DeepNLP/ICLR-2023-Accepted-Papers huggingface dataset:
On Pre-training Language Model for Antibody
Authors: Danqing Wang,Fei YE,Hao Zhou

Antibodies are vital proteins offering robust protection for the human body from pathogens. The development of general protein and antibody-specific pre-trained language models both facilitate antibody prediction tasks. However, there have been limited studies that comprehensively explore the representation capability of distinct pre-trained language models on different antibody tasks. To investigate the problem, we aim to answer several key questions in this paper, such as how pre-trained language models perform in antibody tasks with different specificity and how introducing specific biological mechanisms to the pre-training process can benefit the model. Additionally, we evaluate if the learned antibody pre-trained representations can be applied to real-world antibody problems, like drug discovery and immune process understanding. Previously, no benchmark available largely hindered the study to answer these questions. To aid in our investigation, we provide an AnTibody Understanding Evaluation (ATUE) benchmark. We comprehensively evaluate the performance of protein pre-trained language models by empirical study along with conclusions and new insights. Our ATUE and code are released at https://github.com/dqwang122/EATLM.
Learning to reason over visual objects
Authors: Shanka Subhra Mondal,Taylor Whittington Webb,Jonathan Cohen

A core component of human intelligence is the ability to identify abstract patterns inherent in complex, high-dimensional perceptual data, as exemplified by visual reasoning tasks such as Raven’s Progressive Matrices (RPM). Motivated by the goal of designing AI systems with this capacity, recent work has focused on evaluating whether neural networks can learn to solve RPM-like problems. Previous work has generally found that strong performance on these problems requires the incorporation of inductive biases that are specific to the RPM problem format, raising the question of whether such models might be more broadly useful. Here, we investigated the extent to which a general-purpose mechanism for processing visual scenes in terms of objects might help promote abstract visual reasoning. We found that a simple model, consisting only of an object-centric encoder and a transformer reasoning module, achieved state-of-the-art results on both of two challenging RPM-like benchmarks (PGM and I-RAVEN), as well as a novel benchmark with greater visual complexity (CLEVR-Matrices). These results suggest that an inductive bias for object-centric processing may be a key component of abstract visual reasoning, obviating the need for problem-specific inductive biases.
Imitating Graph-Based Planning with Goal-Conditioned Policies
Authors: Junsu Kim,Younggyo Seo,Sungsoo Ahn,Kyunghwan Son,Jinwoo Shin

Recently, graph-based planning algorithms have gained much attention to solve goal-conditioned reinforcement learning (RL) tasks: they provide a sequence of subgoals to reach the target-goal, and the agents learn to execute subgoal-conditioned policies. However, the sample-efficiency of such RL schemes still remains a challenge, particularly for long-horizon tasks.  To address this issue, we present a simple yet effective self-imitation scheme which distills a subgoal-conditioned policy into the target-goal-conditioned policy. Our intuition here is that to reach a target-goal, an agent should pass through a subgoal, so target-goal- and subgoal- conditioned policies should be similar to each other. We also propose a novel scheme of stochastically skipping executed subgoals in a planned path, which further improves performance. Unlike prior methods that only utilize graph-based planning in an execution phase, our method transfers knowledge from a planner along with a graph into policy learning. We empirically show that our method can significantly boost the sample-efficiency of the existing goal-conditioned RL methods under various long-horizon control tasks.
A theoretical study of inductive biases in contrastive learning
Authors: Jeff Z. HaoChen,Tengyu Ma

