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Jiajun Yu

Publications and source records attributed to Jiajun Yu.

18 recordsLinked to original sources

Pretraining Reusable Inference Across Views with Synthetic Task Priors

Modern pretrained encoders make representations from heterogeneous views increasingly reusable, but the procedure that determines view utility and combines evidence is still relearned for each downstream task. Consequently, knowledge about view relevance, complementarity, reliability, and missingness is repeatedly discarded rather than transferred across tasks. We therefore reformulate multi-view learning as learning a reusable, task-conditioned inference procedure rather than a fixed fusion function. Based on this perspective, we propose SIMPLE, a prior-fitted multi-view in-context learner that predicts query labels by conditioning on a small labeled support set. Since existing real-world datasets cover only a limited range of view configurations and task structures, we construct a controllable synthetic task prior in embedding space. It generates diverse support-query episodes with varying class structures, shared and view-specific factors, representation geometries, cross-view dependencies, reliability levels, missingness patterns, and distribution shifts. A hierarchical inference architecture then performs reasoning within views, across views, and across support and query samples. Experiments on multi-view and multi-omics benchmarks demonstrate that the frozen variant of SIMPLE achieves competitive performance without updating the inference backbone, while lightweight adapter calibration attains leading performance on most evaluated datasets. Together, the results under frozen, one-shot, and missing-view settings support the central hypothesis that multi-view reasoning itself can be pretrained and reused, while lightweight adapter calibration provides task-specific alignment when needed.

cs.LG

Interplay between Nuclear Shell Structure and Pairing around Doubly Magic $^{132}$Sn

Shell structure in finite quantum systems gives rise to sudden changes in observable properties, while pairing correlations often compete against such discontinuities. The region near the doubly magic nucleus $^{132}$Sn provides a fertile ground for testing the combined effect of shell structure and pairing. Here, we provide a novel phenomenological interpretation of existing mass data in the vicinity of the $Z=50$ and $N=82$ shell closures, which we further investigate by performing original Hartree-Fock-Bogolyubov (HFB) mean-field calculations for even-$Z$ nuclei: we find that the proton shell structure enhances an asymmetry of the neutron odd-even staggering in binding energies. We also report mass measurements of $^{137,138}$Sb, including the first experimental mass determination of $^{138}$Sb, performed using TRIUMF's Ion Trap for Atomic and Nuclear Science (TITAN). Together with existing experimental data, our results reveal an interplay between shell structure and pairing in odd-$Z$ nuclei which is more challenging to interpret phenomenologically or using HFB, thereby motivating future experimental and theoretical pairing studies in heavy neutron-rich nuclides.

nucl-ex

DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects

Birth defects are a major cause of fetal loss, neonatal morbidity and long-term disability. In the subset with suspected genetic etiologies, exome and genome sequencing have moved many cases from variant detection to post-sequencing interpretation: clinicians must rank patient-specific candidate variants under incomplete fetal or infant phenotypes and heterogeneous evidence from population genetics, variant-effect prediction, gene-disease validity, phenotype ontologies, cellular and pathway context, protein structure and clinical literature. We present DeepBD, a grounded agentic workflow for variant prioritization and diagnostic interpretation of genetic birth defects. DeepBD organizes the workflow into LLM-assisted case structuring, a pretrained evidence engine, specialist evidence modules and a grounded diagnostic review layer. The evidence engine learns patient-specific variant scores from structured rule evidence, sequence and variant-effect representations and phenotype-conditioned biological context, whereas specialist modules and the agentic layer provide tool-based refinement, candidate-pool review and diagnosis-oriented synthesis from ranked candidates. Developed using an in-house fetal and infant cohort comprising 18,622 cases, DeepBD achieved Recall@1/3/5/10 of 0.658/0.882/0.912/0.929 on an internal held-out solved-case benchmark, outperforming standalone Exomiser, DeepRare and prompted LLM reranking baselines evaluated on Exomiser-derived top-20 candidate variants. Ablation and overlap analyses show that rule evidence, mechanistic context, and specialist refinement provide complementary signals. These findings support a grounded agentic workflow that separates evidence integration, tool-based refinement, and LLM-assisted diagnostic review for retrospective variant prioritization in genetic birth defects.

