arXiv subjects

Jianhua Yao

Publications and source records attributed to Jianhua Yao.

At least 19 recordsLinked to original sources

arXiv2026

Aligning LLMs with Biomedical Knowledge using Balanced Fine-Tuning

Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text exhibits a fundamentally different uncertainty structure from general text: dense low-confidence runs encode epistemic knowledge gaps (dense causal chains, rare entities) rather than the sparse aleatoric stylistic variation typical of general text. Based on this discovery, we propose Balanced Fine-Tuning (BFT), a dual-scale post-training method that combines group-normalized token reweighting with sequence-level reallocation toward knowledge-dense samples exhibiting dense epistemic uncertainty. Across medical evaluation, biological reasoning, sparse-reward RL, and biological representation tasks, BFT provides more consistent gains than SFT and DFT under a shared training setup. When replacing the default closed-source backbones in GeneAgent (GPT-4o) and VCWorld (Gemini-2.5-Flash), the BFT-aligned 70B model delivers stronger performance across biological process reasoning and chemical perturbation prediction. Critically, all BFT variants further improve after subsequent GRPO with sparse rewards, while SFT and DFT degrade, suggesting that epistemic-aware post-training provides a more robust policy initialization. Beyond text generation, BFT-aligned LLMs produce more accurate and professional biomedical profile texts; after encoding these profiles with a text embedding model, the resulting representations support gene-level, cell-level, and perturbation-response tasks, suggesting that BFT-enhanced generation can facilitate biological representation and, in turn, broader biomedical downstream tasks.

cs.LG↗

arXiv2026

Branch-JEPA: Finite-Support Predictive Distributions for JEPA World Models

Joint-embedding predictive architectures (JEPAs) learn dynamics by predicting future observations in representation space. Yet most JEPA world models return one latent successor, even when hidden intent, partial observation, or stochastic dynamics make several futures plausible. We introduce Branch-JEPA, which replaces this point-valued transition with a context-weighted finite set of latent successors. Every branch is decoded independently, and the complete set is retained at inference. The architecture supports two complementary training regimes: specialization for recovering separated successors and full-set Energy-Score training for distributional fidelity. In a locked five-seed evaluation on the Argoverse~2 official validation split, full-set training improves trajectory Energy Score by $5.8$--$6.5\%$ and probability-weighted trajectory distance by $9.3$--$10.4\%$ over matched-$K{=}6$ assignment and transport objectives, while retaining $5.36$ endpoint-deduplicated effective branches. In a parameter-exact official-validation comparison, latent branching retains $10.3\%$ more effective modes and improves Energy Score, expected ADE, and Brier in all five paired seeds over branching only at the output decoder; every paired 95\% interval excludes zero. In an OGBench graph audit, Branch-JEPA increases teleport verified-route existence to $19.2\%$ versus $3.9\%$ for the MDN. Its raw-support advantage also persists with 29-D state and RGB observations. Together, latent branching preserves more distinct futures, while full-set scoring improves the quality of the resulting predictive distribution.

cs.AI↗

arXiv2026

SinAE: A Single-Architecture Flow-Matching Autoencoder for Cross-Domain Atomic Systems

Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture. Cross-domain training would mitigate per-domain data scarcity, but direct generation in 3D coordinate space cannot easily handle the heterogeneous structural priors of all three domains, and no prior latent autoencoder is simultaneously lossless and architecturally general across all three. We introduce SinAE, a single-architecture flow-matching autoencoder for molecules, crystals, and proteins, with vanilla Transformer encoder and decoder and no equivariant, graph, or domain-specific operators. Rather than requiring the encoder to capture fine-grained geometry, SinAE shifts the reconstruction burden into an iterative flow-matching decoder, achieving near-lossless reconstruction across domains and reducing reconstruction errors by orders of magnitude relative to prior latent baselines. The same per-token latent supports a standard Diffusion Transformer prior that reaches strong performance on molecular, crystal, and protein generation benchmarks. Joint molecule--crystal training strictly improves both domains, providing direct evidence of cross-domain transfer through a shared atomic latent. Code is available at https://github.com/BlueWhaleLab/SinAE .

cs.LG↗

arXiv2025

Dynamic Fraud Detection: Integrating Reinforcement Learning into Graph Neural Networks

