Alvin Chan

Wen Tao, Jing Tang, Alvin Chan et al.

Molecule generation is key to drug discovery and materials science, enabling the design of novel compounds with specific properties. Large language models (LLMs) can learn to perform a wide range of tasks from just a few examples. However, generating valid molecules using representations like SMILES is challenging for LLMs in few-shot settings. In this work, we explore how LLMs can generate 100% valid molecules. We evaluate whether LLMs can use SELFIES, a representation where every string corresponds to a valid molecule, for valid molecule generation but find that LLMs perform worse with SELFIES than with SMILES. We then examine LLMs' ability to correct invalid SMILES and find their capacity limited. Finally, we introduce SmiSelf, a cross-chemical language framework for invalid SMILES correction. SmiSelf converts invalid SMILES to SELFIES using grammatical rules, leveraging SELFIES' mechanisms to correct the invalid SMILES. Experiments show that SmiSelf ensures 100% validity while preserving molecular characteristics and maintaining or even enhancing performance on other metrics. SmiSelf helps expand LLMs' practical applications in biomedicine and is compatible with all SMILES-based generative models. Code is available at https://github.com/wentao228/SmiSelf.

Wanlong Fang, Tianle Zhang, Alvin Chan

Multimodal learning often relies on aligning representations across modalities to enable effective information integration, an approach traditionally assumed to be universally beneficial. However, prior research has primarily taken an observational approach, examining naturally occurring alignment in multimodal data and exploring its correlation with model performance, without systematically studying the direct effects of explicitly enforced alignment between representations of different modalities. In this work, we investigate how explicit alignment influences both model performance and representation alignment under different modality-specific information structures. Specifically, we introduce a controllable contrastive learning module that enables precise manipulation of alignment strength during training, allowing us to explore when explicit alignment improves or hinders performance. Our results on synthetic and real datasets under different data characteristics show that the impact of explicit alignment on the performance of unimodal models is related to the characteristics of the data: the optimal level of alignment depends on the amount of redundancy between the different modalities. We identify an optimal alignment strength that balances modality-specific signals and shared redundancy in the mixed information distributions. This work provides practical guidance on when and how explicit alignment should be applied to achieve optimal unimodal encoder performance.

Tianle Zhang, Wanlong Fang, Jonathan Woo et al.

The remarkable performance of Large Language Models (LLMs) can be enhanced with test-time computation, which relies on external tools and even other deep learning models. However, existing approaches for integrating non-text modality representations into LLMs typically require additional costly supervised training, restricting on-the-fly adaptation to new domains and modalities. In this work, we explore the feasibility of integrating representations from non-text foundational models (FMs) into text-based LLMs in a training-free manner. We propose In-Context Representation Learning (ICRL) as a proof-of-concept to allow LLMs to adaptively utilize non-text modality representations with few-shot learning. Unlike traditional in-context learning, which incorporates text-label pairs, ICRL replaces text inputs with FM representations, enabling the LLM to perform multi-modal inference without fine-tuning. We evaluate ICRL on a suite of tasks in the molecular domain, investigating three core research questions: (i) how to map FM representations into LLMs in a training-free manner, (ii) what factors influence ICRL performance, and (iii) what mechanisms underlie the effectiveness of ICRL. To the best of our knowledge, ICRL is the first training-free framework for integrating non-text modality representations into text-based LLMs, presenting a promising direction for adaptable, multi-modal generalization.

Bill Tuck Weng Pung, Alvin Chan

The ability to reason with multiple hierarchical structures is an attractive and desirable property of sequential inductive biases for natural language processing. Do the state-of-the-art Transformers and LSTM architectures implicitly encode for these biases? To answer this, we propose ORCHARD, a diagnostic dataset for systematically evaluating hierarchical reasoning in state-of-the-art neural sequence models. While there have been prior evaluation frameworks such as ListOps or Logical Inference, our work presents a novel and more natural setting where our models learn to reason with multiple explicit hierarchical structures instead of only one, i.e., requiring the ability to do both long-term sequence memorizing, relational reasoning while reasoning with hierarchical structure. Consequently, backed by a set of rigorous experiments, we show that (1) Transformer and LSTM models surprisingly fail in systematic generalization, and (2) with increased references between hierarchies, Transformer performs no better than random.

