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Applications · Robotics

Xiaochen Shang, Pengwei Luo, Xinning Wang, Jiayue Zhao, Huilin Ge, Bo Dong, Xin Yang

Unmanned aerial vehicles could accurately accomplish complex navigation and obstacle avoidance tasks under external control. However, enabling unmanned aerial vehicles (UAVs) to rely solely on onboard computation and sensing for real-time navigation and dynamic obstacle avoidance remains a significant challenge due to stringent latency and energy constraints. Inspired by the efficiency of biological systems, we propose a fully neuromorphic framework achieving end-to-end obstacle avoidance during navigation with an overall latency of just 2.3 milliseconds. Specifically, our bio-inspired approach enables accurate moving object detection and avoidance without requiring target recognition or trajectory computation. Additionally, we introduce the first monocular event-based pose correction dataset with over 50,000 paired and labeled event streams. We validate our system on an autonomous quadrotor using only onboard resources, demonstrating reliable navigation and avoidance of diverse obstacles moving at speeds up to 10 m/s.

Computer Vision · 3D Rendering & Reconstruction

Gang Wan, Qinlong Lan, Zihan Li, Huimin Wang, Wu Yitian, wang zhen, Wanhua Li, Yufei Guo

Spiking Neural Networks (SNNs), as a biologically inspired neural network architecture, have garnered significant attention due to their exceptional energy efficiency and increasing potential for various applications. In this work, we extend the use of SNNs to neural rendering tasks and introduce Spik-NeRF (Spiking Neural Radiance Fields). We observe that the binary spike activation map of traditional SNNs lacks sufficient information capacity, leading to information loss and a subsequent decline in the performance of spiking neural rendering models. To address this limitation, we propose the use of ternary spike neurons, which enhance the information-carrying capacity in the spiking neural rendering model. With ternary spike neurons, Spik-NeRF achieves performance that is on par with, or nearly identical to, traditional ANN-based rendering models. Additionally, we present a re-parameterization technique for inference that allows Spik-NeRF with ternary spike neurons to retain the event-driven, multiplication-free advantages typical of binary spike neurons. Furthermore, to further boost the performance of Spik-NeRF, we employ a distillation method, using an ANN-based NeRF to guide the training of our Spik-NeRF model, which is more compatible with the ternary neurons compared to the standard binary neurons. We evaluate Spik-NeRF on both realistic and synthetic scenes, and the experimental results demonstrate that Spik-NeRF achieves rendering performance comparable to ANN-based NeRF models.

Applications · Everything Else

Sebastian Joseph, Syed M. Husain, Stella Offner, Stéphanie Juneau, Paul Torrey, Adam Bolton, Juan Farias, Niall Gaffney, Greg Durrett, Junyi Jessy Li

Large Language Models (LLMs) are being explored for applications in scientific research, including their capabilities to synthesize literature, answer research questions, generate research ideas, and even conduct computational experiments.Ultimately, our goal is for these to help scientists derive novel scientific insights. In many areas of science, such insights often arise from processing and visualizing data to understand its patterns. However, evaluating whether an LLM-mediated scientific workflow produces outputs conveying the correct scientific insights is challenging to evaluate and has not been addressed in past work.We introduce AstroVisBench, the first benchmark for both scientific computing and visualization in the astronomy domain.AstroVisBench judges a language model’s ability to both (1) create astronomy-specific workflows to process and analyze data and (2) visualize the results of these workflows through complex plots.Our evaluation of visualizations uses a novel LLM-as-a-judge workflow, which is validated against annotation by five professional astronomers.Using AstroVisBench we present an evaluation of state-of-the-art language models, showing a significant gap in their ability to engage in astronomy research as useful assistants.This evaluation provides a strong end-to-end evaluation for AI scientists that offers a path forward for the development of visualization-based workflows, which are central to a broad range of domains from physics to biology.