q-bio.GN

UniField: RBF-Guided Electron Density Fusion for Enhanced Molecular Representations

Current 3D geometric molecular representations predominantly focus on discrete atomic skeletons, inherently overlooking the continuous electron density (ED) field that fundamentally governs microscopic quantum behaviors. Consequently, these purely topological models suffer from critical representational blind spots, particularly in capturing long-range electron delocalization and non-covalent interactions, imposing a severe theoretical ceiling on predicting complex quantum properties. To bridge this physical gap and standardize research in electron density-enhanced molecular learning, we first construct the large-scale UniField-ED Benchmark. Comprising the QM9-ED and QMugs-ED datasets, this benchmark provides natively aligned discrete graphs and high-fidelity ED point clouds. Building upon this data infrastructure, we introduce UniField, an SE(3)-equivariant multimodal architecture that intrinsically intertwines discrete topological graphs with continuous quantum electronic environments. Extensive empirical evaluations across all three benchmarks demonstrate that UniField establishes new state-of-the-art performance. Specifically, UniField achieves a 14.8% improvement in overall predictive performance against the leading topology-only SOTA on the ED5-OE benchmark, alongside a 37.0% performance gain over top pure-ED models. Furthermore, on the complex drug-like dataset QMugs-ED, it yields a striking 28.2% average precision improvement across frontier orbital properties. Alongside new SOTA results on QM9-ED, our method establishes a rigorous foundation for next-generation computational chemistry. Code and datasets are anonymously available at https://anonymous.4open.science/r/UniField-ED-5B1B.

physics.chem-ph

When Molecular Similarity Works: Property Cliffs Reveal Hidden Errors

Accurate prediction of molecular properties underpins drug discovery and material design, yet even state-of-the-art models remain vulnerable to localized failure modes that aggregate metrics cannot detect. The places where molecular similarity should be most helpful are also places where standard evaluation can be most misleading. Property cliffs expose this gap: structurally similar molecules can still differ sharply in target property, so models with competitive overall performance may fail in high-risk local neighborhoods. To expose and mitigate this failure mode, CliffSplit, a cliff-aware evaluation protocol that constructs locally supported, cliff-exposed test cases, and CliffLoss, a model-agnostic train-only mitigation mechanism for cliff-sensitive errors, are introduced. Experiments on three QM9 targets and three MoleculeNet tasks across five backbones show that CliffSplit reveals at least 15% higher error in cliff-heavy QM9 regions, while CliffLoss reduces the cliff-to-smooth error gap by up to 30% on Lipophilicity and improves overall MAE by 9.7%. Together, these results turn molecular similarity failure from a descriptive anomaly into a benchmarked evaluation problem for molecular machine learning. The code is available at https://anonymous.4open.science/r/Cliff_Loss.

cs.LG

Rethinking Molecular OOD Generalization via Target-Aware Source Selection

Robust prediction of molecular properties under extreme out-of-distribution (OOD) scenarios is a pivotal bottleneck in AI-driven drug discovery. Current scaffold-splitting protocols fail to obstruct microscopic semantic overlap, predisposing models to shortcut learning and overestimating their true extrapolation capability; meanwhile, conventional domain adaptation paradigms suffer under extreme structural shifts, as blindly aligning heterogeneous source libraries injects topological noise and triggers negative transfer. To address these two challenges, scaffold-cluster out-of-distribution performance evaluation benchmark (SCOPE-BENCH), a benchmark built on cluster-level partitioning in an explicit physicochemical descriptor space, is proposed alongside policy optimization for multi-source adaptation (POMA), a framework that formulates knowledge transfer as a retrieve-compose-adapt pipeline: labeled source scaffolds structurally close to the unlabeled target are first identified as proxy targets; a reinforcement learning policy then adaptively selects the optimal source subset from an exponentially large candidate pool; and dual-scale domain adaptation is finally performed at macroscopic topological and microscopic pharmacophore scales. Evaluations show that prediction errors of state-of-the-art 3D molecular models surge by up to 8.0x on SCOPE-BENCH with a mean of 5.9x, while POMA achieves up to an 11.2% reduction in mean absolute error with an average relative improvement of 6.2% across diverse backbone architectures. Code is available at https://anonymous.4open.science/r/Molecular-OOD-Code-73F6.

