MedTet: An Online Motion Model for 4D Heart Reconstruction

We present a novel approach to reconstruction of 3D cardiac motion from sparse intraoperative data. While existing methods can accurately reconstruct 3D organ geometries from full 3D volumetric imaging, they cannot be used during surgical interventions where usually limited observed data, such as a few 2D frames or 1D signals, is available in real-time. We propose a versatile framework for reconstructing 3D motion from such partial data. It discretizes the 3D space into a deformable tetrahedral grid with signed distance values, providing implicit unlimited resolution while maintaining explicit control over motion dynamics. Given an initial 3D model reconstructed from pre-operative full volumetric data, our system, equipped with an universal observation encoder, can reconstruct coherent 3D cardiac motion from full 3D volumes, a few 2D MRI slices or even 1D signals. Extensive experiments on cardiac intervention scenarios demonstrate our ability to generate plausible and anatomically consistent 3D motion reconstructions from various sparse real-time observations, highlighting its potential for multimodal cardiac imaging. Our code and model will be made available at https://github.com/Scalsol/MedTet.

Multilingual Pretraining Using a Large Corpus Machine-Translated from a Single Source Language

English, as a very high-resource language, enables the pretraining of high-quality large language models (LLMs). The same cannot be said for most other languages, as leading LLMs still underperform for non-English languages, likely due to a gap in the quality and diversity of the available multilingual pretraining corpora. In this work, we find that machine-translated text from a single high-quality source language can contribute significantly to the pretraining of multilingual LLMs. We translate FineWeb-Edu, a high-quality English web dataset, into French, German, and Spanish, resulting in a final 300B-token dataset, which we call TransWeb-Edu, and pretrain a 1.3B-parameter model, CuatroLLM, from scratch on this dataset. Across five non-English reasoning tasks, we show that CuatroLLM matches or outperforms state-of-the-art multilingual models trained using closed data, such as Llama3.2 and Gemma2, despite using an order of magnitude less data, such as about 6% of the tokens used for Llama3.2's training. We further demonstrate that with additional domain-specific pretraining, amounting to less than 1% of TransWeb-Edu, CuatroLLM surpasses the state of the art in multilingual reasoning. To promote reproducibility, we release our corpus, models, and training pipeline under open licenses at hf.co/britllm/CuatroLLM.

Jet Expansions of Residual Computation

We introduce a framework for expanding residual computational graphs using jets, operators that generalize truncated Taylor series. Our method provides a systematic approach to disentangle contributions of different computational paths to model predictions. In contrast to existing techniques such as distillation, probing, or early decoding, our expansions rely solely on the model itself and requires no data, training, or sampling from the model. We demonstrate how our framework grounds and subsumes logit lens, reveals a (super-)exponential path structure in the recursive residual depth and opens up several applications. These include sketching a transformer large language model with $n$-gram statistics extracted from its computations, and indexing the models' levels of toxicity knowledge. Our approach enables data-free analysis of residual computation for model interpretability, development, and evaluation.

AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction

Epitope identification is vital for antibody design yet challenging due to the inherent variability in antibodies. While many deep learning methods have been developed for general protein binding site prediction tasks, whether they work for epitope prediction remains an understudied research question. The challenge is also heightened by the lack of a consistent evaluation pipeline with sufficient dataset size and epitope diversity. We introduce a filtered antibody-antigen complex structure dataset, AsEP (Antibody-specific Epitope Prediction). AsEP is the largest of its kind and provides clustered epitope groups, allowing the community to develop and test novel epitope prediction methods. AsEP comes with an easy-to-use interface in Python and pre-built graph representations of each antibody-antigen complex while also supporting customizable embedding methods. Based on this new dataset, we benchmarked various representative general protein-binding site prediction methods and find that their performances are not satisfactory as expected for epitope prediction. We thus propose a new method, WALLE, that leverages both protein language models and graph neural networks. WALLE demonstrate about 5X performance gain over existing methods. Our empirical findings evidence that epitope prediction benefits from combining sequential embeddings provided by language models and geometrical information from graph representations, providing a guideline for future method design. In addition, we reformulate the task as bipartite link prediction, allowing easy model performance attribution and interpretability. We open-source our data and code at https://github.com/biochunan/AsEP-dataset.

PISTOL: Dataset Compilation Pipeline for Structural Unlearning of LLMs

Recently, machine unlearning, which seeks to erase specific data stored in the pre-trained or fine-tuned models, has emerged as a crucial protective measure for LLMs. However, unlearning approaches for LLMs that have been considered thus far have focused on the removal of independent data points and have not taken into account that the stored facts are logically connected to one another and form an implicit knowledge graph. To facilitate the development of structural unlearning methods, which are essential for the practical application of unlearning, we propose PISTOL, a pipeline for compiling multi-scenario datasets for benchmarking structural LLM unlearning. Additionally, leveraging sample datasets synthesized using PISTOL, we conducted benchmarks with four distinct unlearning methods on both Llama2-7B and Mistral-7B models. This analysis helps to illustrate the prevailing challenges in effectively and robustly removing highly inter-connected data, batched data, or data skewed towards a specific domain. It also highlights the choice of pre-trained model can impact unlearning performance. This work not only advances our understandings on the limitation of current LLMs unlearning methods and proposes future research directions, but also provides a replicable framework for ongoing exploration and validation in the field.

