Drug Discovery

The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods, and outperforms state-of-the-art learning-based methods, like DiffDock-PP and Alphafold-Multimer, for particularly antibody-antigen docking.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our $\textit{Discrete Walk-Jump Sampling}$ formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the $\textit{distributional conformity score}$ to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100\% of generated samples are successfully expressed and purified and 70\% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reactions and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on all 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making.

Pocket representations play a vital role in various biomedical applications, such as druggability estimation, ligand affinity prediction, and de novo drug design. While existing geometric features and pretrained representations have demonstrated promising results, they usually treat pockets independent of ligands, neglecting the fundamental interactions between them. However, the limited pocket-ligand complex structures available in the PDB database (less than 100 thousand non-redundant pairs) hampers large-scale pretraining endeavors for interaction modeling. To address this constraint, we propose a novel pocket pretraining approach that leverages knowledge from high-resolution atomic protein structures, assisted by highly effective pretrained small molecule representations. By segmenting protein structures into drug-like fragments and their corresponding pockets, we obtain a reasonable simulation of ligand-receptor interactions, resulting in the generation of over 5 million complexes. Subsequently, the pocket encoder is trained in a contrastive manner to align with the representation of pseudo-ligand furnished by some pretrained small molecule encoders. Our method, named ProFSA, achieves state-of-the-art performance across various tasks, including pocket druggability prediction, pocket matching, and ligand binding affinity prediction. Notably, ProFSA surpasses other pretraining methods by a substantial margin. Moreover, our work opens up a new avenue for mitigating the scarcity of protein-ligand complex data through the utilization of high-quality and diverse protein structure databases.

The remarkable success in neural networks provokes the selective rationalization. It explains the prediction results by identifying a small subset of the inputs sufficient to support them. Since existing methods still suffer from adopting the shortcuts in data to compose rationales and limited large-scale annotated rationales by human, in this paper, we propose a Shortcuts-fused Selective Rationalization (SSR) method, which boosts the rationalization by discovering and exploiting potential shortcuts. Specifically, SSR first designs a shortcuts discovery approach to detect several potential shortcuts. Then, by introducing the identified shortcuts, we propose two strategies to mitigate the problem of utilizing shortcuts to compose rationales. Finally, we develop two data augmentations methods to close the gap in the number of annotated rationales. Extensive experimental results on real-world datasets clearly validate the effectiveness of our proposed method.

Generating 3D ligand molecules that bind to specific protein targets via diffusion models has shown great promise for structure-based drug design. The key idea is to disrupt molecules into noise through a fixed forward process and learn its reverse process to generate molecules from noise in a denoising way. However, existing diffusion models primarily focus on incorporating protein-ligand interaction information solely in the reverse process, and neglect the interactions in the forward process. The inconsistency between forward and reverse processes may impair the binding affinity of generated molecules towards target protein. In this paper, we propose a novel Interaction Prior-guided Diffusion model (IPDiff) for the protein-specific 3D molecular generation by introducing geometric protein-ligand interactions into both diffusion and sampling process. Specifically, we begin by pretraining a protein-ligand interaction prior network (IPNet) by utilizing the binding affinity signals as supervision. Subsequently, we leverage the pretrained prior network to (1) integrate interactions between the target protein and the molecular ligand into the forward process for adapting the molecule diffusion trajectories (prior-shifting), and (2) enhance the binding-aware molecule sampling process (prior-conditioning). Empirical studies on CrossDocked2020 dataset show IPDiff can generate molecules with more realistic 3D structures and state-of-the-art binding affinities towards the protein targets, with up to -6.42 Avg. Vina Score, while maintaining proper molecular properties. https://github.com/YangLing0818/IPDiff

Inferring unbiased treatment effects has received widespread attention in the machine learning community. In recent years, our community has proposed numerous solutions in standard settings, high-dimensional treatment settings, and even longitudinal settings. While very diverse, the solution has mostly relied on neural networks for inference and simultaneous correction of assignment bias. New approaches typically build on top of previous approaches by proposing new (or refined) architectures and learning algorithms. However, the end result—a neural-network-based inference machine—remains unchallenged. In this paper, we introduce a different type of solution in the longitudinal setting: a closed-form ordinary differential equation (ODE). While we still rely on continuous optimization to learn an ODE, the resulting inference machine is no longer a neural network. Doing so yields several advantages such as interpretability, irregular sampling, and a different set of identification assumptions. Above all, we consider the introduction of a completely new type of solution to be our most important contribution as it may spark entirely new innovations in treatment effects in general. We facilitate this by formulating our contribution as a framework that can transform any ODE discovery method into a treatment effects method.

