Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets. While initial protein representation learning studies solely focused on either sequence or structural features, recent hybrid architectures have sought to merge these modalities to harness their respective strengths. However, these sequence-structure models have so far achieved only incremental improvements when compared to the leading sequence-only approaches, highlighting unresolved challenges effectively leveraging these modalities together. Moreover, the function of certain proteins is highly dependent on the granular aspects of their surface topology, which have been overlooked by prior models. To address these limitations, we introduce the Sequence-Structure-Surface Fitness (S3F) model -- a novel multimodal representation learning framework that integrates protein features across several scales. Our approach combines sequence representations from a protein language model with Geometric Vector Perceptron networks encoding protein backbone and detailed surface topology. The proposed method achieves state-of-the-art fitness prediction on the ProteinGym benchmark encompassing 217 substitution deep mutational scanning assays, and provides insights into the determinants of protein function.

Efficient and accurate updating of knowledge stored in Large Language Models (LLMs) is one of the most pressing research challenges today. This paper presents Larimar - a novel, brain-inspired architecture for enhancing LLMs with a distributed episodic memory. Larimar's memory allows for dynamic, one-shot updates of knowledge without the need for computationally expensive re-training or fine-tuning. Experimental results on multiple fact editing benchmarks demonstrate that Larimar attains accuracy comparable to most competitive baselines, even in the challenging sequential editing setup, but also excels in speed - yielding speed-ups of 8-10x depending on the base LLM - as well as flexibility due to the proposed architecture being simple, LLM-agnostic, and hence general. We further provide mechanisms for selective fact forgetting, information leakage prevention, and input context length generalization with Larimar and show their effectiveness. Our code is available at https://github.com/IBM/larimar

Protein function annotation is an important yet challenging task in biology. Recent deep learning advancements show significant potential for accurate function prediction by learning from protein sequences and structures. Nevertheless, these predictor-based methods often overlook the modeling of protein similarity, an idea commonly employed in traditional approaches using sequence or structure retrieval tools. To fill this gap, we first study the effect of inter-protein similarity modeling by benchmarking retriever-based methods against predictors on protein function annotation tasks. Our results show that retrievers can match or outperform predictors without large-scale pre-training. Building on these insights, we introduce a novel variational pseudo-likelihood framework, ProtIR, designed to improve function predictors by incorporating inter-protein similarity modeling. This framework iteratively refines knowledge between a function predictor and retriever, thereby combining the strengths of both predictors and retrievers. ProtIR showcases around 10% improvement over vanilla predictor-based methods. Besides, it achieves performance on par with protein language model-based methods, yet without the need for massive pre-training, highlighting the efficacy of our framework. Code will be released upon acceptance.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

We address the problem of learning Granger causality from asynchronous, interdependent, multi-type event sequences. In particular, we are interested in discovering instance-level causal structures in an unsupervised manner. Instance-level causality identifies causal relationships among individual events, providing more fine-grained information for decision-making. Existing work in the literature either requires strong assumptions, such as linearity in the intensity function, or heuristically defined model parameters that do not necessarily meet the requirements of Granger causality. We propose Instance-wise Self-Attentive Hawkes Processes (ISAHP), a novel deep learning framework that can directly infer the Granger causality at the event instance level. ISAHP is the first neural point process model that meets the requirements of Granger causality. It leverages the self-attention mechanism of the transformer to align with the principles of Granger causality. We empirically demonstrate that ISAHP is capable of discovering complex instance-level causal structures that cannot be handled by classical models. We also show that ISAHP achieves state-of-the-art performance in proxy tasks involving type-level causal discovery and instance-level event type prediction.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Our implementation is available at https://github.com/DeepGraphLearning/SiamDiff.

We consider multi-response and multitask regression models, where the parameter matrix to be estimated is expected to have an unknown grouping structure. The groupings can be along tasks, or features, or both, the last one indicating a bi-cluster or "checkerboard" structure. Discovering this grouping structure along with parameter inference makes sense in several applications, such as multi-response Genome-Wide Association Studies. This additional structure can not only can be leveraged for more accurate parameter estimation, but it also provides valuable information on the underlying data mechanisms (e.g. relationships among genotypes and phenotypes in GWAS). In this paper, we propose two formulations to simultaneously learn the parameter matrix and its group structures, based on convex regularization penalties. We present optimization approaches to solve the resulting problems and provide numerical convergence guarantees. Our approaches are validated on extensive simulations and real datasets concerning phenotypes and genotypes of plant varieties.

Innovation is among the key factors driving a country's economic and social growth. But what are the factors that make a country innovative? How do they differ across different parts of the world and different stages of development? In this work done in collaboration with the World Economic Forum (WEF), we analyze the scores obtained through executive opinion surveys that constitute the WEF's Global Competitiveness Index in conjunction with other country-level metrics and indicators to identify actionable levers of innovation. The findings can help country leaders and organizations shape the policies to drive developmental activities and increase the capacity of innovation.