Si Wu

Liang Peng, Haopeng Liu, Yixuan Ye et al.

Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic cellular structure and ignore the pivotal role of cell-gene associations, which limits their ability to distinguish closely related cell types. To this end, we propose a Refinement Contrastive Learning framework (scRCL) that explicitly incorporates cell-gene interactions to derive more informative representations. Specifically, we introduce two contrastive distribution alignment components that reveal reliable intrinsic cellular structures by effectively exploiting cell-cell structural relationships. Additionally, we develop a refinement module that integrates gene-correlation structure learning to enhance cell embeddings by capturing underlying cell-gene associations. This module strengthens connections between cells and their associated genes, refining the representation learning to exploiting biologically meaningful relationships. Extensive experiments on several single-cell RNA-seq and spatial transcriptomics benchmark datasets demonstrate that our method consistently outperforms state-of-the-art baselines in cell-type identification accuracy. Moreover, downstream biological analyses confirm that the recovered cell populations exhibit coherent gene-expression signatures, further validating the biological relevance of our approach. The code is available at https://github.com/THPengL/scRCL.

Rui Li, Qianfen Jiao, Wenming Cao et al.

In this paper, we investigate a challenging unsupervised domain adaptation setting -- unsupervised model adaptation. We aim to explore how to rely only on unlabeled target data to improve performance of an existing source prediction model on the target domain, since labeled source data may not be available in some real-world scenarios due to data privacy issues. For this purpose, we propose a new framework, which is referred to as collaborative class conditional generative adversarial net to bypass the dependence on the source data. Specifically, the prediction model is to be improved through generated target-style data, which provides more accurate guidance for the generator. As a result, the generator and the prediction model can collaborate with each other without source data. Furthermore, due to the lack of supervision from source data, we propose a weight constraint that encourages similarity to the source model. A clustering-based regularization is also introduced to produce more discriminative features in the target domain. Compared to conventional domain adaptation methods, our model achieves superior performance on multiple adaptation tasks with only unlabeled target data, which verifies its effectiveness in this challenging setting.

Si Wu, John Wieting, David A. Smith

While a source sentence can be translated in many ways, most machine translation (MT) models are trained with only a single reference. Previous work has shown that using synthetic paraphrases can improve MT. This paper investigates best practices for employing multiple references by analyzing the semantic similarity among different English translations of world literature in the Par3 dataset. We classify the semantic similarity between paraphrases into three levels: low, medium, and high, and fine-tune three different models (mT5-large, LLaMA-2-7B, and Opus-MT) for literary MT tasks. Across different models, holding the total training instances constant, single-reference but more source texts only marginally outperforms multiple-reference with half of the source texts. Moreover, when fine-tuning an LLM, using paraphrases with medium and high semantic similarity outperforms an unfiltered dataset, with improvements in BLEU (0.3-0.5), COMET (0.1-0.9), and chrF++ (0.17-0.32). Our code is publicly available on GitHub.

Si Wu, Sebastian Bruch

Imageability (potential of text to evoke a mental image) and concreteness (perceptibility of text) are two psycholinguistic properties that link visual and semantic spaces. It is little surprise that computational methods that estimate them do so using parallel visual and semantic spaces, such as collections of image-caption pairs or multi-modal models. In this paper, we work on the supposition that text itself in an image-caption dataset offers sufficient signals to accurately estimate these properties. We hypothesize, in particular, that the peakedness of the neighborhood of a word in the semantic embedding space reflects its degree of imageability and concreteness. We then propose an unsupervised, distribution-free measure, which we call Neighborhood Stability Measure (NSM), that quantifies the sharpness of peaks. Extensive experiments show that NSM correlates more strongly with ground-truth ratings than existing unsupervised methods, and is a strong predictor of these properties for classification. Our code and data are available on GitHub (https://github.com/Artificial-Memory-Lab/imageability).

Yao Lu, Si Wu

The brain is targeted for processing temporal sequence information. It remains largely unclear how the brain learns to store and retrieve sequence memories. Here, we study how recurrent networks of binary neurons learn sequence attractors to store predefined pattern sequences and retrieve them robustly. We show that to store arbitrary pattern sequences, it is necessary for the network to include hidden neurons even though their role in displaying sequence memories is indirect. We develop a local learning algorithm to learn sequence attractors in the networks with hidden neurons. The algorithm is proven to converge and lead to sequence attractors. We demonstrate that the network model can store and retrieve sequences robustly on synthetic and real-world datasets. We hope that this study provides new insights in understanding sequence memory and temporal information processing in the brain.

Xingsi Dong, Xiangyuan Peng, Si Wu

Predictive models are highly advanced in understanding the mechanisms of brain function. Recent advances in machine learning further underscore the power of prediction for optimal representation in learning. However, there remains a gap in creating a biologically plausible model that explains how the neural system achieves prediction. In this paper, we introduce a framework that employs an energy-based model (EBM) to capture the nuanced processes of predicting observation after action within the neural system, encompassing prediction, learning, and inference. We implement the EBM with a hierarchical structure and integrate a continuous attractor neural network for memory, constructing a biologically plausible model. In experimental evaluations, our model demonstrates efficacy across diverse scenarios. The range of actions includes eye movement, motion in environments, head turning, and static observation while the environment changes. Our model not only makes accurate predictions for environments it was trained on, but also provides reasonable predictions for unseen environments, matching the performances of machine learning methods in multiple tasks. We hope that this study contributes to a deep understanding of how the neural system performs prediction.