Financial fraud refers to the act of obtaining financial benefits through dishonest means. Such behavior not only disrupts the order of the financial market but also harms economic and social development and breeds other illegal and criminal activities. With the popularization of the internet and online payment methods, many fraudulent activities and money laundering behaviors in life have shifted from offline to online, posing a great challenge to regulatory authorities. How to efficiently detect these financial fraud activities has become an urgent issue that needs to be resolved. Graph neural networks are a type of deep learning model that can utilize the interactive relationships within graph structures, and they have been widely applied in the field of fraud detection. However, there are still some issues. First, fraudulent activities only account for a very small part of transaction transfers, leading to an inevitable problem of label imbalance in fraud detection. At the same time, fraudsters often disguise their behavior, which can have a negative impact on the final prediction results. In addition, existing research has overlooked the importance of balancing neighbor information and central node information. For example, when the central node has too many neighbors, the features of the central node itself are often neglected. Finally, fraud activities and patterns are constantly changing over time, so considering the dynamic evolution of graph edge relationships is also very important.

cs.LG↗

arXiv2025

Steering Protein Language Models

Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified functionalities or properties due to inherent challenges in controlling their outputs. In this work, we investigate the potential of Activation Steering, a technique originally developed for controlling text generation in Large Language Models (LLMs), to direct PLMs toward generating protein sequences with targeted properties. We propose a simple yet effective method that employs activation editing to steer PLM outputs, and extend this approach to protein optimization through a novel editing site identification module. Through comprehensive experiments on lysozyme-like sequence generation and optimization, we demonstrate that our methods can be seamlessly integrated into both auto-encoding and autoregressive PLMs without requiring additional training. These results highlight a promising direction for precise protein engineering using foundation models.

q-bio.BM↗

arXiv2025

Application of Deep Generative Models for Anomaly Detection in Complex Financial Transactions

This study proposes an algorithm for detecting suspicious behaviors in large payment flows based on deep generative models. By combining Generative Adversarial Networks (GAN) and Variational Autoencoders (VAE), the algorithm is designed to detect abnormal behaviors in financial transactions. First, the GAN is used to generate simulated data that approximates normal payment flows. The discriminator identifies anomalous patterns in transactions, enabling the detection of potential fraud and money laundering behaviors. Second, a VAE is introduced to model the latent distribution of payment flows, ensuring that the generated data more closely resembles real transaction features, thus improving the model's detection accuracy. The method optimizes the generative capabilities of both GAN and VAE, ensuring that the model can effectively capture suspicious behaviors even in sparse data conditions. Experimental results show that the proposed method significantly outperforms traditional machine learning algorithms and other deep learning models across various evaluation metrics, especially in detecting rare fraudulent behaviors. Furthermore, this study provides a detailed comparison of performance in recognizing different transaction patterns (such as normal, money laundering, and fraud) in large payment flows, validating the advantages of generative models in handling complex financial data.

cs.LG↗

arXiv2025

Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from different modalities that may fail to capture fine-grained information, such as molecule-and-text fragments and stereoisomeric nuances, which is crucial for downstream tasks. Furthermore, it is incapable of modeling such information using a similar global alignment strategy due to the lack of annotations about the fine-grained fragments in the existing dataset. In this paper, we propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic levels. Atomas's end-to-end training framework supports understanding and generating molecules, enabling a wider range of downstream tasks. Atomas achieves superior performance across 12 tasks on 11 datasets, outperforming 11 baseline models thus highlighting the effectiveness and versatility of our method. Scaling experiments further demonstrate Atomas's robustness and scalability. Moreover, visualization and qualitative analysis, validated by human experts, confirm the chemical relevance of our approach. Codes are released on https://github.com/yikunpku/Atomas.

q-bio.QM↗

arXiv2025

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

q-bio.OT↗

arXiv2024

Annotation-guided Protein Design with Multi-Level Domain Alignment

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

q-bio.QM↗

arXiv2024

Stock Type Prediction Model Based on Hierarchical Graph Neural Network

This paper introduces a novel approach to stock data analysis by employing a Hierarchical Graph Neural Network (HGNN) model that captures multi-level information and relational structures in the stock market. The HGNN model integrates stock relationship data and hierarchical attributes to predict stock types effectively. The paper discusses the construction of a stock industry relationship graph and the extraction of temporal information from historical price sequences. It also highlights the design of a graph convolution operation and a temporal attention aggregator to model the macro market state. The integration of these features results in a comprehensive stock prediction model that addresses the challenges of utilizing stock relationship data and modeling hierarchical attributes in the stock market.

