ISAAC (Intervention-based Structural Auditing for Computational Models), a post-hoc framework that evaluates model behaviour through controlled, sequence-level interventions grounded in position weight matrices, supports structural auditing as a necessary complement to accuracy and attribution in XAI for genomics.
RegTrust-XAI is developed and evaluated, a trust-aware framework separating these questions using three inference-time signals: ensemble consensus, motif-grounded attribution coherence, and applicability-domain distance, which gives a more complete basis for deciding when to act on a prediction than accuracy alone.
Abdulmujeeb T. Onawole, Sulaimon Basiru, M. Sanni et al.· bioRxiv· 0 citations
It is demonstrated that attention-based protein language models can accurately identify nucleic acid-binding proteins directly from sequence data and reveal biologically meaningful sequence determinants of binding, establishing an interpretable and scalable framework for proteome-wide characterization of protein–nuclei...
Hanjin Kim, Sung-Gwon Lee, Joo-Seong Oh et al.· Bioinformatics Advances· 0 citations
DNA motif discovery and, particularly, computational modeling of transcription factor binding motifs, has been a mecca of algorithmic bioinformatics for several decades. Here, we report the results of the largest open community challenge in Inferring BInding Specificities (IBIS), where participants all over the world w...
Nikita Gryzunov, Dmitry D. Penzar, V. Kamenets et al.· Cell Reports· 0 citations
Sequence-to-function (S2F) deep learning models have become an important aid to decipher the genomic cis-regulatory code. However, current S2F models do not take the cellular trans-environment of transcription factors (TF) into account. Conversely, methods for gene regulatory network (GRN) inference often rely on heuri...
Gabriele Partel, Seppe De Winter, Vasilis Konstantakos et al.· bioRxiv· 0 citations
Identifying transcription factor binding sites (TFBSs) is fundamental to understanding complex gene regulatory mechanisms and the functions of non-coding regions. Although existing methods have achieved substantial strides, capturing both local structural features and long-range spatial dependencies within DNA sequence...
Jingjue Wei, Jie Feng· Match-communications in Math...· 0 citations
This review compares convolutional, Transformer-based and graph architectures used to represent local sequence features, chromatin state and three-dimensional genome organisation to their applications to transcription-factor binding, chromatin accessibility, gene expression, non-coding variant prioritisation and regula...
