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Applications · Genetics, Cell Biology, Health, etc

Pei Liu, Luping Ji, Jiaxiang Gou, Bo Fu, Mao Ye

Histopathology Whole-Slide Images (WSIs) provide an important tool to assess cancer prognosis in computational pathology (CPATH). While existing survival analysis (SA) approaches have made exciting progress, they are generally limited to adopting highly-expressive network architectures and only coarse-grained patient-level labels to learn visual prognostic representations from gigapixel WSIs. Such learning paradigm suffers from critical performance bottlenecks, when facing present scarce training data and standard multi-instance learning (MIL) framework in CPATH. To overcome it, this paper, for the first time, proposes a new Vision-Language-based SA (**VLSA**) paradigm. Concretely, (1) VLSA is driven by pathology VL foundation models. It no longer relies on high-capability networks and shows the advantage of *data efficiency*. (2) In vision-end, VLSA encodes textual prognostic prior and then employs it as *auxiliary signals* to guide the aggregating of visual prognostic features at instance level, thereby compensating for the weak supervision in MIL. Moreover, given the characteristics of SA, we propose i) *ordinal survival prompt learning* to transform continuous survival labels into textual prompts; and ii) *ordinal incidence function* as prediction target to make SA compatible with VL-based prediction. Notably, VLSA's predictions can be interpreted intuitively by our Shapley values-based method. The extensive experiments on five datasets confirm the effectiveness of our scheme. Our VLSA could pave a new way for SA in CPATH by offering weakly-supervised MIL an effective means to learn valuable prognostic clues from gigapixel WSIs. Our source code is available at https://github.com/liupei101/VLSA.

Applications · Genetics, Cell Biology, Health, etc

Xikun ZHANG, Dongjin Song, Yushan Jiang, Yixin Chen, Dacheng Tao

Observation-based trajectory prediction for systems with unknown dynamics is essential in fields such as physics and biology. Most existing approaches are limited to learning within a single system with fixed dynamics patterns. However, many real-world applications require learning across systems with evolving dynamics patterns, a challenge that has been largely overlooked. To address this, we systematically investigate the problem of Continual Dynamics Learning (CDL), examining task configurations and evaluating the applicability of existing techniques, while identifying key challenges. In response, we propose the Mode-switching Graph ODE (MS-GODE) model, which integrates the strengths LG-ODE and sub-network learning with a mode-switching module, enabling efficient learning over varying dynamics. Moreover, we construct a novel benchmark of biological dynamic systems for CDL, Bio-CDL, featuring diverse systems with disparate dynamics and significantly enriching the research field of machine learning for dynamic systems. Our code available at \url{https://github.com/QueuQ/MS-GODE}.

Applications · Genetics, Cell Biology, Health, etc

Xingyu Su, Haiyang Yu, Degui Zhi, Shuiwang Ji

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

Applications · Genetics, Cell Biology, Health, etc

Tianyu Xie, David Harry Tyensoung Richman, Jiansi Gao, Frederick A Matsen, Cheng Zhang

Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used to project phylogenetic trees into Euclidean space, but they are often sensitive to the choice of distance metric and may lack sufficient resolution. In this paper, we introduce *phylogenetic variational autoencoders* (PhyloVAEs), an unsupervised learning framework designed for representation learning and generative modeling of tree topologies. Leveraging an efficient encoding mechanism inspired by autoregressive tree topology generation, we develop a deep latent-variable generative model that facilitates fast, parallelized topology generation. PhyloVAE combines this generative model with a collaborative inference model based on learnable topological features, allowing for high-resolution representations of phylogenetic tree samples. Extensive experiments demonstrate PhyloVAE's robust representation learning capabilities and fast generation of phylogenetic tree topologies.