cs.LG

From Single-Step Edit Response to Multi-Step Molecular Optimization

Conditional molecular optimization aims to edit a molecule to realize a specified property shift. In practice, structurally similar molecule data is scarce, while decisions are inherently action-level: at each step, the system must select one local structural edit from a candidate set that is strictly filtered by chemical feasibility rules. This level mismatch between supervision and decision makes oracle-in-the-loop search unstable in molecular optimization. Regressing on property differences between molecule pairs improves data efficiency but relies on oracle-in-the-loop search, entangling transformation effects with global context and providing limited guidance for selecting the next feasible edit, often resorting to oracle-in-the-loop search. For this reason, we propose a response-oriented discrete edit optimization approach comprising two tightly coupled components: a single-step molecular edit response predictor (SMER) and a multi-step planner that composes local predictions into optimization trajectories via guided tree search (SMER-Opt). The approach learns a directional evaluation model over edit actions to support constraint-aware planning. It mines weakly related molecule pairs and decomposes their structural differences into minimal edit units, turning endpoint property annotations into process-level supervision and yielding reusable, transferable action primitives. A directional edit evaluator then scores feasible candidate edits by their likelihood of moving the molecule toward the desired property change, substantially reducing dependence on external evaluator queries at decision time. Code is available at https://anonymous.4open.science/r/SMER.

cs.AI

Coordination Engineering of Dual-Atom Catalysts for Overall Water Splitting: Mechanistic Insights from Constant-Potential First-Principles and Machine Learning

The rational design of bifunctional electrocatalysts for the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) is essential for achieving efficient and cost-effective overall water splitting. Atomically dispersed transition-metal catalysts, including single-atom catalysts and dual-atom catalysts (DACs), have emerged as a prominent class of heterogeneous catalysts, in which coordination engineering plays a decisive role in tuning catalytic performance. Herein, we explore coordination-engineered bifunctional overall water splitting electrocatalysts using graphene-supported DACs (TM1TM2-C6-xNx) as model systems. By tuning C/N coordination and dual-metal combinations (Fe, Co, Ni, and Cu), a library of 228 structures was constructed. A three-step screening strategy, combining constant-charge and constant-potential density functional theory with kinetic analysis of proton-coupled electron transfer (PCET), identifies 24 highly active candidates (TM1TM2 = CoNi, CoCu and Co2) with mixed C/N coordination for OER. These catalysts exhibit overpotentials comparable to that of IrO2 and low PCET barriers (lower than 0.40 eV), among which 22 also show high HER activity. Machine learning reveals clear coordination-dependent structure-performance relationships. Such bifunctionality arises from coordination engineering that enables the simultaneous optimization of OER intermediate adsorption and the hydrogen binding strength for HER. This work establishes coordination engineering as an effective strategy for designing high-performance bifunctional dual-atom electrocatalysts for overall water splitting.

cond-mat.mtrl-sci

ATRS: Adaptive Trajectory Re-splitting via a Shared Neural Policy for Parallel Optimization