cs.LG↗

arXiv2024

Unveiling the Potential of Graph Neural Networks in SME Credit Risk Assessment

This paper takes the graph neural network as the technical framework, integrates the intrinsic connections between enterprise financial indicators, and proposes a model for enterprise credit risk assessment. The main research work includes: Firstly, based on the experience of predecessors, we selected 29 enterprise financial data indicators, abstracted each indicator as a vertex, deeply analyzed the relationships between the indicators, constructed a similarity matrix of indicators, and used the maximum spanning tree algorithm to achieve the graph structure mapping of enterprises; secondly, in the representation learning phase of the mapped graph, a graph neural network model was built to obtain its embedded representation. The feature vector of each node was expanded to 32 dimensions, and three GraphSAGE operations were performed on the graph, with the results pooled using the Pool operation, and the final output of three feature vectors was averaged to obtain the graph's embedded representation; finally, a classifier was constructed using a two-layer fully connected network to complete the prediction task. Experimental results on real enterprise data show that the model proposed in this paper can well complete the multi-level credit level estimation of enterprises. Furthermore, the tree-structured graph mapping deeply portrays the intrinsic connections of various indicator data of the company, and according to the ROC and other evaluation criteria, the model's classification effect is significant and has good "robustness".

q-fin.RM↗

arXiv2024

Meta-Learn Unimodal Signals with Weak Supervision for Multimodal Sentiment Analysis

Multimodal sentiment analysis aims to effectively integrate information from various sources to infer sentiment, where in many cases there are no annotations for unimodal labels. Therefore, most works rely on multimodal labels for training. However, there exists the noisy label problem for the learning of unimodal signals as multimodal annotations are not always the ideal substitutes for the unimodal ones, failing to achieve finer optimization for individual modalities. In this paper, we explore the learning of unimodal labels under the weak supervision from the annotated multimodal labels. Specifically, we propose a novel meta uni-label generation (MUG) framework to address the above problem, which leverages the available multimodal labels to learn the corresponding unimodal labels by the meta uni-label correction network (MUCN). We first design a contrastive-based projection module to bridge the gap between unimodal and multimodal representations, so as to use multimodal annotations to guide the learning of MUCN. Afterwards, we propose unimodal and multimodal denoising tasks to train MUCN with explicit supervision via a bi-level optimization strategy. We then jointly train unimodal and multimodal learning tasks to extract discriminative unimodal features for multimodal inference. Experimental results suggest that MUG outperforms competitive baselines and can learn accurate unimodal labels.

cs.LG↗

arXiv2024

Relaxing Continuous Constraints of Equivariant Graph Neural Networks for Physical Dynamics Learning

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various scientific and engineering applications, the symmetries of dynamics are frequently discrete due to the boundary conditions. Thus, existing GNNs either overlook necessary symmetry, resulting in suboptimal representation ability, or impose excessive equivariance, which fails to generalize to unobserved symmetric dynamics. In this work, we propose a general Discrete Equivariant Graph Neural Network (DEGNN) that guarantees equivariance to a given discrete point group. Specifically, we show that such discrete equivariant message passing could be constructed by transforming geometric features into permutation-invariant embeddings. Through relaxing continuous equivariant constraints, DEGNN can employ more geometric feature combinations to approximate unobserved physical object interaction functions. Two implementation approaches of DEGNN are proposed based on ranking or pooling permutation-invariant functions. We apply DEGNN to various physical dynamics, ranging from particle, molecular, crowd to vehicle dynamics. In twenty scenarios, DEGNN significantly outperforms existing state-of-the-art approaches. Moreover, we show that DEGNN is data efficient, learning with less data, and can generalize across scenarios such as unobserved orientation.

cs.LG↗

arXiv2024

StableMask: Refining Causal Masking in Decoder-only Transformer

The decoder-only Transformer architecture with causal masking and relative position encoding (RPE) has become the de facto choice in language modeling. Despite its exceptional performance across various tasks, we have identified two limitations: First, it requires all attention scores to be non-zero and sum up to 1, even if the current embedding has sufficient self-contained information. This compels the model to assign disproportional excessive attention to specific tokens. Second, RPE-based Transformers are not universal approximators due to their limited capacity at encoding absolute positional information, which limits their application in position-critical tasks. In this work, we propose StableMask: a parameter-free method to address both limitations by refining the causal mask. It introduces pseudo-attention values to balance attention distributions and encodes absolute positional information via a progressively decreasing mask ratio. StableMask's effectiveness is validated both theoretically and empirically, showing significant enhancements in language models with parameter sizes ranging from 71M to 1.4B across diverse datasets and encoding methods. We further show that it naturally supports (1) efficient extrapolation without special tricks such as StreamingLLM and (2) easy integration with existing attention optimization techniques.