Applications · Genetics, Cell Biology, Health, etc

Stathis Megas, Daniel Chen, Krzysztof Polanski, Moshe Eliasof, Carola-Bibiane Schönlieb, Sarah Teichmann

Models of Virtual Cells and Virtual Tissues at single-cell resolution would allow us to test perturbations in silico and accelerate progress in tissue and cell engineering. However, most such models are not rooted in causal inference and as a result, could mistake correlation for causation.We introduce Celcomen, a novel generative graph neural network grounded in mathematical causality to disentangle intra- and inter-cellular gene regulation in spatial transcriptomics and single-cell data. Celcomen can also be prompted by perturbations to generate spatial counterfactuals, thus offering insights into experimentally inaccessible states, with potential applications in human health. We validate the model's disentanglement and identifiability through simulations, and demonstrate its counterfactual predictions in clinically relevant settings, including human glioblastoma and fetal spleen, recovering inflammation-related gene programs post immune system perturbation. Moreover, it supports mechanistic interpretability, as its parameters can be reverse-engineered from observed behavior, making it an accessible model for understanding both neural networks and complex biological systems.

Applications · Genetics, Cell Biology, Health, etc

Alessandro Palma, Till Richter, Hanyi Zhang, Manuel Lubetzki, Alexander Tong, Andrea Dittadi, Fabian Theis

Generative modeling of single-cell RNA-seq data is crucial for tasks like trajectory inference, batch effect removal, and simulation of realistic cellular data. However, recent deep generative models simulating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, overlooking the discrete nature of single-cell data, which limits their effectiveness and hinders the incorporation of robust noise models. Additionally, aspects like controllable multi-modal and multi-label generation of cellular data remain underexplored. This work introduces CellFlow for Generation (CFGen), a flow-based conditional generative model that preserves the inherent discreteness of single-cell data. CFGen generates whole-genome multi-modal single-cell data reliably, improving the recovery of crucial biological data characteristics while tackling relevant generative tasks such as rare cell type augmentation and batch correction. We also introduce a novel framework for compositional data generation using Flow Matching. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Applications · Genetics, Cell Biology, Health, etc

Jesus de la Fuente Cedeño, Robert Lehmann, Carlos Ruiz-Arenas, Jan Voges, Irene Marín-Goñi, Xabier Martinez de Morentin, David Gomez-Cabrero, Idoia Ochoa, Jesper Tegnér, Vincenzo Lagani 等

Predicting the impact of genomic and drug perturbations in cellular function is crucial for understanding gene functions and drug effects, ultimately leading to improved therapies. To this end, Causal Representation Learning (CRL) constitutes one of the most promising approaches, as it aims to identify the latent factors that causally govern biological systems, thus facilitating the prediction of the effect of unseen perturbations. Yet, current CRL methods fail in reconciling their principled latent representations with known biological processes, leading to models that are not interpretable. To address this major issue, in this work we present SENA-discrepancy-VAE, a model based on the recently proposed CRL method discrepancy-VAE, that produces representations where each latent factor can be interpreted as the (linear) combination of the activity of a (learned) set of biological processes. To this extent, we present an encoder, SENA-$\delta$, that efficiently compute and map biological processes' activity levels to the latent causal factors. We show that SENA-discrepancy-VAE achieves predictive performances on unseen combinations of interventions that are comparable with its original, non-interpretable counterpart, while inferring causal latent factors that are biologically meaningful.

Applications · Genetics, Cell Biology, Health, etc

Lazar Atanackovic, Xi (Nicole) Zhang, Brandon Amos, Mathieu Blanchette, Leo J Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depend on the microenvironment of cells specific to each patient. We propose *Meta Flow Matching* (MFM), a practical approach to integrate along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions, unlike previously proposed methods. We demonstrate the ability of MFM to improve the prediction of individual treatment responses on a large-scale multi-patient single-cell drug screen dataset.