Parallel trajectory optimization via the Alternating Direction Method of Multipliers (ADMM) has emerged as a scalable approach to long-horizon motion planning. However, existing frameworks typically decompose the problem into parallel subproblems based on a predefined fixed structure. Such structural rigidity often causes optimization stagnation in highly constrained regions, where a few lagging subproblems delay global convergence. A natural remedy is to adaptively re-split these stagnating segments online. Yet, deciding when, where, and how to split exceeds the capability of rule-based heuristics. To this end, we propose ATRS, a novel framework that embeds a shared Deep Reinforcement Learning policy into the parallel ADMM loop. We formulate this adaptive adjustment as a Multi-Agent Shared-Policy Markov Decision Process, where all trajectory segments act as homogeneous agents and share a unified neural policy network. This parameter-sharing architecture endows the system with size invariance, enabling it to handle dynamically changing segment counts during re-splitting and generalize to arbitrary trajectory lengths. Furthermore, our formulation inherently supports zero-shot generalization to unseen environments, as our network relies solely on the internal states of the numerical solver rather than on the geometric features of the environment. To ensure solver stability, a Confidence-Based Election mechanism selects only the most stagnating segment for re-splitting at each step. Extensive simulations demonstrate that ATRS accelerates convergence, reducing the number of iterations by up to 26.0% and the computation time by up to 19.1%. Real-world experiments further confirm its applicability to both large-scale offline global planning and real-time onboard replanning within 35 ms per cycle, with no sim-to-real degradation.

cs.RO

Potential-Induced Dynamic Coordination of Nonmetal Atoms Directly Bound to Metal Centers in Graphene-Embedded Single-Atom Catalysts and Its Implications

Electrode-potential-induced dynamic coordination is an essential factor governing the performance of graphene-embedded single-atom catalysts (SACs). While previous studies have primarily centered on structural dynamics at the metal site, the response of its coordinated nonmetal atoms remains largely unexplored. Here, using Ni SACs with mixed nitrogen/carbon coordination (NiN4-xCx) as representatives, we investigate potential-driven hydrogenation of metal-center-coordinated nonmetallic atoms through constant-potential density functional theory and ab initio molecular dynamics. We find that the C sites directly bound to Ni undergo potential-driven hydrogenation, whereas hydrogenation at N sites is thermodynamically unfavorable. Taking NiNC3 as a representative system, we demonstrate that these hydrogenation processes proceed with accessible kinetic barriers and obey the Br{\o}nsted-Evans-Polanyi relation. The resulting dynamic coordination reshapes the Ni 3d and dz2 orbitals, modulates the stability of the active center, and weakens molecular adsorption through combined electronic and steric effects. These findings reveal that electrode potential and solvent not only regulate the metal center but also dynamically reconfigure its coordination environment, offering novel mechanistic insights into potential-induced coordination dynamics and guiding the rational design of coordination-engineered SACs.

cond-mat.mtrl-sci

PCEvo: Path-Consistent Molecular Representation via Virtual Evolutionary

Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are expensive to obtain and therefore limited in availability. Under the few-shot setting, models trained with scarce supervision often learn brittle structure-property relationships, resulting in substantially higher prediction errors and reduced generalization to unseen molecules. To address this limitation, we propose PCEvo, a path-consistent representation method that learns from virtual paths through dynamic structural evolution. PCEvo enumerates multiple chemically feasible edit paths between retrieved similar molecular pairs under topological dependency constraints. It transforms the labels of the two molecules into stepwise supervision along each virtual evolutionary path. It introduces a path-consistency objective that enforces prediction invariance across alternative paths connecting the same two molecules. Comprehensive experiments on the QM9 and MoleculeNet datasets demonstrate that PCEvo substantially improves the few-shot generalization performance of baseline methods. The code is available at https://anonymous.4open.science/r/PCEvo-4BF2.

q-bio.BM

A pathway towards decentralized studies of radioactive post-lead elements and their applications in beyond standard model physics

