OpenRaiser/Intern-Atlas huggingface dataset:
SwiFT: Swin 4D fMRI Transformer
Venue: Conference NeurIPS 2023
Year: 2023

Modeling spatiotemporal brain dynamics from high-dimensional data, such as functional Magnetic Resonance Imaging (fMRI), is a formidable task in neuroscience. Existing approaches for fMRI analysis utilize hand-crafted features, but the process of feature extraction risks losing essential information in fMRI scans. To address this challenge, we present SwiFT (Swin 4D fMRI Transformer), a Swin Transformer architecture that can learn brain dynamics directly from fMRI volumes in a memory and computation-efficient manner. SwiFT achieves this by implementing a 4D window multi-head self-attention mechanism and absolute positional embeddings. We evaluate SwiFT using multiple large-scale resting-state fMRI datasets, including the Human Connectome Project (HCP), Adolescent Brain Cognitive Development (ABCD), and UK Biobank (UKB) datasets, to predict sex, age, and cognitive intelligence. Our experimental outcomes reveal that SwiFT consistently outperforms recent state-of-the-art models. Furthermore, by leveraging its end-to-end learning capability, we show that contrastive loss-based self-supervised pre-training of SwiFT can enhance performance on downstream tasks. Additionally, we employ an explainable AI method to identify the brain regions associated with sex classification. To our knowledge, SwiFT is the first Swin Transformer architecture to process dimensional spatiotemporal brain functional data in an end-to-end fashion. Our work holds substantial potential in facilitating scalable learning of functional brain imaging in neuroscience research by reducing the hurdles associated with applying Transformer models to high-dimensional fMRI.
Consistent Diffusion Models: Mitigating Sampling Drift by Learning to be Consistent
Venue: Conference NeurIPS 2023
Year: 2023

Imperfect score-matching leads to a shift between the training and the sampling distribution of diffusion models. Due to the recursive nature of the generation process, errors in previous steps yield sampling iterates that drift away from the training distribution. Yet, the standard training objective via Denoising Score Matching (DSM) is only designed to optimize over non-drifted data. To train on drifted data, we propose to enforce a \emph{consistency} property which states that predictions of the model on its own generated data are consistent across time. Theoretically, we show that if the score is learned perfectly on some non-drifted points (via DSM) and if the consistency property is enforced everywhere, then the score is learned accurately everywhere. Empirically we show that our novel training objective yields state-of-the-art results for conditional and unconditional generation in CIFAR-10 and baseline improvements in AFHQ and FFHQ. We open-source our code and models: https://github.com/giannisdaras/cdm
AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions
Venue: Conference NeurIPS 2023
Year: 2023

Antibodies have become an important class of therapeutic agents to treat human diseases. To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria. However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences. To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens. By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences. All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method. Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein. This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations. We report experimental benchmark results on AVIDa-hIL6 by using machine learning models. The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants. The dataset is available at https://avida-hil6.cognanous.com.
Token-Scaled Logit Distillation for Ternary Weight Generative Language Models
Venue: Conference NeurIPS 2023
Year: 2023

Generative Language Models (GLMs) have shown impressive performance in tasks such as text generation, understanding, and reasoning. However, the large model size poses challenges for practical deployment. To solve this problem, Quantization-Aware Training (QAT) has become increasingly popular. However, current QAT methods for generative models have resulted in a noticeable loss of accuracy. To counteract this issue, we propose a novel knowledge distillation method specifically designed for GLMs. Our method, called token-scaled logit distillation, prevents overfitting and provides superior learning from the teacher model and ground truth. This research marks the first evaluation of ternary weight quantization-aware training of large-scale GLMs with less than 1.0 degradation in perplexity and achieves enhanced accuracy in tasks like common-sense QA and arithmetic reasoning as well as natural language understanding. Our code is available at https://github.com/aiha-lab/TSLD.
Efficient Exploration in Continuous-time Model-based Reinforcement Learning
Venue: Conference NeurIPS 2023
Year: 2023

Reinforcement learning algorithms typically consider discrete-time dynamics, even though the underlying systems are often continuous in time. In this paper, we introduce a model-based reinforcement learning algorithm that represents continuous-time dynamics using nonlinear ordinary differential equations (ODEs). We capture epistemic uncertainty using well-calibrated probabilistic models, and use the optimistic principle for exploration. Our regret bounds surface the importance of the measurement selection strategy(MSS), since in continuous time we not only must decide how to explore, but also when to observe the underlying system. Our analysis demonstrates that the regret is sublinear when modeling ODEs with Gaussian Processes (GP) for common choices of MSS, such as equidistant sampling. Additionally, we propose an adaptive, data-dependent, practical MSS that, when combined with GP dynamics, also achieves sublinear regret with significantly fewer samples. We showcase the benefits of continuous-time modeling over its discrete-time counterpart, as well as our proposed adaptive MSS over standard baselines, on several applications.
On Learning Necessary and Sufficient Causal Graphs
Venue: Conference NeurIPS 2023
Year: 2023