Conventional causal discovery approaches, which seek to uncover causal relationships among measured variables, are typically fragile to the presence of latent variables. While various methods have been developed to address this confounding issue, they often rely on strong assumptions about the underlying causal structure. In this paper, we consider a general scenario where measured and latent variables collectively form a partially observed causally sufficient linear system and latent variables may be anywhere in the causal structure. We theoretically show that with the aid of high-order statistics, the causal graph is (almost) fully identifiable if, roughly speaking, each latent set has a sufficient number of pure children, which can be either latent or measured. Naturally, LiNGAM, a model without latent variables, is encompassed as a special case. Based on the identification theorem, we develop a principled algorithm to identify the causal graph by testing for statistical independence involving only measured variables in specific manners. Experimental results show that our method effectively recovers the causal structure, even when latent variables are influenced by measured variables.

Conventional causal discovery methods rely on centralized data, which is inconsistent with the decentralized nature of data in many real-world situations. This discrepancy has motivated the development of federated causal discovery (FCD) approaches. However, existing FCD methods may be limited by their potentially restrictive assumptions of identifiable functional causal models or homogeneous data distributions, narrowing their applicability in diverse scenarios. In this paper, we propose a novel FCD method attempting to accommodate arbitrary causal models and heterogeneous data. We first utilize a surrogate variable corresponding to the client index to account for the data heterogeneity across different clients. We then develop a federated conditional independence test (FCIT) for causal skeleton discovery and establish a federated independent change principle (FICP) to determine causal directions. These approaches involve constructing summary statistics as a proxy of the raw data to protect data privacy. Owing to the nonparametric properties, FCIT and FICP make no assumption about particular functional forms, thereby facilitating the handling of arbitrary causal models. We conduct extensive experiments on synthetic and real datasets to show the efficacy of our method. The code is available at https://github.com/lokali/FedCDH.git.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

Machine learning (ML) has been shown to successfully accelerate solving NP-hard combinatorial optimization (CO) problems under the branch and bound framework. However, the high training and inference cost and limited interpretability of ML approaches severely limit their wide application to modern exact CO solvers. In contrast, human-designed policies---though widely integrated in modern CO solvers due to their compactness and reliability---can not capture data-driven patterns for higher performance. To combine the advantages of the two paradigms, we propose the first symbolic discovery framework---namely, deep symbolic discovery for exact combinatorial optimization solver (Symb4CO)---to learn high-performance symbolic policies on the branching task. Specifically, we show the potential existence of small symbolic policies empirically, employ a large neural network to search in the high-dimensional discrete space, and compile the learned symbolic policies directly for fast deployment. Experiments show that the Symb4CO learned purely CPU-based policies consistently achieve *comparable* performance to previous GPU-based state-of-the-art approaches. Furthermore, the appealing features of Symb4CO include its high training (*ten training instances*) and inference (*one CPU core*) efficiency and good interpretability (*one-line expressions*), making it simple and reliable for deployment. The results show encouraging potential for the *wide* deployment of ML to modern CO solvers.

Foundation models (FMs) learn from large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation, we present BioBridge, a parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by ~ 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general-purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs. Code is at https://github.com/RyanWangZf/BioBridge.

We deal with the combinatorial problem of learning directed acyclic graph (DAG) structure from observational data adhering to a linear structural equation model (SEM). Leveraging advances in differentiable, nonconvex characterizations of acyclicity, recent efforts have advocated a continuous constrained optimization paradigm to efficiently explore the space of DAGs. Most existing methods employ lasso-type score functions to guide this search, which (i) require expensive penalty parameter retuning when the $\textit{unknown}$ SEM noise variances change across problem instances; and (ii) implicitly rely on limiting homoscedasticity assumptions. In this work, we propose a new convex score function for sparsity-aware learning of linear DAGs, which incorporates concomitant estimation of scale and thus effectively decouples the sparsity parameter from noise levels. Regularization via a smooth, nonconvex acyclicity penalty term yields CoLiDE ($\textbf{Co}$ncomitant $\textbf{Li}$near $\textbf{D}$AG $\textbf{E}$stimation), a regression-based criterion amenable to efficient gradient computation and closed-form estimation of exogenous noise levels in heteroscedastic scenarios. Our algorithm outperforms state-of-the-art methods without incurring added complexity, especially when the DAGs are larger and the noise level profile is heterogeneous. We also find CoLiDE exhibits enhanced stability manifested via reduced standard deviations in several domain-specific metrics, underscoring the robustness of our novel linear DAG estimator.