Molecules have proven to be sensitive tools for studying physics beyond the standard model, with heavy and deformed nuclei offering decisive sensitivity to parity- and time-reversal-violating effects. However, almost all elements beyond lead, occupying the 6p~to~5f atomic orbitals, lack stable isotopes, hence molecules containing them are referred to as radioactive molecules. Among those, radium monofluoride has seen particular interest, but to date, research on radioactive molecules has mainly been limited to large-scale nuclear facilities. Here, we present a scheme that allows efficient and fast harvest of radioactive ions (including short-lived Ra), and show ion gas-phase reaction studies of singly and doubly charged Ra, Po, and Pb ions with SF$_6$ gas inside an ion trap. Our results show that the chemical reaction rate of Ra$^+$ is in line with trends of other alkaline earth elements, further support by quantum chemical computations. The reaction Ra$^{2+}$ + SF$_6$ $\rightarrow$ RaF${^+}$ + SF$_5^{+}$ achieves an almost unity conversion efficiency, making it particularly suitable for the application for studies in physics beyond the standard model. The scheme enables future decentralized research avenues with short-lived radioactive molecules for fundamental physics research at laboratories without the need for local nuclear reactors or accelerators.

nucl-ex

Multi-Omics Analysis for Cancer Subtype Inference via Unrolling Graph Smoothness Priors

Integrating multi-omics datasets through data-driven analysis offers a comprehensive understanding of the complex biological processes underlying various diseases, particularly cancer. Graph Neural Networks (GNNs) have recently demonstrated remarkable ability to exploit relational structures in biological data, enabling advances in multi-omics integration for cancer subtype classification. Existing approaches often neglect the intricate coupling between heterogeneous omics, limiting their capacity to resolve subtle cancer subtype heterogeneity critical for precision oncology. To address these limitations, we propose a framework named Graph Transformer for Multi-omics Cancer Subtype Classification (GTMancer). This framework builds upon the GNN optimization problem and extends its application to complex multi-omics data. Specifically, our method leverages contrastive learning to embed multi-omics data into a unified semantic space. We unroll the multiplex graph optimization problem in that unified space and introduce dual sets of attention coefficients to capture structural graph priors both within and among multi-omics data. This approach enables global omics information to guide the refining of the representations of individual omics. Empirical experiments on seven real-world cancer datasets demonstrate that GTMancer outperforms existing state-of-the-art algorithms.

cs.LG

TOP: Trajectory Optimization via Parallel Optimization towards Constant Time Complexity

Optimization has been widely used to generate smooth trajectories for motion planning. However, existing trajectory optimization methods show weakness when dealing with large-scale long trajectories. Recent advances in parallel computing have accelerated optimization in some fields, but how to efficiently solve trajectory optimization via parallelism remains an open question. In this paper, we propose a novel trajectory optimization framework based on the Consensus Alternating Direction Method of Multipliers (CADMM) algorithm, which decomposes the trajectory into multiple segments and solves the subproblems in parallel. The proposed framework reduces the time complexity to O(1) per iteration to the number of segments, compared to O(N) of the state-of-the-art (SOTA) approaches. Furthermore, we introduce a closed-form solution that integrates convex linear and quadratic constraints to speed up the optimization, and we also present numerical solutions for general inequality constraints. A series of simulations and experiments demonstrate that our approach outperforms the SOTA approach in terms of efficiency and smoothness. Especially for a large-scale trajectory, with one hundred segments, achieving over a tenfold speedup. To fully explore the potential of our algorithm on modern parallel computing architectures, we deploy our framework on a GPU and show high performance with thousands of segments.

cs.RO

AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy

Protein structure prediction is a critical and longstanding challenge in biology, garnering widespread interest due to its significance in understanding biological processes. A particular area of focus is the prediction of missing loops in proteins, which are vital in determining protein function and activity. To address this challenge, we propose AutoLoop, a novel computational model designed to automatically generate accurate loop backbone conformations that closely resemble their natural structures. AutoLoop employs a bidirectional training approach while merging atom- and residue-level embedding, thus improving robustness and precision. We compared AutoLoop with twelve established methods, including FREAD, NGK, AlphaFold2, and AlphaFold3. AutoLoop consistently outperforms other methods, achieving a median RMSD of 1.12 Angstrom and a 2-Angstrom success rate of 73.23% on the CASP15 dataset, while maintaining strong performance on the HOMSTARD dataset. It demonstrates the best performance across nearly all loop lengths and secondary structural types. Beyond accuracy, AutoLoop is computationally efficient, requiring only 0.10 s per generation. A post-processing module for side-chain packing and energy minimization further improves results slightly, confirming the reliability of the predicted backbone. A case study also highlights AutoLoop's potential for precise predictions based on dominant loop conformations. These advances hold promise for protein engineering and drug discovery.

