Large language models (LLMs) face inherent performance bottlenecks under parameter constraints, particularly in processing critical tokens that demand complex reasoning. Empirical analysis reveals challenging tokens induce abrupt gradient spikes across layers, exposing architectural stress points in standard Transformers. Building on this insight, we propose Inner Thinking Transformer (ITT), which reimagines layer computations as implicit thinking steps. ITT dynamically allocates computation through Adaptive Token Routing, iteratively refines representations via Residual Thinking Connections, and distinguishes reasoning phases using Thinking Step Encoding. ITT enables deeper processing of critical tokens without parameter expansion. Evaluations across 162M-466M parameter models show ITT achieves 96.5\% performance of a 466M Transformer using only 162M parameters, reduces training data by 43.2\%, and outperforms Transformer/Loop variants in 11 benchmarks. By enabling elastic computation allocation during inference, ITT balances performance and efficiency through architecture-aware optimization of implicit thinking pathways.

Transformer models encounter challenges in scaling hidden dimensions efficiently, as uniformly increasing them inflates computational and memory costs while failing to emphasize the most relevant features for each token. For further understanding, we study hidden dimension sparsity and observe that trained Transformers utilize only a small fraction of token dimensions, revealing an "activation flow" pattern. Notably, there are shared sub-dimensions with sustained activation across multiple consecutive tokens and specialized sub-dimensions uniquely activated for each token. To better model token-relevant sub-dimensions, we propose MoHD (Mixture of Hidden Dimensions), a sparse conditional activation architecture. Particularly, MoHD employs shared sub-dimensions for common token features and a routing mechanism to dynamically activate specialized sub-dimensions. To mitigate potential information loss from sparsity, we design activation scaling and group fusion mechanisms to preserve activation flow. In this way, MoHD expands hidden dimensions with negligible increases in computation or parameters, efficient training and inference while maintaining performance. Evaluations across 10 NLP tasks show that MoHD surpasses Vanilla Transformers in parameter efficiency and task performance. It achieves 1.7% higher performance with 50% fewer activation parameters and 3.7% higher performance with a 3x parameter expansion at constant activation cost. MOHD offers a new perspective for scaling the model, showcasing the potential of hidden dimension sparsity to boost efficiency

Low-Rank Adaptation (LoRA) drives research to align its performance with full fine-tuning. However, significant challenges remain: (1) Simply increasing the rank size of LoRA does not effectively capture high-rank information, which leads to a performance bottleneck.(2) MoE-style LoRA methods substantially increase parameters and inference latency, contradicting the goals of efficient fine-tuning and ease of application. To address these challenges, we introduce Mixture of Ranks (MoR), which learns rank-specific information for different tasks based on input and efficiently integrates multi-rank information. We firstly propose a new framework that equates the integration of multiple LoRAs to expanding the rank of LoRA. Moreover, we hypothesize that low-rank LoRA already captures sufficient intrinsic information, and MoR can derive high-rank information through mathematical transformations of the low-rank components. Thus, MoR can reduces the learning difficulty of LoRA and enhances its multi-task capabilities. MoR achieves impressive results, with MoR delivering a 1.31\% performance improvement while using only 93.93\% of the parameters compared to baseline methods.

Large language models (LLMs) with billions of parameters demonstrate impressive performance. However, the widely used Multi-Head Attention (MHA) in LLMs incurs substantial computational and memory costs during inference. While some efforts have optimized attention mechanisms by pruning heads or sharing parameters among heads, these methods often lead to performance degradation or necessitate substantial continued pre-training costs to restore performance. Based on the analysis of attention redundancy, we design a Decoupled-Head Attention (DHA) mechanism. DHA adaptively configures group sharing for key heads and value heads across various layers, achieving a better balance between performance and efficiency. Inspired by the observation of clustering similar heads, we propose to progressively transform the MHA checkpoint into the DHA model through linear fusion of similar head parameters step by step, retaining the parametric knowledge of the MHA checkpoint. We construct DHA models by transforming various scales of MHA checkpoints given target head budgets. Our experiments show that DHA remarkably requires a mere 0.25\% of the original model's pre-training budgets to achieve 97.6\% of performance while saving 75\% of KV cache. Compared to Group-Query Attention (GQA), DHA achieves a 5$\times$ training acceleration, a maximum of 13.93\% performance improvement under 0.01\% pre-training budget, and 4\% relative improvement under 0.05\% pre-training budget.

