Jonas Wallat

Soumyadeep Roy, Jonas Wallat, Sowmya S Sundaram et al. · stanford

Large-scale language models such as DNABert and LOGO aim to learn optimal gene representations and are trained on the entire Human Reference Genome. However, standard tokenization schemes involve a simple sliding window of tokens like k-mers that do not leverage any gene-based semantics and thus may lead to (trivial) masking of easily predictable sequences and subsequently inefficient Masked Language Modeling (MLM) training. Therefore, we propose a novel masking algorithm, GeneMask, for MLM training of gene sequences, where we randomly identify positions in a gene sequence as mask centers and locally select the span around the mask center with the highest Normalized Pointwise Mutual Information (NPMI) to mask. We observe that in the absence of human-understandable semantics in the genomics domain (in contrast, semantic units like words and phrases are inherently available in NLP), GeneMask-based models substantially outperform the SOTA models (DNABert and LOGO) over four benchmark gene sequence classification datasets in five few-shot settings (10 to 1000-shot). More significantly, the GeneMask-based DNABert model is trained for less than one-tenth of the number of epochs of the original SOTA model. We also observe a strong correlation between top-ranked PMI tokens and conserved DNA sequence motifs, which may indicate the incorporation of latent genomic information. The codes (including trained models) and datasets are made publicly available at https://github.com/roysoumya/GeneMask.

Niloy Ganguly, Dren Fazlija, Maryam Badar et al.

State-of-the-art AI models largely lack an understanding of the cause-effect relationship that governs human understanding of the real world. Consequently, these models do not generalize to unseen data, often produce unfair results, and are difficult to interpret. This has led to efforts to improve the trustworthiness aspects of AI models. Recently, causal modeling and inference methods have emerged as powerful tools. This review aims to provide the reader with an overview of causal methods that have been developed to improve the trustworthiness of AI models. We hope that our contribution will motivate future research on causality-based solutions for trustworthy AI.

Jonas Wallat, Tianyi Zhang, Avishek Anand

Language models retain a significant amount of world knowledge from their pre-training stage. This allows knowledgeable models to be applied to knowledge-intensive tasks prevalent in information retrieval, such as ranking or question answering. Understanding how and which factual information is acquired by our models is necessary to build responsible models. However, limited work has been done to understand the effect of pre-training tasks on the amount of knowledge captured and forgotten by language models during pre-training. Building a better understanding of knowledge acquisition is the goal of this paper. Therefore, we utilize a selection of pre-training tasks to infuse knowledge into our model. In the following steps, we test the model's knowledge retention by measuring its ability to answer factual questions. Our experiments show that masking entities and principled masking of correlated spans based on pointwise mutual information lead to more factual knowledge being retained than masking random tokens. Our findings demonstrate that, like the ability to perform a task, the (factual) knowledge acquired from being trained on that task is forgotten when a model is trained to perform another task (catastrophic forgetting) and how to prevent this phenomenon. To foster reproducibility, the code, as well as the data used in this paper, are openly available.

Jonas Wallat, Adam Jatowt, Avishek Anand

Large language models (LLMs) have recently gained significant attention due to their unparalleled ability to perform various natural language processing tasks. These models, benefiting from their advanced natural language understanding capabilities, have demonstrated impressive zero-shot performance. However, the pre-training data utilized in LLMs is often confined to a specific corpus, resulting in inherent freshness and temporal scope limitations. Consequently, this raises concerns regarding the effectiveness of LLMs for tasks involving temporal intents. In this study, we aim to investigate the underlying limitations of general-purpose LLMs when deployed for tasks that require a temporal understanding. We pay particular attention to handling factual temporal knowledge through three popular temporal QA datasets. Specifically, we observe low performance on detailed questions about the past and, surprisingly, for rather new information. In manual and automatic testing, we find multiple temporal errors and characterize the conditions under which QA performance deteriorates. Our analysis contributes to understanding LLM limitations and offers valuable insights into developing future models that can better cater to the demands of temporally-oriented tasks. The code is available\footnote{https://github.com/jwallat/temporalblindspots}.

Jonas Wallat, Abdelrahman Abdallah, Adam Jatowt et al.

Large Language Models (LLMs) encapsulate a surprising amount of factual world knowledge. However, their performance on temporal questions and historical knowledge is limited because they often cannot understand temporal scope and orientation or neglect the temporal aspect altogether. In this study, we aim to measure precisely how robust LLMs are for question answering based on their ability to process temporal information and perform tasks requiring temporal reasoning and temporal factual knowledge. Specifically, we design eight time-sensitive robustness tests for factual information to check the sensitivity of six popular LLMs in the zero-shot setting. Overall, we find LLMs lacking temporal robustness, especially to temporal reformulations and the use of different granularities of temporal references. We show how a selection of these eight tests can be used automatically to judge a model's temporal robustness for user questions on the fly. Finally, we apply the findings of this study to improve the temporal QA performance by up to 55 percent.