Understanding self-supervised learning is important but challenging. Previous theoretical works study the role of pretraining losses, and view neural networks as general black boxes. However, the recent work of [Saunshi et al.] argues that the model architecture --- a component largely ignored by previous works --- also has significant influences on the downstream performance of self-supervised learning. In this work, we provide the first theoretical analysis of self-supervised learning that incorporates the effect of inductive biases originating from the model class. In particular, we focus on contrastive learning --- a popular self-supervised learning method that is widely used in the vision domain. We show that when the model has limited capacity, contrastive representations would recover certain special clustering structures that are compatible with the model architecture, but ignore many other clustering structures in the data distribution. As a result, our theory can capture the more realistic setting where contrastive representations have much lower dimensionality than the number of clusters in the data distribution. We instantiate our theory on several synthetic data distributions, and provide empirical evidence to support the theory.
Combinatorial Pure Exploration of Causal Bandits
Authors: Nuoya Xiong,Wei Chen

The combinatorial pure exploration of causal bandits is the following online learning task: given a causal graph with unknown causal inference distributions, in each round we choose a subset of variables to intervene or do no intervention, and observe the random outcomes of all random variables, with the goal that using as few rounds as possible, we can output an intervention that gives the best (or almost best) expected outcome on the reward variable $Y$ with probability at least $1-\delta$, where $\delta$ is a given confidence level. We provide the first gap-dependent and fully adaptive pure exploration algorithms on two types of causal models --- the binary generalized linear model (BGLM) and general graphs. For BGLM, our algorithm is the first to be designed specifically for this setting and achieves polynomial sample complexity, while all existing algorithms for general graphs have either sample complexity exponential to the graph size or some unreasonable assumptions. For general graphs, our algorithm provides a significant improvement on sample complexity, and it nearly matches the lower bound we prove. Our algorithms achieve such improvement by a novel integration of prior causal bandit algorithms and prior adaptive pure exploration algorithms, the former of which utilize the rich observational feedback in causal bandits but are not adaptive to reward gaps, while the latter of which have the issue in reverse.
Computational Language Acquisition with Theory of Mind
Authors: Andy Liu,Hao Zhu,Emmy Liu,Yonatan Bisk,Graham Neubig

Unlike current state-of-the-art language models, young children actively acquire language through interactions with their surrounding environment and caretakers. One mechanism that has been argued to be critical to language learning is the ability to infer the mental states of other agents in social environments, coined Theory of Mind (ToM) by Premack & Woodruff (1978). Drawing inspiration from the modern operationalized versions of ToM implemented in Rabinowitz et al. (2018) and Zhu et al. (2021), we build language-learning agents equipped with ToM, and measure its effects on the learning process. We model ToM by giving the speaker agent an internal listener model that is trained alongside the speaker and used to rerank potential utterances. We experiment with varying task difficulty, hypothesizing that models will acquire more complex language to adapt to stronger environmental pressures. We find that training speakers with a highly weighted ToM listener component leads to performance gains in our image referential game setting. We also find some evidence that increasing task difficulty in the training process results in more fluent and precise utterances in evaluation. This suggests the potential utility of further incorporating ToM, as well as other insights from child language acquisition, into computational models of language acquisition.
Pareto Invariant Risk Minimization: Towards Mitigating the Optimization Dilemma in Out-of-Distribution Generalization
Authors: Yongqiang Chen,Kaiwen Zhou,Yatao Bian,Binghui Xie,Bingzhe Wu,Yonggang Zhang,MA KAILI,Han Yang,Peilin Zhao,Bo Han,James Cheng

Recently, there has been a growing surge of interest in enabling machine learning systems to generalize well to Out-of-Distribution (OOD) data. Most efforts are devoted to advancing optimization objectives that regularize models to capture the underlying invariance; however, there often are compromises in the optimization process of these OOD objectives: i) Many OOD objectives have to be relaxed as penalty terms of Empirical Risk Minimization (ERM) for the ease of optimization, while the relaxed forms can weaken the robustness of the original objective; ii) The penalty terms also require careful tuning of the penalty weights due to the intrinsic conflicts between ERM and OOD objectives. Consequently, these compromises could easily lead to suboptimal performance of either the ERM or OOD objective. To address these issues, we introduce a multi-objective optimization (MOO) perspective to understand the OOD optimization process, and propose a new optimization scheme called PAreto Invariant Risk Minimization (PAIR). PAIR improves the robustness of OOD objectives by cooperatively optimizing with other OOD objectives, thereby bridging the gaps caused by the relaxations. Then PAIR approaches a Pareto optimal solution that trades off the ERM and OOD objectives properly. Extensive experiments on challenging benchmarks, WILDS, show that PAIR alleviates the compromises and yields top OOD performances.
What Makes Convolutional Models Great on Long Sequence Modeling?
Authors: Yuhong Li,Tianle Cai,Yi Zhang,Deming Chen,Debadeepta Dey

