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Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Large Language Models (LLMs) have become a cornerstone in Natural Language Processing (NLP), achieving impressive performance in text generation. Their token-level representations capture rich, human-aligned semantics. However, pooling…

Interpretable machine learning has exploded as an area of interest over the last decade, sparked by the rise of increasingly large datasets and deep neural networks. Simultaneously, large language models (LLMs) have demonstrated remarkable…

Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual…

This paper introduces VLAP, a novel approach that bridges pretrained vision models and large language models (LLMs) to make frozen LLMs understand the visual world. VLAP transforms the embedding space of pretrained vision models into the…

Machine learning has revolutionized polymer science by enabling rapid property prediction and generative design. Large language models (LLMs) offer further opportunities in polymer informatics by simplifying workflows that traditionally…

Despite outstanding contribution to the significant progress of Artificial Intelligence (AI), deep learning models remain mostly black boxes, which are extremely weak in explainability of the reasoning process and prediction results.…

We show that large language models (LLMs) are remarkably good at working with interpretable models that decompose complex outcomes into univariate graph-represented components. By adopting a hierarchical approach to reasoning, LLMs can…

Aligning visual features with language embeddings is a key challenge in vision-language models (VLMs). The performance of such models hinges on having a good connector that maps visual features generated by a vision encoder to a shared…

Biological multimodal large language models (MLLMs) have emerged as powerful foundation models for scientific discovery. However, existing models are specialized to a single modality, limiting their ability to solve inherently cross-modal…

This paper presents a systematic literature review (SLR) on the explainability and interpretability of machine learning (ML) models within the context of predictive process mining, using the PRISMA framework. Given the rapid advancement of…

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains…

Large Language Models (LLMs) offer a promising approach to enhancing Explainable AI (XAI) by transforming complex machine learning outputs into easy-to-understand narratives, making model predictions more accessible to users, and helping…

Software Engineering (SE) Pre-trained Language Models (PLMs), such as CodeBERT, are pre-trained on large code corpora, and their learned knowledge has shown success in transferring into downstream tasks (e.g., code clone detection) through…

While there has been a recent explosion of work on ExplainableAI ExAI on deep models that operate on imagery and tabular data, textual datasets present new challenges to the ExAI community. Such challenges can be attributed to the lack of…

Despite their success, Large-Language Models (LLMs) still face criticism due to their lack of interpretability. Traditional post-hoc interpretation methods, based on attention and gradient-based analysis, offer limited insights as they only…

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches…

Deep learning is an advanced technology that relies on large-scale data and complex models for feature extraction and pattern recognition. It has been widely applied across various fields, including computer vision, natural language…

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…

Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…