Biologically-informed neural networks (BINNs) are a subclass of physics-informed neural networks tailored for learning partial differential equations in biological systems, where equations are nonlinear and data are sparse. The paper introduces a diagnostic workflow for selecting hyperparameters—network capacity, training epochs, and term stability—without requiring known ground-truth equations. By applying this workflow to synthetic systems, the authors show that validation loss tracks true error and provide practical guidelines and starting values for BINN hyperparameter tuning.
By William Lavery, Jodie A. Cochrane, John T. Nardini, Sara Hamis
arXiv:2606. 30778v1 Announce Type: new Abstract: Mapping a chemical reaction network, the graph of minima and transition states (TS) and the elementary reactions connecting them, is the natural language of chemistry, from catalysis to combustion to the origin of life.
By Stefan Gugler, Max Eissler, Khaled Kahouli, Klaus-Robert M\"uller
KPPax is a new kinetic preprocessor that converts atmospheric chemistry mechanisms written in the Kinetic PreProcessor (KPP) language into differentiable, just‑in‑time compiled, vectorisable code in JAX. It evaluates rate laws in log space to maintain differentiability and integrates stiff systems using implicit solvers with forward‑ and reverse‑mode adjoints from the diffrax library, enabling exact sensitivities without hand‑derived adjoint code. Demonstrations with the POLLU benchmark show that KPPax can predict which rate coefficients are identifiable and improve neural‑network corrections of emission inventories, reducing errors by up to a factor of five.
By Wenqing Peng, Michael Boy, Zhi-Song Liu
Baobab compiles an OWL 2 DL (ΣROIQ) ontology with a finite ABox into a Sentential Decision Diagram (SDD), saturating a propositional core and instantiating remaining DL features over the active domain. The resulting evidence‑conditioned weighted model count trains a perception network to recognize real images under partial ABox supervision, enabling a CNN to recover latent ontology concepts that an independent perception would miss. When supervision allows multiple ontology‑consistent completions, Baobab’s mixture indexed by query justifications represents the calibrated posterior, achieving Bayes‑optimal performance on a real‑image MNIST task where single‑WMC and learned mixtures fail, thereby characterizing and mitigating reasoning shortcuts in a non‑Horn description logic.
By Olga Mashkova, Asaad Mohammedsaleh, Fernando Zhapa-Camacho, Robert Hoehndorf
The paper introduces a fragment‑level graph encoding for molecular property prediction, using BRICS decomposition to represent molecules as graphs of synthetically meaningful fragments. This change of input representation allows any message‑passing GNN and post‑hoc attribution method to produce explanations at the functional‑group level, matching atom‑level accuracy on smaller graphs. Experiments across multiple architectures, tasks, and explainers show that fragment‑level encoding recovers known pharmacophores more reliably than post‑hoc aggregation of atom‑level explanations.
By Rafael Lopes Almeida (School of Pharmacy, University of Eastern Finland, Kuopio, Finland), Ina P\"ohner (School of Pharmacy, University of Eastern Finland, Kuopio, Finland)
arXiv:2606. 31700v1 Announce Type: new Abstract: Biological neural circuits obey Dale's principle: each neuron's synapses are uniformly excitatory or inhibitory.
By Yutaro Yamada, Luca Grillotti, Rujikorn Charakorn, Sebastian Risi, David Ha, Robert Tjarko Lange
arXiv:2607. 26344v1 Announce Type: new Abstract: A gradient-based GNN explainer given a molecule with two chemically equivalent nitro groups assigns them attribution scores that are equal to the last bit.
By Xin Xu, Siru Tao, Kaizhen Tan
arXiv:2608.20965v1 Announce Type: new
Abstract: We define an atomic generation fact f=(u,tau,omega,z;rho), recording the origin, realized transformation, concrete occurrence, generated result and rel...
By Mian Wang
arXiv:2607. 17033v1 Announce Type: new Abstract: Forecasting the outcomes of transition-metal-catalyzed reactions is notoriously complex due to the interplay of diverse physical and chemical variables.
By Qiwei Han, Chi Zhou
arXiv:2607. 18921v1 Announce Type: cross Abstract: Circuit extraction identifies a small set of model components whose presence preserves a target behavior under ablation, and the resulting circuit is often read as the mechanism behind that behavior.
By Yang Sheng, Jie Fu
The paper introduces adVersarial Parameter Decomposition (VPD), a method that splits a language model’s parameters into simple subcomponents, each responsible for a small part of the model’s algorithm. VPD optimizes these decompositions so that the model’s input‑output behavior remains intact even when many subcomponents are removed, including adversarially chosen ones. This approach enables a new form of circuit analysis by tracing how sequences of parameter subcomponents interact to produce outputs for specific inputs.
By Lucius Bushnaq, Dan Braun, Oliver Clive-Griffin, Bart Bussmann, Nathan Hu, Michael Ivanitskiy, Linda Linsefors, Lee Sharkey
arXiv:2607. 12771v1 Announce Type: new Abstract: Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations.
By Xingyu Dang, Haocheng Tang, Junmei Wang, Yanjun Li