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 //github.com/DeepGraphLearning/ESM-GearNet.
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The evaluation of abstractive summarization models typically uses test data that is identically distributed as training data. In real-world practice, documents to be summarized may contain input noise caused by text extraction artifacts or data pipeline bugs. The robustness of model performance under distribution shift caused by such noise is relatively under-studied. We present a large empirical study quantifying the sometimes severe loss in performance (up to 12 ROUGE-1 points) from different types of input noise for a range of datasets and model sizes. We then propose a light-weight method for detecting and removing such noise in the input during model inference without requiring any extra training, auxiliary models, or even prior knowledge of the type of noise. Our proposed approach effectively mitigates the loss in performance, recovering a large fraction of the performance drop, sometimes as large as 11 ROUGE-1 points.
Large language models (LLMs) can be seen as atomic units of computation mapping sequences to a distribution over sequences. Thus, they can be seen as stochastic language layers in a language network, where the learnable parameters are the natural language prompts at each layer. By stacking two such layers and feeding the output of one layer to the next, we obtain a Deep Language Network (DLN). We first show how to effectively perform prompt optimization for a 1-Layer language network (DLN-1). Then, we present an extension that applies to 2-layer DLNs (DLN-2), where two prompts must be learned. The key idea is to consider the output of the first layer as a latent variable, which requires inference, and prompts to be learned as the parameters of the generative distribution. We first test the effectiveness of DLN-1 in multiple reasoning and natural language understanding tasks. Then, we show that DLN-2 can reach higher performance than a single layer, showing promise that we might reach comparable performance to GPT-4, even when each LLM in the network is smaller and less powerful.
We consider the task of allocating indivisible items to agents, when the agents' preferences over the items are identical. The preferences are captured by means of a directed acyclic graph, with vertices representing items and an edge $(a,b)$ meaning that each of the agents prefers item $a$ over item $b$. The dissatisfaction of an agent is measured by the number of items that the agent does not receive and also does not receive any more preferred item. The aim is to allocate the items to the agents in a fair way, i.e., to minimize the maximum dissatisfaction among the agents. We study the status of computational complexity of that problem and establish the following dichotomy: the problem is NP-hard for the case of at least three agents, even on fairly restricted graphs, but polynomially solvable for two agents. We also provide several polynomial-time results with respect to different underlying graph structures, such as graphs of width at most two and tree-like structures such as stars and matchings. These findings are complemented with fixed parameter tractability results related to path modules and independent set modules. Techniques employed in the paper include bottleneck assignment problem, greedy algorithm, dynamic programming, maximum network flow, and integer linear programming.
Many important tasks of large-scale recommender systems can be naturally cast as testing multiple linear forms for noisy matrix completion. These problems, however, present unique challenges because of the subtle bias-and-variance tradeoff of and an intricate dependence among the estimated entries induced by the low-rank structure. In this paper, we develop a general approach to overcome these difficulties by introducing new statistics for individual tests with sharp asymptotics both marginally and jointly, and utilizing them to control the false discovery rate (FDR) via a data splitting and symmetric aggregation scheme. We show that valid FDR control can be achieved with guaranteed power under nearly optimal sample size requirements using the proposed methodology. Extensive numerical simulations and real data examples are also presented to further illustrate its practical merits.
Large language models of code (Code-LLMs) have recently brought tremendous advances to code completion, a fundamental feature of programming assistance and code intelligence. However, most existing works ignore the possible presence of bugs in the code context for generation, which are inevitable in software development. Therefore, we introduce and study the buggy-code completion problem, inspired by the realistic scenario of real-time code suggestion where the code context contains potential bugs -- anti-patterns that can become bugs in the completed program. To systematically study the task, we introduce two datasets: one with synthetic bugs derived from semantics-altering operator changes (buggy-HumanEval) and one with realistic bugs derived from user submissions to coding problems (buggy-FixEval). We find that the presence of potential bugs significantly degrades the generation performance of the high-performing Code-LLMs. For instance, the passing rates of CODEGEN-2B-MONO on test cases of buggy-HumanEval drop more than 50% given a single potential bug in the context. Finally, we investigate several post-hoc methods for mitigating the adverse effect of potential bugs and find that there remains a significant gap in post-mitigation performance.
There is a fast-growing body of research on predicting future links in dynamic networks, with many new algorithms. Some benchmark data exists, and performance evaluations commonly rely on comparing the scores of observed network events (positives) with those of randomly generated ones (negatives). These evaluation measures depend on both the predictive ability of the model and, crucially, the type of negative samples used. Besides, as generally the case with temporal data, prediction quality may vary over time. This creates a complex evaluation space. In this work, we catalog the possibilities for negative sampling and introduce novel visualization methods that can yield insight into prediction performance and the dynamics of temporal networks. We leverage these visualization tools to investigate the effect of negative sampling on the predictive performance, at the node and edge level. We validate empirically, on datasets extracted from recent benchmarks that the error is typically not evenly distributed across different data segments. Finally, we argue that such visualization tools can serve as powerful guides to evaluate dynamic link prediction methods at different levels.
Sonification research is intrinsically interdisciplinary. Consequently, a proper documentation of, and interdisciplinary discourse about a sonification is often hindered by terminology discrepancies between involved disciplines, i.e., the lack of a common sound terminology in sonification research. Without a common ground, a researcher from one discipline may have troubles understanding the implementation and imagining the resulting sound perception of a sonification, if the sonification is described by a researcher from another discipline. To find a common ground, I consulted literature on interdisciplinary research and discourse, identified problems that occur in sonification, and applied the recommended solutions. As a result, I recommend considering three aspects of sonification individually, namely 1.) Sound Design Concept, 2.) Objective and 3.) Method, clarifying which discipline is involved in which aspect, and sticking to this discipline's terminology. As two requirements of sonifications are that they are a) reproducible and b) interpretable, I recommend documenting and discussing every sonification design once using audio engineering terminology, and once using psychoacoustic terminology. The appendix provides comprehensive lists of sound terms from both disciplines, together with relevant literature and a clarification of often misunderstood and misused terms.
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of synthetic biology and molecular computation. This two-part article aims to introduce a programmable biochemical reaction network (BCRN) system endowed with mass action kinetics that realizes the fully connected neural network (FCNN) and has the potential to act automatically in vivo. In part I, the feedforward propagation computation, the backpropagation component, and all bridging processes of FCNN are ingeniously designed as specific BCRN modules based on their dynamics. This approach addresses a design gap in the biochemical assignment module and judgment termination module and provides a novel precise and robust realization of bi-molecular reactions for the learning process. Through equilibrium approaching, we demonstrate that the designed BCRN system achieves FCNN functionality with exponential convergence to target computational results, thereby enhancing the theoretical support for such work. Finally, the performance of this construction is further evaluated on two typical logic classification problems.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.
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