Applications · Physics

Rishal Aggarwal, Jacky Chen, Nicholas Boffi, David Koes

Efficient sampling from the Boltzmann distribution given its energy function is a key challenge for modeling complex physical systems such as molecules. Boltzmann Generators address this problem by leveraging continuous normalizing flows to transform a simple prior into a distribution that can be reweighted to match the target using sample likelihoods. Despite the elegance of this approach, obtaining these likelihoods requires computing costly Jacobians during integration, which is impractical for large molecular systems. To overcome this difficulty, we train an energy-based model (EBM) to approximate likelihoods using both noise contrastive estimation (NCE) and score matching, which we show outperforms the use of either objective in isolation. On 2D synthetic systems where failure can be easily visualized, NCE improves mode weighting relative to score matching alone. On alanine dipeptide, our method yields free energy profiles and energy distributions that closely match those obtained using exact likelihoods while achieving $100\times$ faster inference. By training on multiple dipeptide systems, we show that our approach also exhibits effective transfer learning, generalizing to new systems at inference time and achieving at least a $6\times$ speedup over standard MD with only a bit of fine-tuning. While many recent efforts in generative modeling have prioritized models with fast sampling, our work demonstrates the design of models with accelerated likelihoods, enabling the application of reweighting schemes that ensure unbiased Boltzmann statistics at scale. Our code is available at https://github.com/RishalAggarwal/BoltzNCE.

Computer Vision · Vision Models & Multimodal

Vardhan Dongre, Chi Gui, Shubham Garg, Hooshang Nayyeri, Gokhan Tur, Dilek Hakkani-Tur, Vikram Adve

We introduce MIRAGE, a new benchmark for multimodal expert-level reasoning and decision-making in consultative interaction settings. Designed for the domain of agriculture, MIRAGE captures the full complexity of expert consultations by combining natural user queries, expert-authored responses, and image-based context, offering a high-fidelity benchmark for evaluating models on grounded reasoning, clarification strategies, and long-form generation in a real-world, knowledge-intensive domain. Grounded in over 35,000 real user-expert interactions, and curated through a carefully designed multi-step pipeline, MIRAGE spans diverse crop health, pest diagnosis, and crop management scenarios. The benchmark includes more than 7,000 unique biological entities, covering plant species, pests, and diseases, making it one of the most taxonomically diverse benchmarks available for vision-language models in real-world expert-guided domains. Unlike existing benchmarks that rely on well-specified user inputs, MIRAGE features underspecified, context-rich scenarios, requiring models to infer latent knowledge gaps and either proactively guide the interaction or respond. Our benchmark comprises two core components. The Single-turn Challenge to reason over a single user turn and image set, identify relevant entities, infer causal explanations, and generate actionable recommendations; and a Multi-Turn challenge for dialogue state tracking, goal-driven generation, and expert-level conversational decision-making. We evaluate more than 20 closed and open-source frontier vision-language models (VLMs), using three reasoning language models as evaluators, highlighting the significant challenges posed by MIRAGE in both single-turn and multi-turn interaction settings. Even the advanced GPT4.1 and GPT4o models achieve 44.6% and 40.9% accuracy, respectively, indicating significant room for improvement.

Applications

Julien Martinelli

Physics-Informed Machine Learning (PIML) has successfully integrated mechanistic understanding into machine learning, particularly in domains governed by well-known physical laws.This success has motivated efforts to apply PIML to biology, a field rich in dynamical systems but shaped by different constraints.Biological modeling, however, presents unique challenges: multi-faceted and uncertain prior knowledge, heterogeneous and noisy data, partial observability, and complex, high-dimensional networks.\textbf{In this position paper, we argue that these challenges should not be seen as obstacles to PIML, but as catalysts for its evolution. We propose Biology-Informed Machine Learning (BIML): a principled extension of PIML that retains its structural grounding while adapting to the practical realities of biology.}Rather than replacing PIML, BIML retools its methods to operate under softer, probabilistic forms of prior knowledge.We outline four foundational pillars as a roadmap for this transition: uncertainty quantification, contextualization, constrained latent structure inference, and scalability.Foundation Models and Large Language Models will be key enablers, bridging human expertise with computational modeling.We conclude with concrete recommendations to build the BIML ecosystem and channel PIML-inspired innovation toward challenges of high scientific and societal relevance.

Deep Learning · Algorithms

Fu Feng, Yucheng Xie, Ruixiao Shi, Jianlu Shen, Jingq Wang, Xin Geng

Knowledge in modern neural networks is often entangled and structurally opaque, making current transfer methods—typically based on reusing entire parameter sets—inefficient and inflexible. Efforts to improve flexibility by reusing partial parameters frequently depend on handcrafted heuristics or rigid structural assumptions, which constrain generalization. In contrast, biological evolution enables efficient knowledge transfer by encoding only essential information into genes through iterative refinement under environmental pressure. Inspired by this principle, we propose **ECO**, a framework that **E**volves **CO**re knowledge into modular, reusable neural components—termed *learngenes*—through similar evolutionary dynamics. To this end, we redefine learngenes as neural circuits and introduce Genetic Transfer Learning (GTL), a biologically inspired paradigm that establishes a genetic mechanism within neural networks in the context of supervised learning. GTL simulates evolutionary processes by generating diverse network populations, selecting high-performing individuals, and transferring their learngenes to subsequent generations. Through iterative refinement, GTL enables learngenes to accumulate transferable common knowledge. Extensive experiments show that ECO achieves efficient initialization and strong generalization across diverse models and tasks, while significantly reducing computational and memory costs compared to conventional methods.