NAFRSSR: a Lightweight Recursive Network for Efficient Stereo Image Super-Resolution

Stereo image super-resolution (SR) refers to the reconstruction of a high-resolution (HR) image from a pair of low-resolution (LR) images as typically captured by a dual-camera device. To enhance the quality of SR images, most previous studies focused on increasing the number and size of feature maps and introducing complex and computationally intensive structures, resulting in models with high computational complexity. Here, we propose a simple yet efficient stereo image SR model called NAFRSSR, which is modified from the previous state-of-the-art model NAFSSR by introducing recursive connections and lightweighting the constituent modules. Our NAFRSSR model is composed of nonlinear activation free and group convolution-based blocks (NAFGCBlocks) and depth-separated stereo cross attention modules (DSSCAMs). The NAFGCBlock improves feature extraction and reduces number of parameters by removing the simple channel attention mechanism from NAFBlock and using group convolution. The DSSCAM enhances feature fusion and reduces number of parameters by replacing 1x1 pointwise convolution in SCAM with weight-shared 3x3 depthwise convolution. Besides, we propose to incorporate trainable edge detection operator into NAFRSSR to further improve the model performance. Four variants of NAFRSSR with different sizes, namely, NAFRSSR-Mobile (NAFRSSR-M), NAFRSSR-Tiny (NAFRSSR-T), NAFRSSR-Super (NAFRSSR-S) and NAFRSSR-Base (NAFRSSR-B) are designed, and they all exhibit fewer parameters, higher PSNR/SSIM, and faster speed than the previous state-of-the-art models. In particular, to the best of our knowledge, NAFRSSR-M is the lightest (0.28M parameters) and fastest (50 ms inference time) model achieving an average PSNR/SSIM as high as 24.657 dB/0.7622 on the benchmark datasets. Codes and models will be released at https://github.com/JNUChenYiHong/NAFRSSR.

TPTU-v2: Boosting Task Planning and Tool Usage of Large Language Model-based Agents in Real-world Systems

Large Language Models (LLMs) have demonstrated proficiency in addressing tasks that necessitate a combination of task planning and the usage of external tools that require a blend of task planning and the utilization of external tools, such as APIs. However, real-world complex systems present three prevalent challenges concerning task planning and tool usage: (1) The real system usually has a vast array of APIs, so it is impossible to feed the descriptions of all APIs to the prompt of LLMs as the token length is limited; (2) the real system is designed for handling complex tasks, and the base LLMs can hardly plan a correct sub-task order and API-calling order for such tasks; (3) Similar semantics and functionalities among APIs in real systems create challenges for both LLMs and even humans in distinguishing between them. In response, this paper introduces a comprehensive framework aimed at enhancing the Task Planning and Tool Usage (TPTU) abilities of LLM-based agents operating within real-world systems. Our framework comprises three key components designed to address these challenges: (1) the API Retriever selects the most pertinent APIs for the user task among the extensive array available; (2) LLM Finetuner tunes a base LLM so that the finetuned LLM can be more capable for task planning and API calling; (3) the Demo Selector adaptively retrieves different demonstrations related to hard-to-distinguish APIs, which is further used for in-context learning to boost the final performance. We validate our methods using a real-world commercial system as well as an open-sourced academic dataset, and the outcomes clearly showcase the efficacy of each individual component as well as the integrated framework.

TPTU: Task Planning and Tool Usage of Large Language Model-based AI Agents

With recent advancements in natural language processing, Large Language Models (LLMs) have emerged as powerful tools for various real-world applications. Despite their prowess, the intrinsic generative abilities of LLMs may prove insufficient for handling complex tasks which necessitate a combination of task planning and the usage of external tools. In this paper, we first propose a structured framework tailored for LLM-based AI Agents and discuss the crucial capabilities necessary for tackling intricate problems. Within this framework, we design two distinct types of agents (i.e., one-step agent and sequential agent) to execute the inference process. Subsequently, we instantiate the framework using various LLMs and evaluate their Task Planning and Tool Usage (TPTU) abilities on typical tasks. By highlighting key findings and challenges, our goal is to provide a helpful resource for researchers and practitioners to leverage the power of LLMs in their AI applications. Our study emphasizes the substantial potential of these models, while also identifying areas that need more investigation and improvement.

Improving Language Plasticity via Pretraining with Active Forgetting

Pretrained language models (PLMs) are today the primary model for natural language processing. Despite their impressive downstream performance, it can be difficult to apply PLMs to new languages, a barrier to making their capabilities universally accessible. While prior work has shown it possible to address this issue by learning a new embedding layer for the new language, doing so is both data and compute inefficient. We propose to use an active forgetting mechanism during pretraining, as a simple way of creating PLMs that can quickly adapt to new languages. Concretely, by resetting the embedding layer every K updates during pretraining, we encourage the PLM to improve its ability of learning new embeddings within a limited number of updates, similar to a meta-learning effect. Experiments with RoBERTa show that models pretrained with our forgetting mechanism not only demonstrate faster convergence during language adaptation but also outperform standard ones in a low-data regime, particularly for languages that are distant from English.

Mini-Model Adaptation: Efficiently Extending Pretrained Models to New Languages via Aligned Shallow Training

Prior work has shown that it is possible to expand pretrained Masked Language Models (MLMs) to new languages by learning a new set of embeddings, while keeping the transformer body frozen. Despite learning a small subset of parameters, this approach is not compute-efficient, as training the new embeddings requires a full forward and backward pass over the entire model. In this work, we propose mini-model adaptation, a compute-efficient alternative that builds a shallow mini-model from a fraction of a large model's parameters. New language-specific embeddings can then be efficiently trained over the mini-model, and plugged into the aligned large model for rapid cross-lingual transfer. We explore two approaches to learn mini-models: MiniJoint, which jointly pretrains the primary model and the mini-model using a single transformer with a secondary MLM head at a middle layer; and MiniPost, where we start from a regular pretrained model and build a mini-model by extracting and freezing a few layers and learning a small number of parameters on top. Experiments on XNLI, MLQA and PAWS-X show that mini-model adaptation matches the performance of the standard approach using up to 2.4x less compute.