Bill Tuck Weng Pung, Alvin Chan

Inducing latent tree structures from sequential data is an emerging trend in the NLP research landscape today, largely popularized by recent methods such as Gumbel LSTM and Ordered Neurons (ON-LSTM). This paper proposes FASTTREES, a new general purpose neural module for fast sequence encoding. Unlike most previous works that consider recurrence to be necessary for tree induction, our work explores the notion of parallel tree induction, i.e., imbuing our model with hierarchical inductive biases in a parallelizable, non-autoregressive fashion. To this end, our proposed FASTTREES achieves competitive or superior performance to ON-LSTM on four well-established sequence modeling tasks, i.e., language modeling, logical inference, sentiment analysis and natural language inference. Moreover, we show that the FASTTREES module can be applied to enhance Transformer models, achieving performance gains on three sequence transduction tasks (machine translation, subject-verb agreement and mathematical language understanding), paving the way for modular tree induction modules. Overall, we outperform existing state-of-the-art models on logical inference tasks by +4% and mathematical language understanding by +8%.

Alvin Chan, Ali Madani, Ben Krause et al.

Attribute extrapolation in sample generation is challenging for deep neural networks operating beyond the training distribution. We formulate a new task for extrapolation in sequence generation, focusing on natural language and proteins, and propose GENhance, a generative framework that enhances attributes through a learned latent space. Trained on movie reviews and a computed protein stability dataset, GENhance can generate strongly-positive text reviews and highly stable protein sequences without being exposed to similar data during training. We release our benchmark tasks and models to contribute to the study of generative modeling extrapolation and data-driven design in biology and chemistry.

Alvin Chan, Anna Korsakova, Yew-Soon Ong et al.

A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers. Alternative splicing is determined by the gene's primary sequence and other regulatory factors such as RNA-binding protein levels. With these as input, we formulate the prediction of RNA splicing as a regression task and build a new training dataset (CAPD) to benchmark learned models. We propose discrete compositional energy network (DCEN) which leverages the hierarchical relationships between splice sites, junctions and transcripts to approach this task. In the case of alternative splicing prediction, DCEN models mRNA transcript probabilities through its constituent splice junctions' energy values. These transcript probabilities are subsequently mapped to relative abundance values of key nucleotides and trained with ground-truth experimental measurements. Through our experiments on CAPD, we show that DCEN outperforms baselines and ablation variants.

Aston Zhang, Yi Tay, Shuai Zhang et al.

Recent works have demonstrated reasonable success of representation learning in hypercomplex space. Specifically, "fully-connected layers with Quaternions" (4D hypercomplex numbers), which replace real-valued matrix multiplications in fully-connected layers with Hamilton products of Quaternions, both enjoy parameter savings with only 1/4 learnable parameters and achieve comparable performance in various applications. However, one key caveat is that hypercomplex space only exists at very few predefined dimensions (4D, 8D, and 16D). This restricts the flexibility of models that leverage hypercomplex multiplications. To this end, we propose parameterizing hypercomplex multiplications, allowing models to learn multiplication rules from data regardless of whether such rules are predefined. As a result, our method not only subsumes the Hamilton product, but also learns to operate on any arbitrary nD hypercomplex space, providing more architectural flexibility using arbitrarily $1/n$ learnable parameters compared with the fully-connected layer counterpart. Experiments of applications to the LSTM and Transformer models on natural language inference, machine translation, text style transfer, and subject verb agreement demonstrate architectural flexibility and effectiveness of the proposed approach.

Alvin Chan, Yi Tay, Yew-Soon Ong et al.

This paper demonstrates a fatal vulnerability in natural language inference (NLI) and text classification systems. More concretely, we present a 'backdoor poisoning' attack on NLP models. Our poisoning attack utilizes conditional adversarially regularized autoencoder (CARA) to generate poisoned training samples by poison injection in latent space. Just by adding 1% poisoned data, our experiments show that a victim BERT finetuned classifier's predictions can be steered to the poison target class with success rates of >80% when the input hypothesis is injected with the poison signature, demonstrating that NLI and text classification systems face a huge security risk.

Alvin Chan, Martin D. Levine, Mehrsan Javan

We present a deep recurrent convolutional neural network (CNN) approach to solve the problem of hockey player identification in NHL broadcast videos. Player identification is a difficult computer vision problem mainly because of the players' similar appearance, occlusion, and blurry facial and physical features. However, we can observe players' jersey numbers over time by processing variable length image sequences of players (aka 'tracklets'). We propose an end-to-end trainable ResNet+LSTM network, with a residual network (ResNet) base and a long short-term memory (LSTM) layer, to discover spatio-temporal features of jersey numbers over time and learn long-term dependencies. For this work, we created a new hockey player tracklet dataset that contains sequences of hockey player bounding boxes. Additionally, we employ a secondary 1-dimensional convolutional neural network classifier as a late score-level fusion method to classify the output of the ResNet+LSTM network. This achieves an overall player identification accuracy score over 87% on the test split of our new dataset.

