Yang Yang

Yifei Yang, Runhan Shi, Zuchao Li et al.

Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction types and exploring alternative synthetic pathways. This paper presents BatGPT-Chem, a large language model with 15 billion parameters, tailored for enhanced retrosynthesis prediction. Integrating chemical tasks via a unified framework of natural language and SMILES notation, this approach synthesizes extensive instructional data from an expansive chemical database. Employing both autoregressive and bidirectional training techniques across over one hundred million instances, BatGPT-Chem captures a broad spectrum of chemical knowledge, enabling precise prediction of reaction conditions and exhibiting strong zero-shot capabilities. Superior to existing AI methods, our model demonstrates significant advancements in generating effective strategies for complex molecules, as validated by stringent benchmark tests. BatGPT-Chem not only boosts the efficiency and creativity of retrosynthetic analysis but also establishes a new standard for computational tools in synthetic design. This development empowers chemists to adeptly address the synthesis of novel compounds, potentially expediting the innovation cycle in drug manufacturing and materials science. We release our trial platform at \url{https://www.batgpt.net/dapp/chem}.

Zhenqiao Song, Yunlong Zhao, Wenxian Shi et al.

Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together determine its function. In this paper, we propose NAEPro, a model to jointly design Protein sequence and structure based on automatically detected functional sites. NAEPro is powered by an interleaving network of attention and equivariant layers, which can capture global correlation in a whole sequence and local influence from nearest amino acids in three dimensional (3D) space. Such an architecture facilitates effective yet economic message passing at two levels. We evaluate our model and several strong baselines on two protein datasets, $β$-lactamase and myoglobin. Experimental results show that our model consistently achieves the highest amino acid recovery rate, TM-score, and the lowest RMSD among all competitors. These findings prove the capability of our model to design protein sequences and structures that closely resemble their natural counterparts. Furthermore, in-depth analysis further confirms our model's ability to generate highly effective proteins capable of binding to their target metallocofactors. We provide code, data and models in Github.

Zhenqiao Song, Yunlong Zhao, Yufei Song et al.

Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and structure co-design underexplored. In this paper, we propose GeoPro, a method to design protein backbone structure and sequence jointly. Our motivation is that protein sequence and its backbone structure constrain each other, and thus joint design of both can not only avoid nonfolding and misfolding but also produce more diverse candidates with desired functions. To this end, GeoPro is powered by an equivariant encoder for three-dimensional (3D) backbone structure and a protein sequence decoder guided by 3D geometry. Experimental results on two biologically significant metalloprotein datasets, including $β$-lactamases and myoglobins, show that our proposed GeoPro outperforms several strong baselines on most metrics. Remarkably, our method discovers novel $β$-lactamases and myoglobins which are not present in protein data bank (PDB) and UniProt. These proteins exhibit stable folding and active site environments reminiscent of those of natural proteins, demonstrating their excellent potential to be biologically functional.

Weijia Dou, Xu Zhang, Yi Bin et al.

Recent attempts to transfer features from 2D Vision-Language Models (VLMs) to 3D semantic segmentation expose a persistent trade-off. Directly projecting 2D features into 3D yields noisy and fragmented predictions, whereas enforcing geometric coherence necessitates costly training pipelines and large-scale annotated 3D data. We argue that this limitation stems from the dominant segmentation-and-matching paradigm, which fails to reconcile 2D semantics with 3D geometric structure. The geometric cues are not eliminated during the 2D-to-3D transfer but remain latent within the noisy and view-aggregated features. To exploit this property, we propose GeoPurify that applies a small Student Affinity Network to purify 2D VLM-generated 3D point features using geometric priors distilled from a 3D self-supervised teacher model. During inference, we devise a Geometry-Guided Pooling module to further denoise the point cloud and ensure the semantic and structural consistency. Benefiting from latent geometric information and the learned affinity network, GeoPurify effectively mitigates the trade-off and achieves superior data efficiency. Extensive experiments on major 3D benchmarks demonstrate that GeoPurify achieves or surpasses state-of-the-art performance while utilizing only about 1.5% of the training data. Our codes and checkpoints are available at [https://github.com/tj12323/GeoPurify](https://github.com/tj12323/GeoPurify).

