Multilabel Feature Selection: A Local Causal Structure Learning Approach

ML-FGAT: Identification of multi-label protein subcellular localization by interpretable graph attention networks and feature-generative adversarial networks

The prediction of multi-label protein subcellular localization (SCL) is a pivotal area in bioinformatics research. Recent advancements in protein structure research have facilitated the application of graph neural networks. This paper introduces a novel approach termed ML-FGAT. The approach begins by extracting node information of proteins from sequence data, physical-chemical properties, evolutionary insights, and structural details. Subsequently, various evolutionary techniques are integrated to consolidate multi-view information. A linear discriminant analysis framework, grounded on entropy weight, is then employed to reduce the dimensionality of the merged features. To enhance the robustness of the model, the training dataset is augmented using feature-generative adversarial networks. For the primary prediction step, graph attention networks are employed to determine multi-label protein SCL, leveraging both node and neighboring information. The interpretability is enhanced by analyzing the attention weight parameters. The training is based on the Gram-positive bacteria dataset, while validation employs newly constructed datasets: human, virus, Gram-negative bacteria, plant, and SARS-CoV-2. Following a leave-one-out cross-validation procedure, ML-FGAT demonstrates noteworthy superiority in this domain.

Causal Reasoning Meets Visual Representation Learning: A Prospective Study

Visual representation learning is ubiquitous in various real-world applications, including visual comprehension, video understanding, multi-modal analysis, human-computer interaction, and urban computing. Due to the emergence of huge amounts of multimodal heterogeneous spatial/temporal/spatial-temporal data in the big data era, the lack of interpretability, robustness, and out-of-distribution generalization are becoming the challenges of the existing visual models. The majority of the existing methods tend to fit the original data/variable distributions and ignore the essential causal relations behind the multi-modal knowledge, which lacks unified guidance and analysis about why modern visual representation learning methods easily collapse into data bias and have limited generalization and cognitive abilities. Inspired by the strong inference ability of human-level agents, recent years have therefore witnessed great effort in developing causal reasoning paradigms to realize robust representation and model learning with good cognitive ability. In this paper, we conduct a comprehensive review of existing causal reasoning methods for visual representation learning, covering fundamental theories, models, and datasets. The limitations of current methods and datasets are also discussed. Moreover, we propose some prospective challenges, opportunities, and future research directions for benchmarking causal reasoning algorithms in visual representation learning. This paper aims to provide a comprehensive overview of this emerging field, attract attention, encourage discussions, bring to the forefront the urgency of developing novel causal reasoning methods, publicly available benchmarks, and consensus-building standards for reliable visual representation learning and related real-world applications more efficiently.