main existing methods, our algorithm has a distinct advantage in both the training speed and the robustness of unsupervised representation learning. Furthermore, the proposed method is easily extended to the supervised or unsupervised model for training deep structure networks.

Information-theoretic interpretation of tuning curves for multiple motion directions

We have developed an efficient information-maximization method for computing the optimal shapes of tuning curves of sensory neurons by optimizing the parameters of the underlying feedforward network model. When applied to the problem of population coding of visual motion with multiple directions, our method yields several types of tuning curves with both symmetric and asymmetric shapes that resemble what have been found in the visual cortex. Our result suggests that the diversity or heterogeneity of tuning curve shapes as observed in neurophysiological experiment might actually constitute an optimal population representation of visual motions with multiple components.