cs.CL↗

arXiv2023

Semi-supervised Semantic Segmentation Meets Masked Modeling:Fine-grained Locality Learning Matters in Consistency Regularization

Semi-supervised semantic segmentation aims to utilize limited labeled images and abundant unlabeled images to achieve label-efficient learning, wherein the weak-to-strong consistency regularization framework, popularized by FixMatch, is widely used as a benchmark scheme. Despite its effectiveness, we observe that such scheme struggles with satisfactory segmentation for the local regions. This can be because it originally stems from the image classification task and lacks specialized mechanisms to capture fine-grained local semantics that prioritizes in dense prediction. To address this issue, we propose a novel framework called \texttt{MaskMatch}, which enables fine-grained locality learning to achieve better dense segmentation. On top of the original teacher-student framework, we design a masked modeling proxy task that encourages the student model to predict the segmentation given the unmasked image patches (even with 30\% only) and enforces the predictions to be consistent with pseudo-labels generated by the teacher model using the complete image. Such design is motivated by the intuition that if the predictions are more consistent given insufficient neighboring information, stronger fine-grained locality perception is achieved. Besides, recognizing the importance of reliable pseudo-labels in the above locality learning and the original consistency learning scheme, we design a multi-scale ensembling strategy that considers context at different levels of abstraction for pseudo-label generation. Extensive experiments on benchmark datasets demonstrate the superiority of our method against previous approaches and its plug-and-play flexibility.

cs.CV↗

arXiv2023

DNAGPT: A Generalized Pre-trained Tool for Versatile DNA Sequence Analysis Tasks

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

q-bio.GN↗

arXiv2023

A Noisy-Label-Learning Formulation for Immune Repertoire Classification and Disease-Associated Immune Receptor Sequence Identification

Immune repertoire classification, a typical multiple instance learning (MIL) problem, is a frontier research topic in computational biology that makes transformative contributions to new vaccines and immune therapies. However, the traditional instance-space MIL, directly assigning bag-level labels to instances, suffers from the massive amount of noisy labels and extremely low witness rate. In this work, we propose a noisy-label-learning formulation to solve the immune repertoire classification task. To remedy the inaccurate supervision of repertoire-level labels for a sequence-level classifier, we design a robust training strategy: The initial labels are smoothed to be asymmetric and are progressively corrected using the model's predictions throughout the training process. Furthermore, two models with the same architecture but different parameter initialization are co-trained simultaneously to remedy the known "confirmation bias" problem in the self-training-like schema. As a result, we obtain accurate sequence-level classification and, subsequently, repertoire-level classification. Experiments on the Cytomegalovirus (CMV) and Cancer datasets demonstrate our method's effectiveness and superior performance on sequence-level and repertoire-level tasks.

cs.LG↗

arXiv2023

Reweighted Mixup for Subpopulation Shift

Subpopulation shift exists widely in many real-world applications, which refers to the training and test distributions that contain the same subpopulation groups but with different subpopulation proportions. Ignoring subpopulation shifts may lead to significant performance degradation and fairness concerns. Importance reweighting is a classical and effective way to handle the subpopulation shift. However, recent studies have recognized that most of these approaches fail to improve the performance especially when applied to over-parameterized neural networks which are capable of fitting any training samples. In this work, we propose a simple yet practical framework, called reweighted mixup (RMIX), to mitigate the overfitting issue in over-parameterized models by conducting importance weighting on the ''mixed'' samples. Benefiting from leveraging reweighting in mixup, RMIX allows the model to explore the vicinal space of minority samples more, thereby obtaining more robust model against subpopulation shift. When the subpopulation memberships are unknown, the training-trajectories-based uncertainty estimation is equipped in the proposed RMIX to flexibly characterize the subpopulation distribution. We also provide insightful theoretical analysis to verify that RMIX achieves better generalization bounds over prior works. Further, we conduct extensive empirical studies across a wide range of tasks to validate the effectiveness of the proposed method.

cs.LG↗