Applications · Genetics, Cell Biology, Health, etc

Xiaoyu Cui, Weixing Chen, Jiandong Su

Multiple Instance Learning (MIL) in digital pathology Whole Slide Image (WSI) analysis has shown significant progress. However, due to data bias and unobservable confounders, this paradigm still faces challenges in terms of performance and interpretability. Existing MIL methods might identify patches that do not have true diagnostic significance, leading to false correlations, and experience difficulties in integrating multi-scale features and handling unobservable confounders. To address these issues, we propose a new Multi-Scale Frequency Domain Causal framework (MFC). This framework employs an adaptive memory module to estimate the overall data distribution through multi-scale frequency-domain information during training and simulates causal interventions based on this distribution to mitigate confounders in pathological diagnosis tasks. The framework integrates the Multi-scale Spatial Representation Module (MSRM), Frequency Domain Structure Representation Module (FSRM), and Causal Memory Intervention Module (CMIM) to enhance the model's performance and interpretability. Furthermore, the plug-and-play nature of this framework allows it to be broadly applied across various models. Experimental results on Camelyon16 and TCGA-NSCLC dataset show that, compared to previous work, our method has significantly improved accuracy and generalization ability, providing a new theoretical perspective for medical image analysis and potentially advancing the field further. The code will be released at https://github.com/WissingChen/MFC-MIL.

Applications · Genetics, Cell Biology, Health, etc

Xingyu Su, Haiyang Yu, Degui Zhi, Shuiwang Ji

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

Applications · Genetics, Cell Biology, Health, etc

Zhenyi Zhang, Tiejun Li, Peijie Zhou

Reconstructing dynamics using samples from sparsely time-resolved snapshots is an important problem in both natural sciences and machine learning. Here, we introduce a new deep learning approach for solving regularized unbalanced optimal transport (RUOT) and inferring continuous unbalanced stochastic dynamics from observed snapshots. Based on the RUOT form, our method models these dynamics without requiring prior knowledge of growth and death processes or additional information, allowing them to be learned directly from data. Theoretically, we explore the connections between the RUOT and Schrödinger bridge problem and discuss the key challenges and potential solutions. The effectiveness of our method is demonstrated with a synthetic gene regulatory network, high-dimensional Gaussian Mixture Model, and single-cell RNA-seq data from blood development. Compared with other methods, our approach accurately identifies growth and transition patterns, eliminates false transitions, and constructs the Waddington developmental landscape. Our code is available at: [https://github.com/zhenyiizhang/DeepRUOT](https://github.com/zhenyiizhang/DeepRUOT).

Applications · Genetics, Cell Biology, Health, etc

ZeMing Gong, Austin Wang, Xiaoliang Huo, Joakim Bruslund Haurum, Scott C Lowe, Graham W Taylor, Angel Chang

Measuring biodiversity is crucial for understanding ecosystem health. While prior works have developed machine learning models for taxonomic classification of photographic images and DNA separately, in this work, we introduce a multi-modal approach combining both, using CLIP-style contrastive learning to align images, barcode DNA, and text-based representations of taxonomic labels in a unified embedding space. This allows for accurate classification of both known and unknown insect species without task-specific fine-tuning, leveraging contrastive learning for the first time to fuse DNA and image data. Our method surpasses previous single-modality approaches in accuracy by over 8% on zero-shot learning tasks, showcasing its effectiveness in biodiversity studies.

Applications · Genetics, Cell Biology, etc

Yair Schiff, Chia Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, Volodymyr Kuleshov

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance. Code to reproduce our experiments is available here: https://github.com/kuleshov-group/caduceus.

Applications · Genetics, Cell Biology, etc

Francesca-Zhoufan Li, Ava Amini, Yisong Yue, Kevin Yang, Alex Lu

Large pretrained protein language models (PLMs) have improved protein property and structure prediction from sequences via transfer learning, in which weights and representations from PLMs are repurposed for downstream tasks. Although PLMs have shown great promise, currently there is little understanding of how the features learned by pretraining relate to and are useful for downstream tasks. We perform a systematic analysis of transfer learning using PLMs, conducting 370 experiments across a comprehensive suite of factors including different downstream tasks, architectures, model sizes, model depths, and pretraining time. We observe that while almost all downstream tasks do benefit from pretrained models compared to naive sequence representations, for the majority of tasks performance does not scale with pretraining, and instead relies on low-level features learned early in pretraining. Our results point to a mismatch between current PLM pretraining paradigms and most applications of these models, indicating a need for better pretraining methods.