Convolutional models have been widely used in multiple domains. However, most existing models only use local convolution, making the model unable to handle long-range dependencies efficiently. Attention overcomes this problem by aggregating global information based on the pair-wise attention score but also makes the computational complexity quadratic to the sequence length. Recently, Gu et al. proposed a model called S4 inspired by the state space model. S4 can be efficiently implemented as a global convolutional model whose kernel size equals the input sequence length. With Fast Fourier Transform, S4 can model much longer sequences than Transformers and achieve significant gains over SoTA on several long-range tasks. Despite its empirical success, S4 is involved. It requires sophisticated parameterization and initialization schemes that combine the wisdom from several prior works. As a result, S4 is less intuitive and hard to use for researchers with limited prior knowledge. Here we aim to demystify S4 and extract basic principles that contribute to the success of S4 as a global convolutional model. We focus on the structure of the convolution kernel and identify two critical but intuitive principles enjoyed by S4 that are sufficient to make up an effective global convolutional model: 1) The parameterization of the convolutional kernel needs to be efficient in the sense that the number of parameters should scale sub-linearly with sequence length. 2) The kernel needs to satisfy a decaying structure that the weights for convolving with closer neighbors are larger than the more distant ones. Based on the two principles, we propose a simple yet effective convolutional model called Structured Global Convolution (SGConv). SGConv exhibits strong empirical performance over several tasks: 1) With faster speed, SGConv surpasses the previous SoTA on Long Range Arena and Speech Command datasets. 2) When plugging SGConv into standard language and vision models, it shows the potential to improve both efficiency and performance.
Editing models with task arithmetic
Authors: Gabriel Ilharco,Marco Tulio Ribeiro,Mitchell Wortsman,Ludwig Schmidt,Hannaneh Hajishirzi,Ali Farhadi

Changing how pre-trained models behave---e.g., improving their performance on a downstream task or mitigating biases learned during pre-training---is a common practice when developing machine learning systems. In this work, we propose a new paradigm for steering the behavior of neural networks, centered around task vectors. A task vector specifies a direction in the weight space of a pre-trained model, such that movement in that direction improves performance on the task. We build task vectors by subtracting the weights of a pre-trained model from the weights of the same model after fine-tuning on a task. We show that these task vectors can be modified and combined together through arithmetic operations such as negation and addition, and the behavior of the resulting model is steered accordingly. Moreover, task vectors can be added together to improve performance on multiple tasks at once. Finally, when tasks are linked by an analogy relationship of the form ``A is to B as C is to D", combining task vectors from three of the tasks can improve performance on the fourth, even when no data from the fourth task is used for training.
Neural Systematic Binder
Authors: Gautam Singh,Yeongbin Kim,Sungjin Ahn

The key to high-level cognition is believed to be the ability to systematically manipulate and compose knowledge pieces. While token-like structured knowledge representations are naturally provided in text, it is elusive how to obtain them for unstructured modalities such as scene images. In this paper, we propose a neural mechanism called Neural Systematic Binder or SysBinder for constructing a novel structured representation called Block-Slot Representation. In Block-Slot Representation, object-centric representations known as slots are constructed by composing a set of independent factor representations called blocks, to facilitate systematic generalization. SysBinder obtains this structure in an unsupervised way by alternatingly applying two different binding principles: spatial binding for spatial modularity across the full scene and factor binding for factor modularity within an object. SysBinder is a simple, deterministic, and general-purpose layer that can be applied as a drop-in module in any arbitrary neural network and on any modality.  In experiments, we find that SysBinder provides significantly better factor disentanglement within the slots than the conventional object-centric methods, including, for the first time, in visually complex scene images such as CLEVR-Tex. Furthermore, we demonstrate factor-level systematicity in controlled scene generation by decoding unseen factor combinations.
Training-Free Structured Diffusion Guidance for Compositional Text-to-Image Synthesis
Authors: Weixi Feng,Xuehai He,Tsu-Jui Fu,Varun Jampani,Arjun Reddy Akula,Pradyumna Narayana,Sugato Basu,Xin Eric Wang,William Yang Wang