The causal revolution has stimulated interest in understanding complex relationships in various fields. Most of the existing methods aim to discover causal relationships among all variables within a complex large-scale graph. However, in practice, only a small subset of variables in the graph are relevant to the outcomes of interest. Consequently, causal estimation with the full causal graph -- particularly given limited data -- could lead to numerous falsely discovered, spurious variables that exhibit high correlation with, but exert no causal impact on, the target outcome. In this paper, we propose learning a class of necessary and sufficient causal graphs (NSCG) that exclusively comprises causally relevant variables for an outcome of interest, which we term causal features. The key idea is to employ probabilities of causation to systematically evaluate the importance of features in the causal graph, allowing us to identify a subgraph relevant to the outcome of interest. To learn NSCG from data, we develop a necessary and sufficient causal structural learning (NSCSL) algorithm, by establishing theoretical properties and relationships between probabilities of causation and natural causal effects of features. Across empirical studies of simulated and real data, we demonstrate that NSCSL outperforms existing algorithms and can reveal crucial yeast genes for target heritable traits of interest.
Beyond Unimodal: Generalising Neural Processes for Multimodal Uncertainty Estimation
Venue: Conference NeurIPS 2023
Year: 2023

Uncertainty estimation is an important research area to make deep neural networks (DNNs) more trustworthy. While extensive research on uncertainty estimation has been conducted with unimodal data, uncertainty estimation for multimodal data remains a challenge. Neural processes (NPs) have been demonstrated to be an effective uncertainty estimation method for unimodal data by providing the reliability of Gaussian processes with efficient and powerful DNNs. While NPs hold significant potential for multimodal uncertainty estimation, the adaptation of NPs for multimodal data has not been carefully studied. To bridge this gap, we propose Multimodal Neural Processes (MNPs) by generalising NPs for multimodal uncertainty estimation. Based on the framework of NPs, MNPs consist of several novel and principled mechanisms tailored to the characteristics of multimodal data. In extensive empirical evaluation, our method achieves state-of-the-art multimodal uncertainty estimation performance, showing its appealing robustness against noisy samples and reliability in out-of-distribution detection with faster computation time compared to the current state-of-the-art multimodal uncertainty estimation method.
Plug-and-Play Stability for Intracortical Brain-Computer Interfaces: A One-Year Demonstration of Seamless Brain-to-Text Communication
Venue: Conference NeurIPS 2023
Year: 2023

Intracortical brain-computer interfaces (iBCIs) have shown promise for restoring rapid communication to people with neurological disorders such as amyotrophic lateral sclerosis (ALS). However, to maintain high performance over time, iBCIs typically need frequent recalibration to combat changes in the neural recordings that accrue over days. This requires iBCI users to stop using the iBCI and engage in supervised data collection, making the iBCI system hard to use. In this paper, we propose a method that enables self-recalibration of communication iBCIs without interrupting the user. Our method leverages large language models (LMs) to automatically correct errors in iBCI outputs. The self-recalibration process uses these corrected outputs ("pseudo-labels") to continually update the iBCI decoder online. Over a period of more than one year (403 days), we evaluated our Continual Online Recalibration with Pseudo-labels (CORP) framework with one clinical trial participant. CORP achieved a stable decoding accuracy of 93.84% in an online handwriting iBCI task, significantly outperforming other baseline methods. Notably, this is the longest-running iBCI stability demonstration involving a human participant. Our results provide the first evidence for long-term stabilization of a plug-and-play, high-performance communication iBCI, addressing a major barrier for the clinical translation of iBCIs.
State-Action Similarity-Based Representations for Off-Policy Evaluation
Venue: Conference NeurIPS 2023
Year: 2023

