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Shihao Ma

dblp:263/8146 · DBLP profile ↗
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4ranked-venue papers
0as first author
4since 2021 · last 2025
0009-0000-3336-8248ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 4 · 4 since 2021Systems, architecture and hardware · 2 · 2 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Vision and language · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Computer vision › Vision and language
multimodal reasoning
0.912025
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model · NeurIPS 2025
Bioinformatics and computational biology › sequence analysis
genomic sequence analysis
0.912025
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model · NeurIPS 2025
Bioinformatics and computational biology › statistical genetics
variant effect prediction
0.912025
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model · NeurIPS 2025

Methods — techniques the papers use, named apart from their topics

supervised fine-tuning · 1.7reinforcement learning · 1.7DNA foundation model · 1.7
YearPublicationVenuePosition
2025 A Modified Resistance Model for Magnetic Honeycomb Robots to Navigate in Low Reynolds Number Fluids
abstract
In recent years, magnetically controlled microrobots have garnered significant attention. This paper presents the H-robot, a self-designed microrobot featuring an innovative structure. The H-robot features a honeycomb porous spherical design specifically engineered to enhance cargo capacity. A new dynamic model for this structure has been developed for low Reynolds number fluid environments, along with a robust backstepping sliding mode control (RBSMC) strategy. Experiments were conducted in a calibrated magnetic field generated by a magnetic field generator to achieve precise motion control. The results demonstrate that the H-robot accurately tracks standard trajectories, with root mean square errors (RMSE) of$9.09 \times 10^{-4} \mathbf{~ m}$for the Number-8 path and$8.29 \times 10^{-4} \mathbf{~ m}$for the S-shaped path. Additionally, the proposed resistance model enhances tracking accuracy by 73.61% compared to traditional models, effectively adjusting the dynamic behavior of the H-robot in low Reynolds number fluids and significantly improving its motion performance. Finally, path planning experiments in a maze demonstrate the H-robot's ability to navigate and avoid obstacles.
Leyao Zou, Shihao Ma, Yi Liu 0027, Xinyang Dong, Ziqing Zhou, Chun Ouyang 0002, Zhongxue Gan 0001
ICRA2
2025 Ctrl-DNA: Controllable Cell-Type-Specific Regulatory DNA Design via Constrained RL
abstract
Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can effectively capture patterns in regulatory DNA, their generative approaches often struggle to produce novel sequences with reliable cell-specific activity. Here, we introduce Ctrl-DNA, a novel constrained reinforcement learning (RL) framework tailored for designing regulatory DNA sequences with controllable cell-type specificity. By formulating regulatory sequence design as a biologically informed constrained optimization problem, we apply RL to autoregressive genomic LMs, enabling the models to iteratively refine sequences that maximize regulatory activity in targeted cell types while constraining off-target effects. Our evaluation on human promoters and enhancers demonstrates that Ctrl-DNA consistently outperforms existing generative and RL-based approaches, generating high-fitness regulatory sequences and achieving state-of-the-art cell-type specificity. Moreover, Ctrl-DNA-generated sequences capture key cell-type-specific transcription factor binding sites (TFBS), short DNA motifs recognized by regulatory proteins that control gene expression, demonstrating the biological plausibility of the generated sequences.
Shihao Ma, Runsheng Lin, Jiecong Lin
NeurIPS2
2025 BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
abstract
Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology. All data, code, and checkpoints are available at [https://github.com/bowang-lab/BioReason](https://github.com/bowang-lab/BioReason).
Adibvafa Fallahpour, Andrew Magnuson, Purav Gupta, Shihao Ma, Jack Naimer, Arnav Shah, Haonan Duan 0002, Omar Ibrahim, Hani Goodarzi, Chris J. Maddison, Bo Wang 0044
NeurIPS4
2022 Design and Experiments of Snake Robots with Docking Function
abstract
This paper presents a novel snake robot with the docking function, which can help the snake robots to connect with each other to achieve a stronger one with double length and double degrees of freedom. First, the mechanical design of the snake robot with docking function is introduced, including the body link and the head-tail passive docking mechanical structure. Second, the control system is built, and the control strategies of locomotion and docking are separately proposed. Then, the visual perception function is implemented for the target recognition during the docking process. Finally, the prototype is developed. The mobility and the docking function are fully verified and analyzed through the physical experiments.
Fatao Qin, Xiaojie Duan, Shihao Ma, Jinglun Yuan
IROS3