This paper describes our winning system on SemEval 2022 Task 7: Identifying Plausible Clarifications of Implicit and Underspecified Phrases in Instructional Texts. A replaced token detection pre-trained model is utilized with minorly different task-specific heads for SubTask-A: Multi-class Classification and SubTask-B: Ranking. Incorporating a pattern-aware ensemble method, our system achieves a 68.90% accuracy score and 0.8070 spearman's rank correlation score surpassing the 2nd place with a large margin by 2.7 and 2.2 percent points for SubTask-A and SubTask-B, respectively. Our approach is simple and easy to implement, and we conducted ablation studies and qualitative and quantitative analyses for the working strategies used in our system.

Gaining more comprehensive knowledge about drug-drug interactions (DDIs) is one of the most important tasks in drug development and medical practice. Recently graph neural networks have achieved great success in this task by modeling drugs as nodes and drug-drug interactions as links and casting DDI predictions as link prediction problems. However, correlations between link labels (e.g., DDI types) were rarely considered in existing works. We propose the graph energy neural network ( GENN) to explicitly model link type correlations. We formulate the DDI prediction task as a structure prediction problem, and introduce a new energy-based model where the energy function is defined by graph neural networks. Experiments on two real world DDI datasets demonstrated that GENN is superior to many baselines without consideration of link type correlations and achieved 13. 77% and 5.01% PR-AUC improvement on the two datasets, respectively. We also present a case study in which GENN can better capture meaningful DDI correlations compared with baseline models. The use of drug combinations is common and often necessary for treating patients with complex diseases.

Medication recommendation is an important healthcare application. It is commonly formulated as a temporal prediction task. Hence, most existing works only utilize longitudinal electronic health records (EHRs) from a small number of patients with multiple visits ignoring a large number of patients with a single visit (selection bias). Moreover, important hierarchical knowledge such as diagnosis hierarchy is not leveraged in the representation learning process. To address these challenges, we propose G-BERT, a new model to combine the power of Graph Neural Networks (GNNs) and BERT (Bidirectional Encoder Representations from Transformers) for medical code representation and medication recommendation. We use GNNs to represent the internal hierarchical structures of medical codes. Then we integrate the GNN representation into a transformer-based visit encoder and pre-train it on EHR data from patients only with a single visit. The pre-trained visit encoder and representation are then fine-tuned for downstream predictive tasks on longitudinal EHRs from patients with multiple visits. G-BERT is the first to bring the language model pre-training schema into the healthcare domain and it achieved state-of-the-art performance on the medication recommendation task.

Recent progress in deep learning is revolutionizing the healthcare domain including providing solutions to medication recommendations, especially recommending medication combination for patients with complex health conditions. Existing approaches either do not customize based on patient health history, or ignore existing knowledge on drug-drug interactions (DDI) that might lead to adverse outcomes. To fill this gap, we propose the Graph Augmented Memory Networks (GAMENet), which integrates the drug-drug interactions knowledge graph by a memory module implemented as a graph convolutional networks, and models longitudinal patient records as the query. It is trained end-to-end to provide safe and personalized recommendation of medication combination. We demonstrate the effectiveness and safety of GAMENet by comparing with several state-of-the-art methods on real EHR data. GAMENet outperformed all baselines in all effectiveness measures, and also achieved 3.60% DDI rate reduction from existing EHR data.