Isaac Shi, Zeyuan Li, Fan Liu et al.

We present the DEREK (Deep Extraction & Reasoning Engine for Knowledge) Module, a secure and scalable Retrieval-Augmented Generation pipeline designed specifically for enterprise document question answering. Designed and implemented by eSapiens, the system ingests heterogeneous content (PDF, Office, web), splits it into 1,000-token overlapping chunks, and indexes them in a hybrid HNSW+BM25 store. User queries are refined by GPT-4o, retrieved via combined vector+BM25 search, reranked with Cohere, and answered by an LLM using CO-STAR prompt engineering. A LangGraph verifier enforces citation overlap, regenerating answers until every claim is grounded. On four LegalBench subsets, 1000-token chunks improve Recall@50 by approximately 1 pp and hybrid+rerank boosts Precision@10 by approximately 7 pp; the verifier raises TRACe Utilization above 0.50 and limits unsupported statements to less than 3%. All components run in containers, enforce end-to-end TLS 1.3 and AES-256. These results demonstrate that the DEREK module delivers accurate, traceable, and production-ready document QA with minimal operational overhead. The module is designed to meet enterprise demands for secure, auditable, and context-faithful retrieval, providing a reliable baseline for high-stakes domains such as legal and finance.

Sheng Zheng, Chaoning Zhang, Dongshen Han et al.

Implicit neural representations (INRs), which leverage neural networks to represent signals by mapping coordinates to their corresponding attributes, have garnered significant attention. They are extensively utilized for image representation, with pixel coordinates as input and pixel values as output. In contrast to prior works focusing on investigating the effect of the model's inside components (activation function, for instance), this work pioneers the exploration of the effect of kernel transformation of input/output while keeping the model itself unchanged. A byproduct of our findings is a simple yet effective method that combines scale and shift to significantly boost INR with negligible computation overhead. Moreover, we present two perspectives, depth and normalization, to interpret the performance benefits caused by scale and shift transformation. Overall, our work provides a new avenue for future works to understand and improve INR through the lens of kernel transformation.

Hao Xu, Jinglong Lin, Qianyi Liu et al.

As an essential attribute of organic compounds, polarity has a profound influence on many molecular properties such as solubility and phase transition temperature. Thin layer chromatography (TLC) represents a commonly used technique for polarity measurement. However, current TLC analysis presents several problems, including the need for a large number of attempts to obtain suitable conditions, as well as irreproducibility due to non-standardization. Herein, we describe an automated experiment system for TLC analysis. This system is designed to conduct TLC analysis automatically, facilitating high-throughput experimentation by collecting large experimental data under standardized conditions. Using these datasets, machine learning (ML) methods are employed to construct surrogate models correlating organic compounds' structures and their polarity using retardation factor (Rf). The trained ML models are able to predict the Rf value curve of organic compounds with high accuracy. Furthermore, the constitutive relationship between the compound and its polarity can also be discovered through these modeling methods, and the underlying mechanism is rationalized through adsorption theories. The trained ML models not only reduce the need for empirical optimization currently required for TLC analysis, but also provide general guidelines for the selection of conditions, making TLC an easily accessible tool for the broad scientific community.

Yang Yang, Ke Deng, Michael Zhu

Hyperparameters play a critical role in the performances of many machine learning methods. Determining their best settings or Hyperparameter Optimization (HPO) faces difficulties presented by the large number of hyperparameters as well as the excessive training time. In this paper, we develop an effective approach to reducing the total amount of required training time for HPO. In the initialization, the nested Latin hypercube design is used to select hyperparameter configurations for two types of training, which are, respectively, heavy training and light training. We propose a truncated additive Gaussian process model to calibrate approximate performance measurements generated by light training, using accurate performance measurements generated by heavy training. Based on the model, a sequential model-based algorithm is developed to generate the performance profile of the configuration space as well as find optimal ones. Our proposed approach demonstrates competitive performance when applied to optimize synthetic examples, support vector machines, fully connected networks and convolutional neural networks.