Bio2Token: All-atom tokenization of any biomolecular structure with Mamba

Efficient encoding and representation of large 3D molecular structures with high fidelity is critical for biomolecular design applications. Despite this, many representation learning approaches restrict themselves to modeling smaller systems or use coarse-grained approximations of the systems, for example modeling proteins at the resolution of amino acid residues rather than at the level of individual atoms. To address this, we develop quantized auto-encoders that learn atom-level tokenizations of complete proteins, RNA and small molecule structures with reconstruction accuracies below and around 1 Angstrom. We demonstrate that the Mamba state space model architecture employed is comparatively efficient, requiring a fraction of the training data, parameters and compute needed to reach competitive accuracies and can scale to systems with almost 100,000 atoms. The learned structure tokens of bio2token may serve as the input for all-atom language models in the future.

A Role of Environmental Complexity on Representation Learning in Deep Reinforcement Learning Agents

The environments where individuals live can present diverse navigation challenges, resulting in varying navigation abilities and strategies. Inspired by differing urban layouts and the Dual Solutions Paradigm test used for human navigators, we developed a simulated navigation environment to train deep reinforcement learning agents in a shortcut usage task. We modulated the frequency of exposure to a shortcut and navigation cue, leading to the development of artificial agents with differing abilities. We examined the encoded representations in artificial neural networks driving these agents, revealing intricate dynamics in representation learning, and correlated them with shortcut use preferences. Furthermore, we demonstrated methods to analyze representations across a population of nodes, which proved effective in finding patterns in what would otherwise be noisy single-node data. These techniques may also have broader applications in studying neural activity. From our observations in representation learning dynamics, we propose insights for human navigation learning, emphasizing the importance of navigation challenges in developing strong landmark knowledge over repeated exposures to landmarks alone.

What does the Knowledge Neuron Thesis Have to do with Knowledge?

We reassess the Knowledge Neuron (KN) Thesis: an interpretation of the mechanism underlying the ability of large language models to recall facts from a training corpus. This nascent thesis proposes that facts are recalled from the training corpus through the MLP weights in a manner resembling key-value memory, implying in effect that "knowledge" is stored in the network. Furthermore, by modifying the MLP modules, one can control the language model's generation of factual information. The plausibility of the KN thesis has been demonstrated by the success of KN-inspired model editing methods (Dai et al., 2022; Meng et al., 2022). We find that this thesis is, at best, an oversimplification. Not only have we found that we can edit the expression of certain linguistic phenomena using the same model editing methods but, through a more comprehensive evaluation, we have found that the KN thesis does not adequately explain the process of factual expression. While it is possible to argue that the MLP weights store complex patterns that are interpretable both syntactically and semantically, these patterns do not constitute "knowledge." To gain a more comprehensive understanding of the knowledge representation process, we must look beyond the MLP weights and explore recent models' complex layer structures and attention mechanisms.

Large Language Models in Healthcare: A Comprehensive Benchmark

The adoption of large language models (LLMs) to assist clinicians has attracted remarkable attention. Existing works mainly adopt the close-ended question-answering task with answer options for evaluation. However, in real clinical settings, many clinical decisions, such as treatment recommendations, involve answering open-ended questions without pre-set options. Meanwhile, existing studies mainly use accuracy to assess model performance. In this paper, we comprehensively benchmark diverse LLMs in healthcare, to clearly understand their strengths and weaknesses. Our benchmark contains seven tasks and thirteen datasets across medical language generation, understanding, and reasoning. We conduct a detailed evaluation of the existing sixteen LLMs in healthcare under both zero-shot and few-shot (i.e., 1,3,5-shot) learning settings. We report the results on five metrics (i.e. matching, faithfulness, comprehensiveness, generalizability, and robustness) that are critical in achieving trust from clinical users. We further invite medical experts to conduct human evaluation.

Qilin-Med: Multi-stage Knowledge Injection Advanced Medical Large Language Model

Integrating large language models (LLMs) into healthcare presents potential but faces challenges. Directly pre-training LLMs for domains like medicine is resource-heavy and sometimes unfeasible. Sole reliance on Supervised Fine-tuning (SFT) can result in overconfident predictions and may not tap into domain specific insights. Addressing these challenges, we present a multi-stage training method combining Domain-specific Continued Pre-training (DCPT), SFT, and Direct Preference Optimization (DPO). A notable contribution of our study is the introduction of a 3Gb Chinese Medicine (ChiMed) dataset, encompassing medical question answering, plain texts, knowledge graphs, and dialogues, segmented into three training stages. The medical LLM trained with our pipeline, Qilin-Med, exhibits significant performance boosts. In the CPT and SFT phases, it achieves 38.4% and 40.0% accuracy on the CMExam, surpassing Baichuan-7B's 33.5%. In the DPO phase, on the Huatuo-26M test set, it scores 16.66 in BLEU-1 and 27.44 in ROUGE1, outperforming the SFT's 12.69 and 24.21. This highlights the strength of our training approach in refining LLMs for medical applications.