Applications · Genetics, Cell Biology, etc

Ashesh Ashesh, Florian Jug

Fluorescence microscopy, while being a key driver for progress in the life sciences, is also subject to technical limitations. To overcome them, computational multiplexing techniques have recently been proposed, which allow multiple cellular structures to be captured in a single image and later be unmixed. Existing image decomposition methods are trained on a set of superimposed input images and the respective unmixed target images. It is critical to note that the relative strength (mixing ratio) of the superimposed images for a given input is a priori unknown. However, existing methods are trained on a fixed intensity ratio of superimposed inputs, making them not cognizant of the range of relative intensities that can occur in fluorescence microscopy. In this work, we propose a novel method called scSplit that is cognizant of the severity of the above-mentioned mixing ratio. Our idea is based on InDI, a popular iterative method for image restoration, and an ideal starting point to embrace the unknown mixing ratio in any given input. We introduce (i) a suitably trained regressor network that predicts the degradation level (mixing asymmetry) of a given input image and (ii) a degradation-specific normalization module, enabling degradation-aware inference across all mixing ratios. We show that this method solves two relevant tasks in fluorescence microscopy, namely image splitting and bleedthrough removal, and empirically demonstrate the applicability of scSplit on 5 public datasets. The source code with pre-trained models is hosted at https://github.com/juglab/scSplit/.

Computer Vision · Segmentation

Sheida Rahnamai Kordasiabi, Damian Nogare, Florian Jug

Semantic segmentation of electron microscopy (EM) images of biological samples remains a challenge in the life sciences. EM data captures details of biological structures, sometimes with such complexity that even human observers can find it overwhelming. We introduce $\epsilon$-Seg, a method based on hierarchical variational autoencoders (HVAEs), employing center-region masking, sparse label contrastive learning (CL), a Gaussian mixture model (GMM) prior, and clustering-free label prediction. Center-region masking and the inpainting loss encourage the model to learn robust and representative embeddings to distinguish the desired classes, even if training labels are sparse ($0.05$\% of the total image data or less). For optimal performance, we employ CL and a GMM prior to shape the latent space of the HVAE such that encoded input patches tend to cluster w.r.t. the semantic classes we wish to distinguish. Finally, instead of clustering latent embeddings for semantic segmentation, we propose a MLP semantic segmentation head to directly predict class labels from latent embeddings. We show empirical results of $\epsilon$-Seg and baseline methods on $2$ dense EM datasets of biological tissues and demonstrate the applicability of our method also on fluorescence microscopy data. Our results show that $\epsilon$-Seg is capable of achieving competitive sparsely-supervised segmentation results on complex biological image data, even if only limited amounts of training labels are available. Code available at https://github.com/juglab/eps-Seg.

Applications · Neuroscience, Cognitive Science

Jia Nuo Liew, Shenghan Lin, Bowen Chen, Wei Zhang, Xiaowei Zhu, Wei Zhang, Xiaolin Hu

The ability to extract oriented edges from visual input is a core computation across animal vision systems. Orientation maps, long associated with the layered architecture of the mammalian visual cortex, systematically organise neurons by their preferred edge orientation. Despite lacking cortical structures, the *Drosophila melanogaster* brain contains feature-selective neurons and exhibits complex visual detection capacity, raising the question of whether map-like vision representations can emerge without cortical infrastructure. We integrate a complete fruit fly brain connectome with biologically grounded spiking neuron models to simulate neuroprocessing in the fly visual system. By driving the network with oriented stimuli and analysing downstream responses, we show that coherent orientation maps can emerge from purely connectome-constrained dynamics. These results suggest that species of independent origin could evolve similar visual structures.

