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Publications
MiRGraph: A transformer-based feature learning approach to identify microRNA-target interactions by integrating heterogeneous graph network and sequence information
MicroRNAs (miRNAs) play a crucial role in the regulation of gene expression by targeting specific mRNAs. They can function as both tumor sup… (see more)pressors and oncogenes depending on the specific miRNA and its target genes. Detecting miRNA-target interactions (MTIs) is critical for unraveling the complex mechanisms of gene regulation and identifying therapeutic targets and diagnostic markers. There is currently a lack of MTIs prediction method that simultaneously performs feature learning on heterogeneous graph network and sequence information. To improve the prediction performance of MTIs, we present a novel transformer-based multi-view feature learning method, named MiRGraph. It consists of two main modules for learning the sequence and heterogeneous graph network, respectively. For learning the sequence-based feaature embedding, we utilize the mature miRNA sequence and the complete 3’UTR sequence of the target mRNAs to encode sequence features. Specifically, a transformer-based CNN (TransCNN) module is designed for miRNAs and genes respectively to extract their personalized sequence features. For learning the network-based feature embedding, we utilize a heterogeneous graph transformer (HGT) module to extract the relational and structural information in a heterogeneous graph consisting of miRNA-miRNA, gene-gene and miRNA-target interactions. We learn the TransCNN and HGT modules end-to-end by utilizing a feedforward network, which takes the combined embedded features of the miRNA-gene pair to predict MTIs. Comparisons with other existing MTIs prediction methods illustrates the superiority of MiRGraph under standard criteria. In a case study on breast cancer, we identified plausible target genes of an oncomir hsa-MiR-122-5p and plausible miRNAs that regulate the oncogene BRCA1.
We study the depth of grade-school math (GSM) problem-solving capabilities of LLMs. To this end, we evaluate their performance on pairs of e… (see more)xisting math word problems together so that the answer to the second problem depends on correctly answering the first problem. Our findings reveal a significant reasoning gap in most LLMs, that is performance difference between solving the compositional pairs and solving each question independently. This gap is more pronounced in smaller, more cost-efficient, and math-specialized models. Moreover, instruction-tuning recipes and code generation have varying effects across LLM sizes, while finetuning on GSM can lead to task overfitting. Our analysis indicates that large reasoning gaps are not because of test-set leakage, but due to distraction from additional context and poor second-hop reasoning. Overall, LLMs exhibit systematic differences in their reasoning abilities, despite what their performance on standard benchmarks indicates.
Autonomous robots navigating in off-road terrain like forests open new opportunities for automation. While off-road navigation has been stud… (see more)ied, existing work often relies on clearly delineated pathways. We present a method allowing for long-range planning, exploration and low-level control in unknown off-trail forest terrain, using vision and GPS only. We represent outdoor terrain with a topological map, which is a set of panoramic snapshots connected with edges containing traversability information. A novel traversability analysis method is demonstrated, predicting the existence of a safe path towards a target in an image. Navigating between nodes is done using goal-conditioned behavior cloning, leveraging the power of a pretrained vision transformer. An exploration planner is presented, efficiently covering an unknown off-road area with unknown traversability using a frontiers-based approach. The approach is successfully deployed to autonomously explore two 400 meters squared forest sites unseen during training, in difficult conditions for navigation.
Large language models (LLMs) are increasingly applied to complex reasoning tasks that require executing several complex steps before receivi… (see more)ng any reward. Properly assigning credit to these steps is essential for enhancing model performance. Proximal Policy Optimization (PPO), a common reinforcement learning (RL) algorithm used for LLM finetuning, employs value networks to tackle credit assignment. However, recent approaches achieve strong results without it, raising questions about the efficacy of value networks in practice. In this work, we systematically evaluate the efficacy of value networks and reveal their significant shortcomings in reasoning-heavy LLM tasks, showing that they often produce poor estimate of expected return and barely outperform a random baseline when comparing alternative steps. This motivates our key question: Can improved credit assignment enhance RL training for LLMs? To address this, we propose VinePPO, a straightforward approach that leverages the flexibility of language environments to compute unbiased Monte Carlo-based estimates. Our method consistently outperforms PPO and other baselines across MATH and GSM8K datasets in less wall-clock time (up to 3.0x). Crucially, it achieves higher test accuracy for a given training accuracy, capturing more generalization signal per sample. These results emphasize the importance of accurate credit assignment in RL training of LLM.