Benchmarking Large Language Models on CMExam -- A Comprehensive Chinese Medical Exam Dataset

Recent advancements in large language models (LLMs) have transformed the field of question answering (QA). However, evaluating LLMs in the medical field is challenging due to the lack of standardized and comprehensive datasets. To address this gap, we introduce CMExam, sourced from the Chinese National Medical Licensing Examination. CMExam consists of 60K+ multiple-choice questions for standardized and objective evaluations, as well as solution explanations for model reasoning evaluation in an open-ended manner. For in-depth analyses of LLMs, we invited medical professionals to label five additional question-wise annotations, including disease groups, clinical departments, medical disciplines, areas of competency, and question difficulty levels. Alongside the dataset, we further conducted thorough experiments with representative LLMs and QA algorithms on CMExam. The results show that GPT-4 had the best accuracy of 61.6% and a weighted F1 score of 0.617. These results highlight a great disparity when compared to human accuracy, which stood at 71.6%. For explanation tasks, while LLMs could generate relevant reasoning and demonstrate improved performance after finetuning, they fall short of a desired standard, indicating ample room for improvement. To the best of our knowledge, CMExam is the first Chinese medical exam dataset to provide comprehensive medical annotations. The experiments and findings of LLM evaluation also provide valuable insights into the challenges and potential solutions in developing Chinese medical QA systems and LLM evaluation pipelines. The dataset and relevant code are available at https://github.com/williamliujl/CMExam.

Investigating Navigation Strategies in the Morris Water Maze through Deep Reinforcement Learning

Navigation is a complex skill with a long history of research in animals and humans. In this work, we simulate the Morris Water Maze in 2D to train deep reinforcement learning agents. We perform automatic classification of navigation strategies, analyze the distribution of strategies used by artificial agents, and compare them with experimental data to show similar learning dynamics as those seen in humans and rodents. We develop environment-specific auxiliary tasks and examine factors affecting their usefulness. We suggest that the most beneficial tasks are potentially more biologically feasible for real agents to use. Lastly, we explore the development of internal representations in the activations of artificial agent neural networks. These representations resemble place cells and head-direction cells found in mouse brains, and their presence has correlation to the navigation strategies that artificial agents employ.

AICOM-MP: an AI-based Monkeypox Detector for Resource-Constrained Environments

Under the Autonomous Mobile Clinics (AMCs) initiative, we are developing, open sourcing, and standardizing health AI technologies to enable healthcare access in least developed countries (LDCs). We deem AMCs as the next generation of health care delivery platforms, whereas health AI engines are applications on these platforms, similar to how various applications expand the usage scenarios of smart phones. Facing the recent global monkeypox outbreak, in this article, we introduce AICOM-MP, an AI-based monkeypox detector specially aiming for handling images taken from resource-constrained devices. Compared to existing AI-based monkeypox detectors, AICOM-MP has achieved state-of-the-art (SOTA) performance. We have hosted AICOM-MP as a web service to allow universal access to monkeypox screening technology. We have also open sourced both the source code and the dataset of AICOM-MP to allow health AI professionals to integrate AICOM-MP into their services. Also, through the AICOM-MP project, we have generalized a methodology of developing health AI technologies for AMCs to allow universal access even in resource-constrained environments.

Urban Radiance Fields

The goal of this work is to perform 3D reconstruction and novel view synthesis from data captured by scanning platforms commonly deployed for world mapping in urban outdoor environments (e.g., Street View). Given a sequence of posed RGB images and lidar sweeps acquired by cameras and scanners moving through an outdoor scene, we produce a model from which 3D surfaces can be extracted and novel RGB images can be synthesized. Our approach extends Neural Radiance Fields, which has been demonstrated to synthesize realistic novel images for small scenes in controlled settings, with new methods for leveraging asynchronously captured lidar data, for addressing exposure variation between captured images, and for leveraging predicted image segmentations to supervise densities on rays pointing at the sky. Each of these three extensions provides significant performance improvements in experiments on Street View data. Our system produces state-of-the-art 3D surface reconstructions and synthesizes higher quality novel views in comparison to both traditional methods (e.g.~COLMAP) and recent neural representations (e.g.~Mip-NeRF).

Depth-supervised NeRF: Fewer Views and Faster Training for Free

One common failure mode of Neural Radiance Field (NeRF) models is fitting incorrect geometries when given an insufficient number of input views. We propose DS-NeRF (Depth-supervised Neural Radiance Fields), a loss for learning neural radiance fields that takes advantage of readily-available depth supervision. Our key insight is that sparse depth supervision can be used to regularize the learned geometry, a crucial component for effectively rendering novel views using NeRF. We exploit the fact that current NeRF pipelines require images with known camera poses that are typically estimated by running structure-from-motion (SFM). Crucially, SFM also produces sparse 3D points that can be used as ``free" depth supervision during training: we simply add a loss to ensure that depth rendered along rays that intersect these 3D points is close to the observed depth. We find that DS-NeRF can render more accurate images given fewer training views while training 2-6x faster. With only two training views on real-world images, DS-NeRF significantly outperforms NeRF as well as other sparse-view variants. We show that our loss is compatible with these NeRF models, demonstrating that depth is a cheap and easily digestible supervisory signal. Finally, we show that DS-NeRF supports other types of depth supervision such as scanned depth sensors and RGBD reconstruction outputs.