In reinforcement learning, off-policy evaluation (OPE) is the problem of estimating the expected return of an evaluation policy given a fixed dataset that was collected by running one or more different policies. One of the more empirically successful algorithms for OPE has been the fitted q-evaluation (FQE) algorithm that uses temporal difference updates to learn an action-value function, which is then used to estimate the expected return of the evaluation policy. Typically, the original fixed dataset is fed directly into FQE to learn the action-value function of the evaluation policy. Instead, in this paper, we seek to enhance the data-efficiency of FQE by first transforming the fixed dataset using a learned encoder, and then feeding the transformed dataset into FQE. To learn such an encoder, we introduce an OPE-tailored state-action behavioral similarity metric, and use this metric and the fixed dataset to learn an encoder that models this metric. Theoretically, we show that this metric allows us to bound the error in the resulting OPE estimate. Empirically, we show that other state-action similarity metrics lead to representations that cannot represent the action-value function of the evaluation policy, and that our state-action representation method boosts the data-efficiency of FQE and lowers OPE error relative to other OPE-based representation learning methods on challenging OPE tasks. We also empirically show that the learned representations significantly mitigate divergence of FQE under varying distribution shifts. Our code is available here: https://github.com/Badger-RL/ROPE.
Can LLM Already Serve as A Database Interface? A BIg Bench for Large-Scale Database Grounded Text-to-SQLs
Venue: Conference NeurIPS 2023
Year: 2023

Text-to-SQL parsing, which aims at converting natural language instructions into executable SQLs, has gained increasing attention in recent years. In particular, Codex and ChatGPT have shown impressive results in this task. However, most of the prevalent benchmarks, i.e., Spider, and WikiSQL, focus on database schema with few rows of database contents leaving the gap between academic study and real-world applications. To mitigate this gap, we present Bird, a big benchmark for large-scale database grounded in text-to-SQL tasks, containing 12,751 pairs of text-to-SQL data and 95 databases with a total size of 33.4 GB, spanning 37 professional domains. Our emphasis on database values highlights the new challenges of dirty database contents, external knowledge between NL questions and database contents, and SQL efficiency, particularly in the context of massive databases. To solve these problems, text-to-SQL models must feature database value comprehension in addition to semantic parsing. The experimental results demonstrate the significance of database values in generating accurate text-to-SQLs for big databases. Furthermore, even the most effective text-to-SQL models, i.e. ChatGPT, only achieves 40.08% in execution accuracy, which is still far from the human result of 92.96%, proving that challenges still stand. Besides, we also provide an efficiency analysis to offer insights into generating text-to-efficient-SQLs that are beneficial to industries. We believe that BIRD will contribute to advancing real-world applications of text-to-SQL research. The leaderboard and source code are available: https://bird-bench.github.io/.
CARE-MI: Chinese Benchmark for Misinformation Evaluation in Maternity and Infant Care
Venue: Conference NeurIPS 2023
Year: 2023

The recent advances in natural language processing (NLP), have led to a new trend of applying large language models (LLMs) to real-world scenarios. While the latest LLMs are astonishingly fluent when interacting with humans, they suffer from the misinformation problem by unintentionally generating factually false statements. This can lead to harmful consequences, especially when produced within sensitive contexts, such as healthcare. Yet few previous works have focused on evaluating misinformation in the long-form (LF) generation of LLMs, especially for knowledge-intensive topics. Moreover, although LLMs have been shown to perform well in different languages, misinformation evaluation has been mostly conducted in English. To this end, we present a benchmark, CARE-MI, for evaluating LLM misinformation in: 1) a sensitive topic, specifically the maternity and infant care domain; and 2) a language other than English, namely Chinese. Most importantly, we provide an innovative paradigm for building LF generation evaluation benchmarks that can be transferred to other knowledge-intensive domains and low-resourced languages. Our proposed benchmark fills the gap between the extensive usage of LLMs and the lack of datasets for assessing the misinformation generated by these models. It contains 1,612 expert-checked questions, accompanied with human-selected references. Using our benchmark, we conduct extensive experiments and found that current Chinese LLMs are far from perfect in the topic of maternity and infant care. In an effort to minimize the reliance on human resources for performance evaluation, we offer off-the-shelf judgment models for automatically assessing the LF output of LLMs given benchmark questions. Moreover, we compare potential solutions for LF generation evaluation and provide insights for building better automated metrics.
Explore In-Context Learning for 3D Point Cloud Understanding
Venue: Conference NeurIPS 2023
Year: 2023

With the rise of large-scale models trained on broad data, in-context learning has become a new learning paradigm that has demonstrated significant potential in natural language processing and computer vision tasks. Meanwhile, in-context learning is still largely unexplored in the 3D point cloud domain. Although masked modeling has been successfully applied for in-context learning in 2D vision, directly extending it to 3D point clouds remains a formidable challenge. In the case of point clouds, the tokens themselves are the point cloud positions (coordinates) that are masked during inference. Moreover, position embedding in previous works may inadvertently introduce information leakage. To address these challenges, we introduce a novel framework, named Point-In-Context, designed especially for in-context learning in 3D point clouds, where both inputs and outputs are modeled as coordinates for each task. Additionally, we propose the Joint Sampling module, carefully designed to work in tandem with the general point sampling operator, effectively resolving the aforementioned technical issues. We conduct extensive experiments to validate the versatility and adaptability of our proposed methods in handling a wide range of tasks.
Interactive Visual Reasoning under Uncertainty
Venue: Conference NeurIPS 2023
Year: 2023