Large-scale diffusion models have achieved state-of-the-art results on text-to-image synthesis (T2I) tasks. Despite their ability to generate high-quality yet creative images, we observe that attribution-binding and compositional capabilities are still considered major challenging issues, especially when involving multiple objects. Attribute-binding requires the model to associate objects with the correct attribute descriptions, and compositional skills require the model to combine and generate multiple concepts into a single image. In this work, we improve these two aspects of T2I models to achieve more accurate image compositions. To do this, we incorporate linguistic structures with the diffusion guidance process based on the controllable properties of manipulating cross-attention layers in diffusion-based T2I models. We observe that keys and values in cross-attention layers have strong semantic meanings associated with object layouts and content. Therefore, by manipulating the cross-attention representations based on linguistic insights, we can better preserve the compositional semantics in the generated image. Built upon Stable Diffusion, a SOTA T2I model, our structured cross-attention design is efficient that requires no additional training samples. We achieve better compositional skills in qualitative and quantitative results, leading to a significant 5-8\% advantage in head-to-head user comparison studies. Lastly, we conduct an in-depth analysis to reveal potential causes of incorrect image compositions and justify the properties of cross-attention layers in the generation process.
Can Agents Run Relay Race with Strangers? Generalization of RL to Out-of-Distribution Trajectories
Authors: Li-Cheng Lan,Huan Zhang,Cho-Jui Hsieh

In this paper, we evaluate and improve the generalization performance for reinforcement learning (RL) agents on the set of ``controllable'' states, where good policies exist on these states to achieve the goal. An RL agent that generally masters a task should reach its goal starting from any controllable state of the environment instead of memorizing a small set of trajectories. To practically evaluate this type of generalization, we propose relay evaluation, which starts the test agent from the middle of other independently well-trained stranger agents' trajectories. With extensive experimental evaluation, we show the prevalence of generalization failure on controllable states from stranger agents. For example, in the Humanoid environment, we observed that a well-trained Proximal Policy Optimization (PPO) agent, with only 3.9\% failure rate during regular testing, failed on 81.6\% of the states generated by well-trained stranger PPO agents. To improve "relay generalization," we propose a novel method called Self-Trajectory Augmentation (STA), which will reset the environment to the agent's old states according to the Q function during training. After applying STA to the Soft Actor Critic's (SAC) training procedure, we reduced the failure rate of SAC under relay-evaluation by more than three times in most settings without impacting agent performance and increasing the needed number of environment interactions. Our code is available at https://github.com/lan-lc/STA.
CktGNN:  Circuit Graph Neural Network for Electronic Design Automation
Authors: Zehao Dong,Weidong Cao,Muhan Zhang,Dacheng Tao,Yixin Chen,Xuan Zhang

The electronic design automation of analog circuits has been a longstanding challenge in the integrated circuit field due to the huge design space and complex design trade-offs among circuit specifications. In the past decades, intensive research efforts have only been paid to automate the transistor sizing with a given circuit topology. By recognizing the graph nature of circuits, this paper presents a Circuit Graph Neural Network (CktGNN) that simultaneously automates the circuit topology generation and device sizing based on the encoder-dependent optimization subroutines. Particularly, CktGNN encodes circuit graphs using a two-level GNN framework (of nested GNN) where circuits are represented as combinations of subgraphs in a known subgraph basis. In this way, it significantly improves efficiency by reducing the number of subgraphs to perform message passing.

