Sijie Chen

Tong Lin, Sijie Chen, Ruchira Basu et al.

Despite the prevalence and many successes of deep learning applications in de novo molecular design, the problem of peptide generation targeting specific proteins remains unsolved. A main barrier for this is the scarcity of the high-quality training data. To tackle the issue, we propose a novel machine learning based peptide design architecture, called Latent Space Approximate Trajectory Collector (LSATC). It consists of a series of samplers on an optimization trajectory on a highly non-convex energy landscape that approximates the distributions of peptides with desired properties in a latent space. The process involves little human intervention and can be implemented in an end-to-end manner. We demonstrate the model by the design of peptide extensions targeting Beta-catenin, a key nuclear effector protein involved in canonical Wnt signalling. When compared with a random sampler, LSATC can sample peptides with $36\%$ lower binding scores in a $16$ times smaller interquartile range (IQR) and $284\%$ less hydrophobicity with a $1.4$ times smaller IQR. LSATC also largely outperforms other common generative models. Finally, we utilized a clustering algorithm to select 4 peptides from the 100 LSATC designed peptides for experimental validation. The result confirms that all the four peptides extended by LSATC show improved Beta-catenin binding by at least $20.0\%$, and two of the peptides show a $3$ fold increase in binding affinity as compared to the base peptide.

Yifan Sun, Lei Cheng, Sijie Chen et al.

Learning-based surrogates have become increasingly effective for wave-field prediction, and neural operators in particular have shown strong performance within observed frequency regimes. However, higher-frequency prediction under scarce target supervision remains comparatively underexplored, especially in wave problems where higher-frequency data are substantially more expensive to simulate or measure than lower-frequency data. A central difficulty is that cross-frequency transfer is inherently asymmetric: coarse amplitude structure remains relatively stable across frequencies, whereas phase-sensitive oscillatory structure deteriorates much more rapidly as frequency increases. Motivated by this asymmetry, we propose APEX, Amplitude-anchored and Phase-prior-guided Enhancement from eXtrapolated coarse predictions, a framework for target-scarce higher-frequency wave-field prediction. A lower-frequency neural operator first provides a coarse prediction in the target-frequency regime, from which we retain only the amplitude as a transferable structural anchor. A conditional flow-matching enhancer then reconstructs the target higher-frequency field under the guidance of a Green's-function-inspired phase prior. Experiments on SimpleWave, Helmholtz, and Maxwell benchmarks show that APEX consistently outperforms direct lower-to-higher extrapolation, target-adapted operator, and joint generative baselines under limited target-frequency supervision. Our results suggest that reliable higher-frequency prediction of oscillatory wave fields should not rely on direct end-to-end transfer of the full complex field, but instead on explicitly reusing transferable coarse structure while separately recovering the missing oscillatory detail.

Jingru Chen, Yiming Liu, Mingtao Chen et al.

Frontier multimodal large language models (MLLMs) have been reported to achieve over 90% accuracy on fine-grained perception benchmarks. However, such scores do not necessarily imply faithful use of visual evidence. Prior studies have identified three shortcuts that inflate benchmark performance. First, linguistic priors and lexical cues in questions often enable models to infer plausible answers without seeing the image. Second, coarse global semantics from the visual encoder can bypass fine-grained local details. Third, in some ``think-with-images'' benchmarks, corrupting the intermediate images returned by visual tools barely affects the final answer. These findings suggest that higher input resolution or larger question pools alone do not elicit genuine active visual search. To address this, we introduce VisualNeedle, a challenging, information-dense, and fine-grained benchmark for scenes where critical evidence is spatially constrained to minute regions and not discernible at a glance. We further propose a counterfactual crop-black setting, which replaces crops returned by tools with black images of the same size, to test whether tool-enabled performance truly relies on intermediate visual evidence. We evaluate 9 promninent MLLMs across three settings: no-tool, standard tool-enabled, and crop-black. No-tool accuracy stays below 20\%, and the best tool-enabled model reaches only 56.01\%, still trailing the 63.00% human majority-vote accuracy. These results reveal persistent limitations in fine-grained visual search, while the crop-black ablation confirms that success on VisualNeedle hinges on genuine intermediate visual evidence.

Alessandro Magnani, Feng Liu, Suthee Chaidaroon et al.

In product search, the retrieval of candidate products before re-ranking is more critical and challenging than other search like web search, especially for tail queries, which have a complex and specific search intent. In this paper, we present a hybrid system for e-commerce search deployed at Walmart that combines traditional inverted index and embedding-based neural retrieval to better answer user tail queries. Our system significantly improved the relevance of the search engine, measured by both offline and online evaluations. The improvements were achieved through a combination of different approaches. We present a new technique to train the neural model at scale. and describe how the system was deployed in production with little impact on response time. We highlight multiple learnings and practical tricks that were used in the deployment of this system.

Dian Chen, Yunkai Chen, Tong Lin et al.

Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the inherent conformational flexibility of peptides and the limited availability of structural data that hinder direct training of structure-aware models. To address these limitations, we introduce GeoPep, a novel framework for peptide binding site prediction that leverages transfer learning from ESM3, a multimodal protein foundation model. GeoPep fine-tunes ESM3's rich pre-learned representations from protein-protein binding to address the limited availability of protein-peptide binding data. The fine-tuned model is further integrated with a parameter-efficient neural network architecture capable of learning complex patterns from sparse data. Furthermore, the model is trained using distance-based loss functions that exploit 3D structural information to enhance binding site prediction. Comprehensive evaluations demonstrate that GeoPep significantly outperforms existing methods in protein-peptide binding site prediction by effectively capturing sparse and heterogeneous binding patterns.

Qiangang Jia, Zhaoyu Hu, Yiyan Li et al.

Q learning is widely used to simulate the behaviors of generation companies (GenCos) in an electricity market. However, existing Q learning method usually requires numerous iterations to converge, which is time-consuming and inefficient in practice. To enhance the calculation efficiency, a novel Q learning algorithm improved by dichotomy is proposed in this paper. This method modifies the update process of the Q table by dichotomizing the state space and the action space step by step. Simulation results in a repeated Cournot game show the effectiveness of the proposed algorithm.