Large language models (LLMs) are increasingly applied to complex reasoning tasks that require executing several complex steps before receivi… (see more)ng any reward. Properly assigning credit to these steps is essential for enhancing model performance. Proximal Policy Optimization (PPO), a common reinforcement learning (RL) algorithm used for LLM finetuning, employs value networks to tackle credit assignment. However, recent approaches achieve strong results without it, raising questions about the efficacy of value networks in practice. In this work, we systematically evaluate the efficacy of value networks and reveal their significant shortcomings in reasoning-heavy LLM tasks, showing that they often produce poor estimate of expected return and barely outperform a random baseline when comparing alternative steps. This motivates our key question: Can improved credit assignment enhance RL training for LLMs? To address this, we propose VinePPO, a straightforward approach that leverages the flexibility of language environments to compute unbiased Monte Carlo-based estimates. Our method consistently outperforms PPO and other baselines across MATH and GSM8K datasets in less wall-clock time (up to 3.0x). Crucially, it achieves higher test accuracy for a given training accuracy, capturing more generalization signal per sample. These results emphasize the importance of accurate credit assignment in RL training of LLM.
Large language models (LLMs) are increasingly applied to complex reasoning tasks that require executing several complex steps before receivi… (see more)ng any reward. Properly assigning credit to these steps is essential for enhancing model performance. Proximal Policy Optimization (PPO), a state-of-the-art reinforcement learning (RL) algorithm used for LLM finetuning, employs value networks to tackle credit assignment. However, value networks face challenges in predicting the expected cumulative rewards accurately in complex reasoning tasks, often leading to high-variance updates and suboptimal performance. In this work, we systematically evaluate the efficacy of value networks and reveal their significant shortcomings in reasoning-heavy LLM tasks, showing that they barely outperform a random baseline when comparing alternative steps. To address this, we propose VinePPO, a straightforward approach that leverages the flexibility of language environments to compute unbiased Monte Carlo-based estimates, bypassing the need for large value networks. Our method consistently outperforms PPO and other RL-free baselines across MATH and GSM8K datasets with fewer gradient updates (up to 9x), less wall-clock time (up to 3.0x). These results emphasize the importance of accurate credit assignment in RL finetuning of LLM and demonstrate VinePPO's potential as a superior alternative.
Large language models (LLMs) are increasingly applied to complex reasoning tasks that require executing several complex steps before receivi… (see more)ng any reward. Properly assigning credit to these steps is essential for enhancing model performance. Proximal Policy Optimization (PPO), a state-of-the-art reinforcement learning (RL) algorithm used for LLM finetuning, employs value networks to tackle credit assignment. However, value networks face challenges in predicting the expected cumulative rewards accurately in complex reasoning tasks, often leading to high-variance updates and suboptimal performance. In this work, we systematically evaluate the efficacy of value networks and reveal their significant shortcomings in reasoning-heavy LLM tasks, showing that they barely outperform a random baseline when comparing alternative steps. To address this, we propose VinePPO, a straightforward approach that leverages the flexibility of language environments to compute unbiased Monte Carlo-based estimates, bypassing the need for large value networks. Our method consistently outperforms PPO and other RL-free baselines across MATH and GSM8K datasets with fewer gradient updates (up to 9x), less wall-clock time (up to 3.0x). These results emphasize the importance of accurate credit assignment in RL finetuning of LLM and demonstrate VinePPO's potential as a superior alternative.
The introduction of Transformers in 2017 reshaped the landscape of deep learning. Originally proposed for sequence modelling, Transformers h… (see more)ave since achieved widespread success across various domains. However, the scalability limitations of Transformers - particularly with respect to sequence length - have sparked renewed interest in novel recurrent models that are parallelizable during training, offer comparable performance, and scale more effectively. In this work, we revisit sequence modelling from a historical perspective, focusing on Recurrent Neural Networks (RNNs), which dominated the field for two decades before the rise of Transformers. Specifically, we examine LSTMs (1997) and GRUs (2014). We demonstrate that by simplifying these models, we can derive minimal versions (minLSTMs and minGRUs) that (1) use fewer parameters than their traditional counterparts, (2) are fully parallelizable during training, and (3) achieve surprisingly competitive performance on a range of tasks, rivalling recent models including Transformers.
The introduction of Transformers in 2017 reshaped the landscape of deep learning. Originally proposed for sequence modelling, Transformers h… (see more)ave since achieved widespread success across various domains. However, the scalability limitations of Transformers - particularly with respect to sequence length - have sparked renewed interest in novel recurrent models that are parallelizable during training, offer comparable performance, and scale more effectively. In this work, we revisit sequence modelling from a historical perspective, focusing on Recurrent Neural Networks (RNNs), which dominated the field for two decades before the rise of Transformers. Specifically, we examine LSTMs (1997) and GRUs (2014). We demonstrate that by simplifying these models, we can derive minimal versions (minLSTMs and minGRUs) that (1) use fewer parameters than their traditional counterparts, (2) are fully parallelizable during training, and (3) achieve surprisingly competitive performance on a range of tasks, rivalling recent models including Transformers.
