Related papers: Structural Interpretations of Protein Language Mod…

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language…

Accurate protein function prediction requires integrating heterogeneous intrinsic signals (e.g., sequence and structure) with noisy extrinsic contexts (e.g., protein-protein interactions and GO term annotations). However, two key challenges…

Equivariant graph neural network (GNN) methods for antibody complementarity-determining region (CDR) design achieve the highest sequence recovery but suffer from severe vocabulary collapse. The current best GNN methods over-predict very few…

With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…

Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…

Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have…

Among interpretable machine learning methods, the class of Generalised Additive Neural Networks (GANNs) is referred to as Self-Explaining Neural Networks (SENN) because of the linear dependence on explicit functions of the inputs. In binary…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

Patterns of brain activity are associated with different brain processes and can be used to identify different brain states and make behavioral predictions. However, the relevant features are not readily apparent and accessible. To mine…

In the early days of machine learning (ML), the emphasis was on developing complex algorithms to achieve best predictive performance. To understand and explain the model results, one had to rely on post hoc explainability techniques, which…

Multimodal protein features play a crucial role in protein function prediction. However, these features encompass a wide range of information, ranging from structural data and sequence features to protein attributes and interaction…

Protein dynamics play a crucial role in many biological processes and drug interactions. However, measuring, and simulating protein dynamics is challenging and time-consuming. While machine learning holds promise in deciphering the…

Prototypical part learning is emerging as a promising approach for making semantic segmentation interpretable. The model selects real patches seen during training as prototypes and constructs the dense prediction map based on the similarity…

Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…

Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed…

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key idea behind FARM is the incorporation of…

Adversarial vulnerability and lack of interpretability are critical limitations of deep neural networks, especially in safety-sensitive settings such as autonomous driving. We introduce \DesignII, a neuro-symbolic framework that integrates…

Pre-trained seq2seq models excel at graph semantic parsing with rich annotated data, but generalize worse to out-of-distribution (OOD) and long-tail examples. In comparison, symbolic parsers under-perform on population-level metrics, but…

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…