Evaluating Agentic Bioinformatics through Function, Evidence, and Validation

Large language model agents increasingly plan, execute, and interpret biological analyses, yet fluent responses, successful tool calls, and benchmark performance alone do not establish scientific credibility. Existing reviews primarily organize biological agents by application, architecture, and agentic capability, but do not jointly operationalize the accountability of agent-generated workflows. We address this gap by treating the inspectable workflow trajectory, rather than architecture or final output alone, as the primary unit of analysis. We introduce the Function--Evidence--Validation (FEV) framework, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation. Using FEV, we map 109 agentic or agent-adjacent systems and 28 benchmark or evaluation resources, representing 128 unique publications across genomics, single-cell and spatial omics, protein science, drug discovery, computational pathology, and general bioinformatics automation. Across domains, planning and tool-mediated execution have advanced more rapidly than replayability, provenance, robust scientific assessment, external validation, and prospective empirical testing. We therefore argue that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone. FEV provides a practical basis for comparing systems and designing transparent, auditable, and scientifically accountable bioinformatics workflows.

SwiftTailor: Efficient 3D Garment Generation with Geometry Image Representation

Realistic and efficient 3D garment generation remains a longstanding challenge in computer vision and digital fashion. Existing methods typically rely on large vision- language models to produce serialized representations of 2D sewing patterns, which are then transformed into simulation-ready 3D meshes using garment modeling framework such as GarmentCode. Although these approaches yield high-quality results, they often suffer from slow inference times, ranging from 30 seconds to a minute. In this work, we introduce SwiftTailor, a novel two-stage framework that unifies sewing-pattern reasoning and geometry-based mesh synthesis through a compact geometry image representation. SwiftTailor comprises two lightweight modules: PatternMaker, an efficient vision-language model that predicts sewing patterns from diverse input modalities, and GarmentSewer, an efficient dense prediction transformer that converts these patterns into a novel Garment Geometry Image, encoding the 3D surface of all garment panels in a unified UV space. The final 3D mesh is reconstructed through an efficient inverse mapping process that incorporates remeshing and dynamic stitching algorithms to directly assemble the garment, thereby amortizing the cost of physical simulation. Extensive experiments on the Multimodal GarmentCodeData demonstrate that SwiftTailor achieves state-of-the-art accuracy and visual fidelity while significantly reducing inference time. This work offers a scalable, interpretable, and high-performance solution for next-generation 3D garment generation.

LINKER: Learning Interactions Between Functional Groups and Residues With Chemical Knowledge-Enhanced Reasoning and Explainability

Accurate identification of interactions between protein residues and ligand functional groups is essential to understand molecular recognition and guide rational drug design. Existing deep learning approaches for protein-ligand interpretability often rely on 3D structural input or use distance-based contact labels, limiting both their applicability and biological relevance. We introduce LINKER, the first sequence-based model to predict residue-functional group interactions in terms of biologically defined interaction types, using only protein sequences and the ligand SMILES as input. LINKER is trained with structure-supervised attention, where interaction labels are derived from 3D protein-ligand complexes via functional group-based motif extraction. By abstracting ligand structures into functional groups, the model focuses on chemically meaningful substructures while predicting interaction types rather than mere spatial proximity. Crucially, LINKER requires only sequence-level input at inference time, enabling large-scale application in settings where structural data is unavailable. Experiments on the LP-PDBBind benchmark demonstrate that structure-informed supervision over functional group abstractions yields interaction predictions closely aligned with ground-truth biochemical annotations.