Alvin Chan, Yew-Soon Ong, Bill Pung et al.

Pretrained Transformer-based language models (LMs) display remarkable natural language generation capabilities. With their immense potential, controlling text generation of such LMs is getting attention. While there are studies that seek to control high-level attributes (such as sentiment and topic) of generated text, there is still a lack of more precise control over its content at the word- and phrase-level. Here, we propose Content-Conditioner (CoCon) to control an LM's output text with a content input, at a fine-grained level. In our self-supervised approach, the CoCon block learns to help the LM complete a partially-observed text sequence by conditioning with content inputs that are withheld from the LM. Through experiments, we show that CoCon can naturally incorporate target content into generated texts and control high-level text attributes in a zero-shot manner.

Alvin Chan, Yi Tay, Yew Soon Ong et al.

Adversarial examples are crafted with imperceptible perturbations with the intent to fool neural networks. Against such attacks, adversarial training and its variants stand as the strongest defense to date. Previous studies have pointed out that robust models that have undergone adversarial training tend to produce more salient and interpretable Jacobian matrices than their non-robust counterparts. A natural question is whether a model trained with an objective to produce salient Jacobian can result in better robustness. This paper answers this question with affirmative empirical results. We propose Jacobian Adversarially Regularized Networks (JARN) as a method to optimize the saliency of a classifier's Jacobian by adversarially regularizing the model's Jacobian to resemble natural training images. Image classifiers trained with JARN show improved robust accuracy compared to standard models on the MNIST, SVHN and CIFAR-10 datasets, uncovering a new angle to boost robustness without using adversarial training examples.

Alvin Chan, Yi Tay, Yew-Soon Ong

Adversarial perturbations are imperceptible changes to input pixels that can change the prediction of deep learning models. Learned weights of models robust to such perturbations are previously found to be transferable across different tasks but this applies only if the model architecture for the source and target tasks is the same. Input gradients characterize how small changes at each input pixel affect the model output. Using only natural images, we show here that training a student model's input gradients to match those of a robust teacher model can gain robustness close to a strong baseline that is robustly trained from scratch. Through experiments in MNIST, CIFAR-10, CIFAR-100 and Tiny-ImageNet, we show that our proposed method, input gradient adversarial matching, can transfer robustness across different tasks and even across different model architectures. This demonstrates that directly targeting the semantics of input gradients is a feasible way towards adversarial robustness.

Alvin Chan, Yew-Soon Ong

Deep learning models have recently shown to be vulnerable to backdoor poisoning, an insidious attack where the victim model predicts clean images correctly but classifies the same images as the target class when a trigger poison pattern is added. This poison pattern can be embedded in the training dataset by the adversary. Existing defenses are effective under certain conditions such as a small size of the poison pattern, knowledge about the ratio of poisoned training samples or when a validated clean dataset is available. Since a defender may not have such prior knowledge or resources, we propose a defense against backdoor poisoning that is effective even when those prerequisites are not met. It is made up of several parts: one to extract a backdoor poison signal, detect poison target and base classes, and filter out poisoned from clean samples with proven guarantees. The final part of our defense involves retraining the poisoned model on a dataset augmented with the extracted poison signal and corrective relabeling of poisoned samples to neutralize the backdoor. Our approach has shown to be effective in defending against backdoor attacks that use both small and large-sized poison patterns on nine different target-base class pairs from the CIFAR10 dataset.

Alvin Chan, Lei Ma, Felix Juefei-Xu et al.

Deep neural networks (DNN), while becoming the driving force of many novel technology and achieving tremendous success in many cutting-edge applications, are still vulnerable to adversarial attacks. Differentiable neural computer (DNC) is a novel computing machine with DNN as its central controller operating on an external memory module for data processing. The unique architecture of DNC contributes to its state-of-the-art performance in tasks which requires the ability to represent variables and data structure as well as to store data over long timescales. However, there still lacks a comprehensive study on how adversarial examples affect DNC in terms of robustness. In this paper, we propose metamorphic relation based adversarial techniques for a range of tasks described in the natural processing language domain. We show that the near-perfect performance of the DNC in bAbI logical question answering tasks can be degraded by adversarially injected sentences. We further perform in-depth study on the role of DNC's memory size in its robustness and analyze the potential reason causing why DNC fails. Our study demonstrates the current challenges and potential opportunities towards constructing more robust DNCs.