Nonetheless, another critical roadblock to advancing learning-assisted circuit design automation is a lack of public benchmarks to perform canonical assessment and reproducible research. To tackle the challenge, we introduce Open Circuit Benchmark (OCB), an open-sourced dataset that contains $10$K distinct operational amplifiers with carefully-extracted circuit specifications from physical implementations. OCB also equips with communicative circuit generation and evaluation capabilities such that it can be used to generalize the applicability of CktGNN to design various analog circuits by efficiently producing corresponding datasets. Experiments on OCB show the extraordinary advantages of CktGNN through representation-based optimization frameworks over other recent powerful GNN baselines and manual design from human experts. Our work paves the way toward a learning-based open-sourced design automation flow for analog circuits.
Specformer: Spectral Graph Neural Networks Meet Transformers
Authors: Deyu Bo,Chuan Shi,Lele Wang,Renjie Liao

Spectral graph neural networks (GNNs) learn graph representations via spectral-domain graph convolutions. However, most existing spectral graph filters are scalar-to-scalar functions, i.e., mapping a single eigenvalue to a single filtered value, thus ignoring the global pattern of the spectrum. Furthermore, these filters are often constructed based on some fixed-order polynomials, which have limited expressiveness and flexibility. To tackle these issues, we introduce Specformer, which effectively encodes the set of all eigenvalues and performs self-attention in the spectral domain, leading to a learnable set-to-set spectral filter. We also design a decoder with learnable bases to enable non-local graph convolution. Importantly, Specformer is equivariant to permutation. By stacking multiple Specformer layers, one can build a powerful spectral GNN. On synthetic datasets, we show that our Specformer can better recover ground-truth spectral filters than other spectral GNNs. Extensive experiments of both node-level and graph-level tasks on real-world graph datasets show that our Specformer outperforms state-of-the-art GNNs and learns meaningful spectrum patterns. Code and data are available at https://github.com/bdy9527/Specformer.
Language Models Are Greedy Reasoners: A Systematic Formal Analysis of Chain-of-Thought
Authors: Abulhair Saparov,He He

Large language models (LLMs) have shown remarkable reasoning capabilities given chain-of-thought prompts (examples with intermediate reasoning steps). Existing benchmarks measure reasoning ability indirectly, by evaluating accuracy on downstream tasks such as mathematical reasoning. However, it is unclear how these models obtain the answers and whether they rely on simple heuristics rather than the generated chain-of-thought. To enable systematic exploration of the reasoning ability of LLMs, we present a new synthetic question-answering dataset called PrOntoQA, where each example is generated from a synthetic world model represented in first-order logic. This allows us to parse the generated chain-of-thought into symbolic proofs for formal analysis. Our analysis on InstructGPT and GPT-3 shows that LLMs are quite capable of making correct individual deduction steps, and so are generally capable of reasoning, even in fictional contexts. However, they have difficulty with proof planning: When multiple valid deduction steps are available, they are not able to systematically explore the different options.
Recursive Time Series Data Augmentation
Authors: Amine Mohamed Aboussalah,Minjae Kwon,Raj G Patel,Cheng Chi,Chi-Guhn Lee

Time series observations can be seen as realizations of an underlying dynamical system governed by rules that we typically do not know. For time series learning tasks we create our model using available data. Training on available realizations, where data is limited, often induces severe over-fitting thereby preventing generalization. To address this issue, we introduce a general recursive framework for time series augmentation, which we call the Recursive Interpolation Method (RIM). New augmented time series are generated using a recursive interpolation function from the original time series for use in training. We perform theoretical analysis to characterize the proposed RIM and to guarantee its performance under certain conditions. We apply RIM to diverse synthetic and real-world time series cases to achieve strong performance over non-augmented data on a variety of learning tasks. Our method is also computationally more efficient and leads to better performance when compared to state of the art time series data augmentation.