Developing deep learning models that effectively learn object-centric representations, akin to human cognition, remains a challenging task. Existing approaches facilitate object discovery by representing objects as fixed-size vectors, called ``slots'' or ``object files''. While these approaches have shown promise in certain scenarios, they still exhibit certain limitations. First, they rely on architectural priors which can be unreliable and usually require meticulous engineering to identify the correct objects. Second, there has been a notable gap in investigating the practical utility of these representations in downstream tasks. To address the first limitation, we introduce a method that explicitly optimizes the constraint that each object in a scene should be associated with a distinct slot. We formalize this constraint by introducing consistency objectives which are cyclic in nature. By integrating these consistency objectives into various existing slot-based object-centric methods, we showcase substantial improvements in object-discovery performance. These enhancements consistently hold true across both synthetic and real-world scenes, underscoring the effectiveness and adaptability of the proposed approach. To tackle the second limitation, we apply the learned object-centric representations from the proposed method to two downstream reinforcement learning tasks, demonstrating considerable performance enhancements compared to conventional slot-based and monolithic representation learning methods. Our results suggest that the proposed approach not only improves object discovery, but also provides richer features for downstream tasks.

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the main goals in drug discovery -- designing novel ligands with desired properties, e.g., high binding affinity, easily synthesizable, etc. This challenge becomes particularly pronounced when the target-ligand pairs used for training do not align with these desired properties. Moreover, most existing methods aim at solving de novo design task, while many generative scenarios requiring flexible controllability, such as R-group optimization and scaffold hopping, have received little attention. In this work, we propose DecompOpt, a structure-based molecular optimization method based on a controllable and decomposed diffusion model. DecompOpt presents a new generation paradigm which combines optimization with conditional diffusion models to achieve desired properties while adhering to the molecular grammar. Additionally, DecompOpt offers a unified framework covering both de novo design and controllable generation. To achieve so, ligands are decomposed into substructures which allows fine-grained control and local optimization. Experiments show that DecompOpt can efficiently generate molecules with improved properties than strong de novo baselines, and demonstrate great potential in controllable generation tasks.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a comprehensive instruction dataset designed for the biomolecular domain. Mol-Instructions encompasses three key components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions. Each component aims to improve the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on LLMs, we demonstrate the effectiveness of Mol-Instructions in enhancing large models' performance in the intricate realm of biomolecular studies, thus fostering progress in the biomolecular research community. Mol-Instructions is publicly available for ongoing research and will undergo regular updates to enhance its applicability (https://github.com/zjunlp/Mol-Instructions).

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional connectivity. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional connectivity can change over time. To model dynamically changing functional connectivity, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional connectivities are shaped and confined by the underlying anatomical connectome. Here, we propose two novel prior-informed state-switching GLMs, called Gaussian HMM-GLM (Gaussian prior) and one-hot HMM-GLM (Gumbel-Softmax one-hot prior). We show that the learned prior should capture the state-invariant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood, and enhance the interpretability of interaction patterns and hidden states when applied to real neural data. The code is available at \url{https://github.com/JerrySoybean/onehot-hmmglm}.

Most existing causal discovery methods rely on the assumption of no latent confounders, limiting their applicability in solving real-life problems. In this paper, we introduce a novel, versatile framework for causal discovery that accommodates the presence of causally-related hidden variables almost everywhere in the causal network (for instance, they can be effects of measured variables), based on rank information of covariance matrix over measured variables. We start by investigating the efficacy of rank in comparison to conditional independence and, theoretically, establish necessary and sufficient conditions for the identifiability of certain latent structural patterns. Furthermore, we develop a Rank-based Latent Causal Discovery algorithm, RLCD, that can efficiently locate hidden variables, determine their cardinalities, and discover the entire causal structure over both measured and hidden ones. We also show that, under certain graphical conditions, RLCD correctly identifies the Markov Equivalence Class of the whole latent causal graph asymptotically. Experimental results on both synthetic and real-world personality data sets demonstrate the efficacy of the proposed approach in finite-sample cases. Our code will be publicly available.

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e. atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.