The study fine‑tunes the Uni‑Mol2 molecular foundation model on the GS‑LF benchmark for multi‑label odor descriptor prediction. The resulting model matches or surpasses state‑of‑the‑art baselines on the primary benchmark and successfully transfers to four downstream olfactory tasks—including cross‑dataset prediction, odorless vs. odorous classification, enantiomer evaluation, and odor mixture discriminability—without further deep‑learning training. The enantiomer analysis demonstrates that 3D molecular representations can distinguish mirror‑image molecules, a capability lacking in 2D graph models, though predicting stereochemistry’s perceptual effects remains unresolved.
By Yikun Han, Yi Wang, Neil Mankodi, Stephen Yang, Ambuj Tewari
arXiv:2609.05694v1 Announce Type: new
Abstract: Predicting olfactory qualities from molecular structure is an open problem in chemoinformatics. Although linear models can link molecular features to o...
By Mrityunjay Sharma, Sarabeshwar Balaji, Valentina Parma, Ritesh Kumar
The paper introduces Competitive Dimerization Networks (CDNs) as a chemical learning framework where molecular species bind reversibly to form dimers, with binding affinities acting as tunable synaptic weights. Through a directed evolution protocol involving mutation, selection, and amplification of DNA-based components, CDNs can be trained in vitro to perform complex tasks such as multiclass classification, achieving strong output contrast and high mutual information. Comparative studies with in silico gradient descent show closely correlated performance, positioning CDNs as a promising platform for analog physical computation that bridges synthetic biology and machine learning.
By Alexei V. Tkachenko, Bortolo Matteo Mognetti, Sergei Maslov
The paper introduces Align-React, a chemical reaction representation learning framework that incorporates atomic correspondence between reactants and products, an adapter for embedding reaction conditions, and a Reaction-Center-Aware attention mechanism. These components enable the model to capture precise molecular transformations and focus on critical functional groups, leading to improved performance across a variety of organic reaction tasks. The framework outperforms existing architectures on most benchmark datasets.
By Kaipeng Zeng, Xianbin Liu, Yu Zhang, Xiaokang Yang, Yaohui Jin, Yanyan Xu
arXiv:2607. 24848v1 Announce Type: cross Abstract: Pretrained molecular encoders are commonly evaluated through downstream prediction, but predictive accuracy alone does not establish that a learned representation captures reproducible scientific structure, adds information beyond strong conventional baselines, or transfers out of distribution.
By Kai Lun Huang (California State University, Fullerton), Wei Chieh Sun (University of Washington)
arXiv:2606. 18469v1 Announce Type: cross Abstract: Neuroscientific research has revealed that the brain encodes complex behaviors by leveraging structured, low-dimensional manifolds and dynamically fusing multiple sources of information through adaptive gating mechanisms.
By Somjit Nath, Jackson J Cone, Derek Nowrouzezahrai, Samira Ebrahimi Kahou
arXiv:2605. 16823v2 Announce Type: replace Abstract: Large language models succeed by combining large-scale pretraining with meaningful discrete tokens.
By Takayuki Kimura
arXiv:2607. 28079v1 Announce Type: new Abstract: Chemical property prediction plays a critical role in accelerating scientific discovery in chemistry, materials science, and drug development.
By Tianyou Bai, Huan Wang, Mingchen Gao, Fangyue Lin, Pinze Ren, Zhenlin Zhao, Siming Dong
arXiv:2511. 19264v2 Announce Type: replace-cross Abstract: Generative Flow Networks (GFlowNets) construct molecules through sequential decisions, but their internal policies remain opaque, limiting adoption in drug discovery, where chemists need interpretable rationales for proposed structures.
By Amirtha Varshini A S, Duminda S. Ranasinghe, Hok Hei Tam
The paper presents a deep learning approach that converts nanopore resistive pulse signals into scaleograms using continuous wavelet transforms, enabling the classification of peptides as an image‑classification problem. On a dataset of 42 peptides, the method achieves an 82% macro‑averaged accuracy, outperforming previous descriptor‑based techniques by 8.6 percentage points. The models also remain accurate after significant weight pruning and 8‑bit quantization, making them suitable for deployment on embedded sensing hardware.
By Julian Ho{\ss}bach, Samuel Tovey, Sandro Kuppel, Tobias Ensslen, Jan C. Behrends, Christian Holm
arXiv:2606. 09770v1 Announce Type: cross Abstract: Nearby neurons in cortex share similar response profiles, producing systematic spatial organization across sensory and cognitive systems.
By Badr AlKhamissi, Johannes Mehrer, Lara Marinov, Ahmed Abdelaal, Abdulkadir Gokce, Martin Schrimpf
arXiv:2606. 11508v1 Announce Type: new Abstract: Accurate prediction of absorption, distribution, metabolism, and excretion (ADME) properties is critical to drug discovery, but remains challenging because ADME endpoints are noisy, interdependent, and often data-limited.
By Yifan Xue, Srimukh Prasad Veccham, Saee Paliwal, Tyler Shimko, Micha Livne