One of the fundamental cognitive abilities of humans is to quickly resolve uncertainty by generating hypotheses and testing them via active trials. Encountering a novel phenomenon accompanied by ambiguous cause-effect relationships, humans make hypotheses against data, conduct inferences from observation, test their theory via experimentation, and correct the proposition if inconsistency arises. These iterative processes persist until the underlying mechanism becomes clear. In this work, we devise the IVRE (pronounced as "ivory") environment for evaluating artificial agents' reasoning ability under uncertainty. IVRE is an interactive environment featuring rich scenarios centered around Blicket detection. Agents in IVRE are placed into environments with various ambiguous action-effect pairs and asked to determine each object's role. They are encouraged to propose effective and efficient experiments to validate their hypotheses based on observations and actively gather new information. The game ends when all uncertainties are resolved or the maximum number of trials is consumed. By evaluating modern artificial agents in IVRE, we notice a clear failure of today's learning methods compared to humans. Such inefficacy in interactive reasoning ability under uncertainty calls for future research in building human-like intelligence.
Lie Point Symmetry and Physics-Informed Networks
Venue: Conference NeurIPS 2023
Year: 2023

Symmetries have been leveraged to improve the generalization of neural networks through different mechanisms from data augmentation to equivariant architectures. However, despite their potential, their integration into neural solvers for partial differential equations (PDEs) remains largely unexplored. We explore the integration of PDE symmetries, known as Lie point symmetries, in a major family of neural solvers known as physics-informed neural networks (PINNs). We propose a loss function that informs the network about Lie point symmetries in the same way that PINN models try to enforce the underlying PDE through a loss function. Intuitively, our symmetry loss ensures that the infinitesimal generators of the Lie group conserve the PDE solutions. Effectively, this means that once the network learns a solution, it also learns the neighbouring solutions generated by Lie point symmetries. Empirical evaluations indicate that the inductive bias introduced by the Lie point symmetries of the PDEs greatly boosts the sample efficiency of PINNs.
Intelligent Knee Sleeves: A Real-time Multimodal Dataset for 3D Lower Body Motion Estimation Using Smart Textile
Venue: Conference NeurIPS 2023
Year: 2023

The kinematics of human movements and locomotion are closely linked to the activation and contractions of muscles. To investigate this, we present a multimodal dataset with benchmarks collected using a novel pair of Intelligent Knee Sleeves (Texavie MarsWear Knee Sleeves) for human pose estimation. Our system utilizes synchronized datasets that comprise time-series data from the Knee Sleeves and the corresponding ground truth labels from the visualized motion capture camera system. We employ these to generate 3D human models solely based on the wearable data of individuals performing different activities. We demonstrate the effectiveness of this camera-free system and machine learning algorithms in the assessment of various movements and exercises, including extension to unseen exercises and individuals. The results show an average error of 7.21 degrees across all eight lower body joints when compared to the ground truth, indicating the effectiveness and reliability of the Knee Sleeve system for the prediction of different lower body joints beyond the knees. The results enable human pose estimation in a seamless manner without being limited by visual occlusion or the field of view of cameras. Our results show the potential of multimodal wearable sensing in a variety of applications from home fitness to sports, healthcare, and physical rehabilitation focusing on pose and movement estimation.
Neural Injective Functions for Multisets, Measures and Graphs via a Finite Witness Theorem
Venue: Conference NeurIPS 2023
Year: 2023

Injective multiset functions have a key role in the theoretical study of machine learning on multisets and graphs. Yet, there remains a gap between the provably injective multiset functions considered in theory, which typically rely on polynomial moments, and the multiset functions used in practice, which rely on $\textit{neural moments}$ $\unicode{x2014}$ whose injectivity on multisets has not been studied to date. In this paper, we bridge this gap by showing that moments of neural networks do define injective multiset functions, provided that an analytic non-polynomial activation is used. The number of moments required by our theory is optimal essentially up to a multiplicative factor of two. To prove this result, we state and prove a $\textit{finite witness theorem}$, which is of independent interest. As a corollary to our main theorem, we derive new approximation results for functions on multisets and measures, and new separation results for graph neural networks. We also provide two negative results: (1) moments of piecewise-linear neural networks cannot be injective multiset functions; and (2) even when moment-based multiset functions are injective, they can never be bi-Lipschitz.