FoldPipe: Bounded Remote Streaming of Native Molecular Shards with Asynchronous Prefetch

Training molecular machine-learning models on ephemeral or memory-constrained accelerator instances can require repeatedly retrieving preprocessed molecular graphs from remote storage. FoldPipe is a lightweight Python orchestration layer for already-sharded PyTorch and PyTorch Geometric data. It retrieves one shard ahead in a background thread while the consumer trains on the current shard, keeping the number of live shard payloads bounded with respect to total dataset size. Asynchronous prefetch and bounded buffering are established systems techniques rather than novel scheduling algorithms. FoldPipe's contribution is a small integration targeted at native .pt molecular shards together with a source-pinned empirical characterization of its operating regime. We evaluate a SchNet energy-and-force workload on MD17 aspirin using 20 paired, order-alternating benchmark passes on a Tesla T4. Each pass processes five pinned shards containing 25,000 structures. FoldPipe records 16.33 s mean I/O-compute overlap, compared with zero by construction for the sequential bounded baseline. Mean pass time is 76.78 s for FoldPipe and 83.37 s for the baseline. However, the geometric mean paired speedup is $1.059\times$ with a 95% bootstrap interval from $0.878\times$ to $1.288\times$. The experiment therefore verifies the overlap mechanism but is inconclusive about a reliable wall-clock speed advantage under the observed public-network variability.

Semi-Supervised Learning for Molecular Graphs via Ensemble Consensus

Machine learning is transforming molecular sciences by accelerating property prediction, simulation, and the discovery of new molecules and materials. Acquiring labeled data in these domains is often costly and time-consuming, whereas large collections of unlabeled molecular data are readily available. Standard semi-supervised learning methods often rely on label-preserving augmentations, which are challenging to design in the molecular domain, where minor changes can drastically alter properties. In this work, we show that semi-supervised methods that rely on an ensemble consensus can boost predictive accuracy across a diverse range of molecular datasets, task types, and graph neural network architectures. We find that training with an ensemble consensus objective increases robustness in models and exhibits an effect similar to knowledge distillation; an individual member of an ensemble trained this way outperforms a full ensemble trained in a traditional supervised fashion in almost all cases. In addition, this type of semi-supervised training reduces calibration error.

GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

Predicting tandem mass spectra (MS/MS) from molecular structures represents a central task in analytical chemistry with direct relevance to clinical metabolomics, systems biology, and adjacent disciplines. In this work, we revisit the problem through the lens of object detection on molecular graphs. Molecular fragmentation, a central step in MS/MS prediction, can be approximated as detecting a set of subgraphs (i.e., fragments) and their associated spectral contributions. Existing fragment-based models follow a two-stage paradigm -- first generating candidate fragments and then scoring them -- analogous to two-stage R-CNNs in computer vision. Towards higher accuracy and faster inference, we introduce GLACIER, a single-stage transformer-based fragment detection neural network for molecular graphs. This unified formulation eliminates the need for candidate enumeration, enabling scalable and globally consistent modeling of molecular fragmentation. GLACIER is faster and more accurate than existing state-of-the-art by a significant margin, achieving 70.0% and 69.7% Top-1 retrieval accuracy with and without contrastive finetuning on the MassSpecGym dataset (from the previous SOTA of 64.0%) and 52.5% and 38.5% respectively on the NIST'20 dataset (from 33.2%). Furthermore, GLACIER provides nearly 8-fold inference speedup over our prior two-stage model. Code is available at https://github.com/coleygroup/ms-pred

Rethinking Molecular Graph Backdoors under Chemistry-aware Admission

Backdoor attacks on molecular graph neural networks (GNNs) are typically evaluated as abstract graph edits, but real molecular learning pipelines do not train on arbitrary graphs. Molecular records must first survive parsing, sanitization, canonicalization, and graph-string consistency checks. We formalize this overlooked admission stage as ChemGuard, an operational protocol for testing whether a submitted molecular record can enter a realistic learning pipeline, while complementing existing defenses. ChemGuard admits a record only when its molecular string is sanitizable and the graph reconstructed from that string matches the submitted molecular graph. Under this operational view, many existing graph-based backdoors lose much of their apparent efficacy because their poisons are chemically invalid or representation-inconsistent. We then show that admission checks alone are insufficient to rule out molecular backdoors. We propose ChemBack, an admission-aware molecular backdoor attack that constructs chemically feasible motif-anchor attachments and ranks admitted candidates by fingerprint-based Tanimoto similarity to clean target-class molecules. ChemBack is model-free during trigger selection, using molecular structures, target labels, fingerprints, and public validity checks, but no victim model, surrogate GNN, learned embedding, gradient, logit, or training-code access. Across molecular benchmarks, validators, architectures, and defenses, \textbf{ChemBack} achieves high attack success with fully admitted poisons while preserving clean accuracy. Our results reveal a two-sided lesson, chemistry-aware admission suppresses many graph-only backdoors, yet chemically valid and target-aligned molecular backdoors remain a practical threat.