Abdelrahman Abdallah, Bhawna Piryani, Jonas Wallat et al.

Temporal awareness is crucial in many information retrieval tasks, particularly in scenarios where the relevance of documents depends on their alignment with the query's temporal context. Traditional approaches such as BM25 and Dense Passage Retrieval (DPR) focus on lexical or semantic similarity but tend to neglect the temporal alignment between queries and documents, which is essential for time-sensitive tasks like temporal question answering (TQA). We propose TempRetriever, a novel extension of DPR that explicitly incorporates temporal information by embedding both the query date and document timestamp into the retrieval process. This allows retrieving passages that are not only contextually relevant but also aligned with the temporal intent of queries. We evaluate TempRetriever on two large-scale datasets ArchivalQA and ChroniclingAmericaQA demonstrating its superiority over baseline retrieval models across multiple metrics. TempRetriever achieves a 6.63\% improvement in Top-1 retrieval accuracy and a 3.79\% improvement in NDCG@10 compared to the standard DPR on ArchivalQA. Similarly, for ChroniclingAmericaQA, TempRetriever exhibits a 9.56\% improvement in Top-1 retrieval accuracy and a 4.68\% improvement in NDCG@10. We also propose a novel, time-based negative sampling strategy which further enhances retrieval performance by addressing temporal misalignment during training. Our results underline the importance of temporal aspects in dense retrieval systems and establish a new benchmark for time-aware passage retrieval.

Jonas Wallat, Maria Heuss, Maarten de Rijke et al.

Retrieving relevant context is a common approach to reduce hallucinations and enhance answer reliability. Explicitly citing source documents allows users to verify generated responses and increases trust. Prior work largely evaluates citation correctness - whether cited documents support the corresponding statements. But citation correctness alone is insufficient. To establish trust in attributed answers, we must examine both citation correctness and citation faithfulness. In this work, we first disentangle the notions of citation correctness and faithfulness, which have been applied inconsistently in previous studies. Faithfulness ensures that the model's reliance on cited documents is genuine, reflecting actual reference use rather than superficial alignment with prior beliefs, which we call post-rationalization. We design an experiment that reveals the prevalent issue of post-rationalization, which undermines reliable attribution and may result in misplaced trust. Our findings suggest that current attributed answers often lack citation faithfulness (up to 57 percent of the citations), highlighting the need to evaluate correctness and faithfulness for trustworthy attribution in language models.

Jonas Wallat, Jaspreet Singh, Avishek Anand

Probing complex language models has recently revealed several insights into linguistic and semantic patterns found in the learned representations. In this article, we probe BERT specifically to understand and measure the relational knowledge it captures in its parametric memory. While probing for linguistic understanding is commonly applied to all layers of BERT as well as fine-tuned models, this has not been done for factual knowledge. We utilize existing knowledge base completion tasks (LAMA) to probe every layer of pre-trained as well as fine-tuned BERT models(ranking, question answering, NER). Our findings show that knowledge is not just contained in BERT's final layers. Intermediate layers contribute a significant amount (17-60%) to the total knowledge found. Probing intermediate layers also reveals how different types of knowledge emerge at varying rates. When BERT is fine-tuned, relational knowledge is forgotten. The extent of forgetting is impacted by the fine-tuning objective and the training data. We found that ranking models forget the least and retain more knowledge in their final layer compared to masked language modeling and question-answering. However, masked language modeling performed the best at acquiring new knowledge from the training data. When it comes to learning facts, we found that capacity and fact density are key factors. We hope this initial work will spur further research into understanding the parametric memory of language models and the effect of training objectives on factual knowledge. The code to repeat the experiments is publicly available on GitHub.

Jonas Wallat, Jaspreet Singh, Avishek Anand

Probing complex language models has recently revealed several insights into linguistic and semantic patterns found in the learned representations. In this paper, we probe BERT specifically to understand and measure the relational knowledge it captures. We utilize knowledge base completion tasks to probe every layer of pre-trained as well as fine-tuned BERT (ranking, question answering, NER). Our findings show that knowledge is not just contained in BERT's final layers. Intermediate layers contribute a significant amount (17-60%) to the total knowledge found. Probing intermediate layers also reveals how different types of knowledge emerge at varying rates. When BERT is fine-tuned, relational knowledge is forgotten but the extent of forgetting is impacted by the fine-tuning objective but not the size of the dataset. We found that ranking models forget the least and retain more knowledge in their final layer. We release our code on github to repeat the experiments.