Applications · Chemistry and Drug Discovery

Shayan Shekarforoush, David Lindell, Marcus Brubaker, David Fleet

Cryo-EM is a transformational paradigm in molecular biology where computational methods are used to infer 3D molecular structure at atomic resolution from extremely noisy 2D electron microscope images. At the forefront of research is how to model the structure when the imaged particles exhibit non-rigid conformational flexibility and compositional variation where parts are sometimes missing. We introduce a novel 3D reconstruction framework with a hierarchical Gaussian mixture model, inspired in part by Gaussian Splatting for 4D scene reconstruction. In particular, the structure of the model is grounded in an initial process that infers a part-based segmentation of the particle, providing essential inductive bias in order to handle both conformational and compositional variability. The framework, called \methodName, is shown to reveal biologically meaningful structures on complex experimental datasets, and establishes a new state-of-the-art on CryoBench, a benchmark for cryo-EM heterogeneity methods.

Chengwei Qin, Wenhan Xia, Tan Wang, Fangkai Jiao, Yuchen Hu, Bosheng Ding, Ruirui Chen, Shafiq Joty

Analogical reasoning is a unique ability of humans to address unfamiliar challenges by transferring strategies from relevant past experiences. One key finding in psychology is that compared with irrelevant past experiences, recalling relevant ones can help humans better handle new tasks. Coincidentally, the NLP community has also recently found that self-generating relevant examples in the context can help large language models (LLMs) better solve a given problem than hand-crafted prompts. However, it is yet not clear whether relevance is the key factor eliciting such capability, i.e., can LLMs benefit more from self-generated relevant examples than irrelevant ones? In this work, we systematically explore whether LLMs can truly perform analogical reasoning on a diverse set of reasoning tasks. With extensive experiments and analysis, we show that self-generated random examples can surprisingly achieve comparable or even better performance on certain tasks, e.g., 4% performance boost on GSM8K with random biological examples. We find that the accuracy of self-generated examples is the key factor and subsequently design two novel methods with improved performance and significantly reduced inference costs. Overall, we aim to advance a deeper understanding of LLM analogical reasoning and hope this work stimulates further research in the design of self-generated contexts.

Chi-Jane Chen, Yuhang Chen, Sukwon Yun, Natalie Stanley, Tianlong Chen

Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry’s analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information—they struggle to generalize spatial coordinates and effectively encode spatial context as text, and (2) Treating each cell independently—they overlook cell-cell interactions, limiting their ability to capture biological relationships. To address these limitations, we propose Spatial2Sentence, a novel framework that integrates both single-cell expression and spatial information into natural language using a multi-sentence approach. Given an expression matrix and spatial coordinates, Spatial2Sentence constructs expression similarity and distance matrices, pairing spatially adjacent and expressionally similar cells as positive pairs while using distant and dissimilar cells as negatives. These multi-sentence representations are processed by LLMs, enabling them to learn cellular interactions in both expression and spatial contexts. Equipped with multi-task learning, Spatial2Sentence outperforms existing single-cell LLMs on preprocessed IMC datasets for diabetes and brain tumors, improving cell-type classification by 5.98% and clinical status prediction by 4.18% on the diabetes dataset while enhancing interpretability. The source code can be found here: https://github.com/UNITES-Lab/Spatial2Sentence.

Mufan Qiu, Xinyu Hu, Fengwei Zhan, Sukwon Yun, Jie Peng, Ruichen Zhang, Bhavya Kailkhura, Jiekun Yang, Tianlong Chen

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: \mathbf{3.6\\\%} increase in drug response prediction correlation, \mathbf{9.6\\\%} improvement in single-cell drug classification AUC, and \mathbf{1.1\\\%} average gain in gene perturbation prediction accuracy.

Ziyan Wang, Zhankun Xiong, Feng Huang, Wen Zhang

Drug-drug interactions (DDIs) arise when multiple drugs are administered concurrently. Accurately predicting the specific mechanisms underlying DDIs (named DDI events or DDIEs) is critical for the safe clinical use of drugs. DDIEs are typically represented as textual descriptions. However, most computational methods focus more on predicting the DDIE class label over generating human-readable natural language increasing clinicians’ interpretation costs. Furthermore, current methods overlook the fact that each drug assumes distinct biological functions in a DDI, which, when used as input context, can enhance the understanding of the DDIE process and benefit DDIE generation by the language model (LM). In this work, we propose a novel pairwise knowledge-augmented generative method (termed PKAG-DDI) for DDIE text generation. It consists of a pairwise knowledge selector efficiently injecting structural information between drugs bidirectionally and simultaneously to select pairwise biological functions from the knowledge set, and a pairwise knowledge integration strategy that matches and integrates the selected biological functions into the LM. Experiments on two professional datasets show that PKAG-DDI outperforms existing methods in DDIE text generation, especially in challenging inductive scenarios, indicating its practicality and generalization.