Applications · Genetics, Cell Biology, etc

Daniel Levine, Syed Rizvi, Sacha Lévy, Nazreen Pallikkavaliyaveetil MohammedSheriff, David Zhang, Xingyu Chen, SINA GHADERMARZI, Ruiming Wu, Zihe Zheng, Ivan Vrkic 等

We introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentences," C2S bridges the gap between natural language processing and biology. We demonstrate cell sentences enable the fine-tuning of language models for diverse tasks in biology, including cell generation, complex cell-type annotation, and direct data-driven text generation. Our experiments reveal that GPT-2, when fine-tuned with C2S, can generate biologically valid cells based on cell type inputs, and accurately predict cell types from cell sentences. This illustrates that language models, through C2S fine-tuning, can acquire a significant understanding of single-cell biology while maintaining robust text generation capabilities. C2S offers a flexible, accessible framework to integrate natural language processing with transcriptomics, utilizing existing models and libraries for a wide range of biological applications.

Applications · Genetics, Cell Biology, etc

Pedro A. Campana, Paul Prasse, Tobias Scheffer

Dose-response curves characterize the relationship between the concentration of drugs and their inhibitory effect on the growth of specific types of cells. The predominant Hill-equation model of an ideal enzymatic inhibition unduly simplifies the biochemical reality of many drugs; and for these drugs the widely-used drug performance indicator of the half-inhibitory concentration $IC_{50}$ can lead to poor therapeutic recommendations and poor selections of promising drug candidates. We develop a neural model that uses an embedding of the interaction between drug molecules and the tissue transcriptome to estimate the entire dose-response curve rather than a scalar aggregate. We find that, compared to the prior state of the art, this model excels at interpolating and extrapolating the inhibitory effect of untried concentrations. Unlike prevalent parametric models, it it able to accurately predict dose-response curves of drugs on previously unseen tumor tissues as well as of previously untested drug molecules on established tumor cell lines.

Applications · Genetics, Cell Biology, etc

Hannes Stärk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that naive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in $O(L)$ speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets.

Applications · Genetics, Cell Biology, etc

Suyuan Zhao, Jiahuan Zhang, Yushuai Wu, YIZHEN LUO, Zaiqing Nie

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce **LangCell**, the first **Lang**uage-**Cell** pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Applications · Genetics, Cell Biology, etc

Albane Ruaud, Cansu Sancaktar, Marco Bagatella, Christoph Ratzke, Georg Martius

Understanding the interactions and interplay of microorganisms is a great challenge with many applications in medical and environmental settings. In this work, we model bacterial communities directly from their genomes using graph neural networks (GNNs). GNNs leverage the inductive bias induced by the set nature of bacteria, enforcing permutation invariance and granting combinatorial generalization. We propose to learn the dynamics implicitly by directly predicting community relative abundance profiles at steady state, thus escaping the need for growth curves. On two real-world datasets, we show for the first time generalization to unseen bacteria and different community structures. To investigate the prediction results more deeply, we create a simulation for flexible data generation and analyze effects of bacteria interaction strength, community size, and training data amount.

Applications · Genetics, Cell Biology, etc

Siyuan Li, Zedong Wang, Zicheng Liu, Di Wu, Cheng Tan, Jiangbin Zheng, Yufei Huang, Stan Z Li

Similar to natural language models, pre-trained genome language models are proposed to capture the underlying intricacies within genomes with unsupervised sequence modeling. They have become essential tools for researchers and practitioners in biology. However, the hand-crafted tokenization policies used in these models may not encode the most discriminative patterns from the limited vocabulary of genomic data. In this paper, we introduce VQDNA, a general-purpose framework that renovates genome tokenization from the perspective of genome vocabulary learning. By leveraging vector-quantized codebook as learnable vocabulary, VQDNA can adaptively tokenize genomes into pattern-aware embeddings in an end-to-end manner. To further push its limits, we propose Hierarchical Residual Quantization (HRQ), where varying scales of codebooks are designed in a hierarchy to enrich the genome vocabulary in a coarse-to-fine manner. Extensive experiments on 32 genome datasets demonstrate VQDNA's superiority and favorable parameter efficiency compared to existing genome language models. Notably, empirical analysis of SARS-CoV-2 mutations reveals the fine-grained pattern awareness and biological significance of learned HRQ vocabulary, highlighting its untapped potential for broader applications in genomics.