Probabilistic Contrastive Pretraining for Multi-task ADME Property Prediction

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. We propose a molecular graph-transformer pretraining framework that combines chemistry-specific self-supervision with contrastive mutual information machine learning (cMIM). Our method encodes molecular graphs into latent variables, reconstructs SMILES strings from the graph-derived latent codes, and augments the contrastive objective with domain-specific self-supervised chemistry tasks. Rather than treating these tasks as auxiliary regularizers with separately tuned loss weights, we formulate reconstruction, contrastive discrimination, and chemistry-specific supervision as unit-weighted log-probability factors in a single probabilistic latent-variable objective. For fine-tuning, we propose a multi-task GNN readout architecture with task-specific multilayer perceptron heads, preserving shared representation learning while mitigating negative transfer and improving the modeling of heterogeneous, nonlinear task relationships. Across Biogen, ExpansionRX, and ChEMBL-MT, the resulting Contrastive KERMT pretraining improves over the KERMT baseline by 7.6%, 9.9%, and 9.5% respectively (averaged over significantly-improved endpoints). Adding ADME-adjacent molecules to the pretraining corpus further improves transfer, and the contrastive component sharpens chemically meaningful latent neighborhoods.

GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction

Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds. However, the computational burden to develop and deploy state-of-the-art models continuously increases, limiting their scalability. Most large-scale models are unimodal in nature and overlook the potential to leverage complementary molecular data modalities. To address these shortcomings, this paper introduces the Graph-Language Alignment for Chemical Inference and Exploration using Representations (GLACIER) model, a student-teacher framework that integrates molecular graphs, SMILES strings, and physicochemical descriptors to learn rich molecular embeddings. Our framework consists of three stages: (1) we pretrain three student encoders on 100,000 drug-like molecules: a message-passing neural network for molecular graphs, a transformer-based encoder for SMILES strings, and a multilayer perceptron for physicochemical descriptors, (2) we fuse these student modalities using a novel Finsler geometry-aware module, and (3) distill complementary knowledge from large teacher models, including MiniMol and MolFormer, into a single lightweight model via contrastive learning. We demonstrate that GLACIER is a robust framework that delivers high predictive performance and computational efficiency in complex molecular property prediction tasks. Our code is publicly available at https://github.com/eemokey/glacier.

End-to-End Subgraph Detection with GraphDETR

Subgraph detection seeks to identify whether and where instances of query patterns occur within a larger graph. This problem is fundamental across scientific domains and is closely related to subgraph isomorphism, which is NP-complete, limiting combinatorial approaches to small patterns or moderately sized graphs. We introduce GraphDETR, a deep learning framework that formulates subgraph detection as a set prediction problem, analogous to DETR in object detection. GraphDETR encodes the target graph with a graph neural network, and employs a fixed set of learnable query vectors, decoded via a transformer decoder, to predict all pattern occurrences jointly in a single forward pass. This is enabled by training the model end-to-end with bipartite matching. Unlike traditional combinatorial methods that only solve exact structural matching, GraphDETR naturally extends to approximate matching, enabling detection beyond exact pattern correspondence. Empirically, we show that GraphDETR can detect diverse patterns, such as molecular structures, cycles, cliques, and fuzzy patterns of up to 50 nodes, in target graphs with up to 1000 nodes. We further evaluate on molecular functional group detection over the ChEMBL dataset, where GraphDETR predicts the complete set of functional groups per molecule, achieving a strong performance of $\text{AP}_{100} = 91.2$.

Scaling Novel Graph Generation via Lightweight Structure-Guided Autoregressive Models

Generating realistic and diverse graphs is a key problem in machine learning, with applications in molecular discovery, circuit design, cybersecurity, and beyond. However, current graph generative models remain limited by scalability and novelty. Diffusion-based methods often require costly full-adjacency operations and long denoising chains, while many autoregressive and hybrid models have at least quadratic complexity. In addition, these models often imitate training graphs rather than generalize beyond them. We propose a lightweight autoregressive framework to address these issues. It uses a structure-guided topological ordering to serialize graphs into regular edge sequences, enabling near log-linear generation, and a two-phase training strategy that combines exploration-oriented augmentation with iterative refinement to reduce overfitting and promote controlled novelty. Experiments on molecular and non-molecular benchmarks show that our approach improves novelty while preserving high validity and uniqueness. The framework also supports both LSTM and Mamba-style causal sequence backbones, with large-memory accelerators enabling longer graph-sequence experiments beyond typical GPU limits.