q-bio.BM

Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization

Molecular optimization is a crucial yet complex and time-intensive process that often acts as a bottleneck for drug development. Traditional methods rely heavily on trial and error, making multi-objective optimization both time-consuming and resource-intensive. Current AI-based methods have shown limited success in handling multi-objective optimization tasks, hampering their practical utilization. To address this challenge, we present MultiMol, a collaborative large language model (LLM) system designed to guide multi-objective molecular optimization. MultiMol comprises two agents, including a data-driven worker agent and a literature-guided research agent. The data-driven worker agent is a large language model being fine-tuned to learn how to generate optimized molecules considering multiple objectives, while the literature-guided research agent is responsible for searching task-related literature to find useful prior knowledge that facilitates identifying the most promising optimized candidates. In evaluations across six multi-objective optimization tasks, MultiMol significantly outperforms existing methods, achieving a 82.30% success rate, in sharp contrast to the 27.50% success rate of current strongest methods. To further validate its practical impact, we tested MultiMol on two real-world challenges. First, we enhanced the selectivity of Xanthine Amine Congener (XAC), a promiscuous ligand that binds both A1R and A2AR, successfully biasing it towards A1R. Second, we improved the bioavailability of Saquinavir, an HIV-1 protease inhibitor with known bioavailability limitations. Overall, these results indicate that MultiMol represents a highly promising approach for multi-objective molecular optimization, holding great potential to accelerate the drug development process and contribute to the advancement of pharmaceutical research.

q-bio.BM

Navigating Brain Language Representations: A Comparative Analysis of Neural Language Models and Psychologically Plausible Models

Neural language models, particularly large-scale ones, have been consistently proven to be most effective in predicting brain neural activity across a range of studies. However, previous research overlooked the comparison of these models with psychologically plausible ones. Moreover, evaluations were reliant on limited, single-modality, and English cognitive datasets. To address these questions, we conducted an analysis comparing encoding performance of various neural language models and psychologically plausible models. Our study utilized extensive multi-modal cognitive datasets, examining bilingual word and discourse levels. Surprisingly, our findings revealed that psychologically plausible models outperformed neural language models across diverse contexts, encompassing different modalities such as fMRI and eye-tracking, and spanning languages from English to Chinese. Among psychologically plausible models, the one incorporating embodied information emerged as particularly exceptional. This model demonstrated superior performance at both word and discourse levels, exhibiting robust prediction of brain activation across numerous regions in both English and Chinese.

cs.CL

Optimal Rendezvous Strategies for Different Environments in Cognitive Radio Networks

In Cognitive Radio Networks (CRNs), the secondary users (SUs) are allowed to access the licensed channels opportunistically. A fundamental and essential operation for SUs is to establish communication through choosing a common channel at the same time slot, which is referred to as rendezvous problem. In this paper, we study strategies to achieve fast rendezvous for two secondary users. The channel availability for secondary nodes is subject to temporal and spatial variation. Moreover, in a distributed system, one user is oblivious of the other user's channel status. Therefore, a fast rendezvous is not trivial. Recently, a number of rendezvous strategies have been proposed for different system settings, but rarely have they taken the temporal variation of the channels into account. In this work, we first derive a time-adaptive strategy with optimal expected time-to-rendezvous (TTR) for synchronous systems in stable environments, where channel availability is assumed to be static over time. Next, in dynamic environments, which better represent temporally dynamic channel availability in CRNs, we first derive optimal strategies for two special cases, and then prove that our strategy is still asymptotically optimal in general dynamic cases. Numerous simulations are conducted to demonstrate the performance of our strategies, and validate the theoretical analysis. The impacts of different parameters on the TTR are also investigated, such as the number of channels, the channel open possibilities, the extent of the environment being dynamic, and the existence of an intruder.

cs.NI