Fan Zhang, Hao Chen, Zhihong Zhu, Ziheng Zhang, Zhenxi Lin, Ziyue Qiao, Yefeng Zheng, Xian Wu

The recent advancements in language models have significantly catalyzed progress in computational biology. A growing body of research strives to construct unified foundation models for single-cell biology, with language models serving as the cornerstone. In this paper, we systematically review the developments in foundation language models designed specifically for single-cell biology. Our survey offers a thorough analysis of various incarnations of single-cell foundation language models, viewed through the lens of both pre-trained language models (PLMs) and large language models (LLMs). This includes an exploration of data tokenization strategies, pre-training/tuning paradigms, and downstream single-cell data analysis tasks. Additionally, we discuss the current challenges faced by these pioneering works and speculate on future research directions. Overall, this survey provides a comprehensive overview of the existing single-cell foundation language models, paving the way for future research endeavors.

Position · Methodology

Frithjof Gressmann, Ashley Chen, Lily Xie, Nancy Amato, Lawrence Rauchwerger

Recent advances in bioengineering have enabled the creation of biological neural networks in vitro, significantly reducing the cost, ethical hurdles, and complexity of experimentation with genuine biological neural computation. In this position paper, we argue that this trend offers a unique and timely opportunity to put our understanding of neural computation to the test. By designing artificial neural networks that can interact and control living neural systems, it is becoming possible to validate computational models beyond simulation and gain empirical insights to help unlock more robust and energy-efficient next-generation AI systems. We provide an overview of key technologies, challenges, and principles behind this development and describe strategies and opportunities for novel machine learning research in this emerging field. We also discuss implications and fundamental questions that could be answered as this technology advances, exemplifying the longer-term impact of increasingly sophisticated in vitro neural networks.

Applications · Chemistry, Physics, and Earth Sciences

Wenyin Zhou, Christopher I Sprague, Vsevolod Viliuga, Matteo Tadiello, Arne Elofsson, Hossein Azizpour

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design.Recent advances in generative modeling, such as diffusion models and flow matching, have made great progress on these tasks by modeling molecular conformations as a distribution.In this work, we focus on flow matching and adopt an energy-based perspective to improve training and inference of structure generation models. Our view results in a mapping function, represented by a deep network, that is directly learned to \textit{iteratively} map random configurations, i.e. samples from the source distribution, to target structures, i.e. points in the data manifold. This yields a conceptually simple and empirically effective flow matching setup that is theoretically justified and has interesting connections to fundamental properties such as idempotency and stability, as well as the empirically useful techniques such as structure refinement in AlphaFold. Experiments on protein docking as well as protein backbone generation consistently demonstrate the method's effectiveness, where it outperforms recent baselines of task-associated flow matching and diffusion models, using a similar computational budget.

Applications · Computer Vision

Jiawen Wang, Yinda Chen, Xiaoyu Liu, che liu, Dong Liu, Jianqing Gao, Zhiwei Xiong

Recent works have correlated Masked Image Modeling (MIM) with consistency regularization in Unsupervised Domain Adaptation (UDA). However, they merely treat masking as a special form of deformation on the input images and neglect the theoretical analysis, which leads to a superficial understanding of masked reconstruction and insufficient exploitation of its potential in enhancing feature extraction and representation learning. In this paper, we reframe masked reconstruction as a sparse signal reconstruction problem and theoretically prove that the dual form of complementary masks possesses superior capabilities in extracting domain-agnostic image features. Based on this compelling insight, we propose MaskTwins, a simple yet effective UDA framework that integrates masked reconstruction directly into the main training pipeline. MaskTwins uncovers intrinsic structural patterns that persist across disparate domains by enforcing consistency between predictions of images masked in complementary ways, enabling domain generalization in an end-to-end manner. Extensive experiments verify the superiority of MaskTwins over baseline methods in natural and biological image segmentation.These results demonstrate the significant advantages of MaskTwins in extracting domain-invariant features without the need for separate pre-training, offering a new paradigm for domain-adaptive segmentation. The source code is available at https://github.com/jwwang0421/masktwins.

Applications · Health / Medicine

Yuhui Zhang, Yuchang Su, Chenyu Wang, Tianhong Li, Zoe Wefers, Jeffrey J. Nirschl, James Burgess, Daisy Yi Ding, Alejandro Lozano, Emma Lundberg 等

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects—a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.