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KnowledgeHub: An end-to-end Tool for Assisted Scientific Discovery

arXiv.org Artificial Intelligence

This paper describes the KnowledgeHub tool, a scientific literature Information Extraction (IE) and Question Answering (QA) pipeline. This is achieved by supporting the ingestion of PDF documents that are converted to text and structured representations. An ontology can then be constructed where a user defines the types of entities and relationships they want to capture. A browser-based annotation tool enables annotating the contents of the PDF documents according to the ontology. Named Entity Recognition (NER) and Relation Classification (RC) models can be trained on the resulting annotations and can be used to annotate the unannotated portion of the documents. A knowledge graph is constructed from these entity and relation triples which can be queried to obtain insights from the data. Furthermore, we integrate a suite of Large Language Models (LLMs) that can be used for QA and summarisation that is grounded in the included documents via a retrieval component. KnowledgeHub is a unique tool that supports annotation, IE and QA, which gives the user full insight into the knowledge discovery pipeline.


Bayesian Networks and Machine Learning for COVID-19 Severity Explanation and Demographic Symptom Classification

arXiv.org Machine Learning

With the prevailing efforts to combat the coronavirus disease 2019 (COVID-19) pandemic, there are still uncertainties that are yet to be discovered about its spread, future impact, and resurgence. In this paper, we present a three-stage data-driven approach to distill the hidden information about COVID-19. The first stage employs a Bayesian network structure learning method to identify the causal relationships among COVID-19 symptoms and their intrinsic demographic variables. As a second stage, the output from the Bayesian network structure learning, serves as a useful guide to train an unsupervised machine learning (ML) algorithm that uncovers the similarities in patients' symptoms through clustering. The final stage then leverages the labels obtained from clustering to train a demographic symptom identification (DSID) model which predicts a patient's symptom class and the corresponding demographic probability distribution. We applied our method on the COVID-19 dataset obtained from the Centers for Disease Control and Prevention (CDC) in the United States. Results from the experiments show a testing accuracy of 99.99%, as against the 41.15% accuracy of a heuristic ML method. This strongly reveals the viability of our Bayesian network and ML approach in understanding the relationship between the virus symptoms, and providing insights on patients' stratification towards reducing the severity of the virus.


DistPred: A Distribution-Free Probabilistic Inference Method for Regression and Forecasting

arXiv.org Machine Learning

Traditional regression and prediction tasks often only provide deterministic point estimates. To estimate the uncertainty or distribution information of the response variable, methods such as Bayesian inference, model ensembling, or MC Dropout are typically used. These methods either assume that the posterior distribution of samples follows a Gaussian process or require thousands of forward passes for sample generation. We propose a novel approach called DistPred for regression and forecasting tasks, which overcomes the limitations of existing methods while remaining simple and powerful. Specifically, we transform proper scoring rules that measure the discrepancy between the predicted distribution and the target distribution into a differentiable discrete form and use it as a loss function to train the model end-to-end. This allows the model to sample numerous samples in a single forward pass to estimate the potential distribution of the response variable. We have compared our method with several existing approaches on multiple datasets and achieved state-of-the-art performance. Additionally, our method significantly improves computational efficiency. For example, compared to state-of-the-art models, DistPred has a 90x faster inference speed. Experimental results can be reproduced through https://github.com/Anoise/DistPred.


Joint Linked Component Analysis for Multiview Data

arXiv.org Machine Learning

Recent technological advances have led to increased availability of multiple sources of highcontent data. In particular, multiview data refers to different types of variables collected from the same set of individuals. One typical example is the Roadmap Epigenomics Project (Kundaje et al., 2015) which integrates information about histone marks, DNA methylation, DNA accessibility and RNA expression to infer high-resolution maps of regulatory elements annotated jointly across a total of 127 reference epigenomes spanning diverse cell and tissue types. Another example is the data used in NCI-DREAM drug sensitivity prediction challenge (Costello et al. (2014)) which contains gene expression (GE), RNA, DNA methylation (MET), copy number variation (CNV), protein abundance (RPPA) and exome sequence (EX) measurements for 53 human breast cancer cell lines. The prevalence of multiview data has motivated research on uncovering associations between different data views.


Sam Bankman-Fried funded a group with racist ties. FTX wants its 5m back

The Guardian

Multiple events hosted at a historic former hotel in Berkeley, California, have brought together people from intellectual movements popular at the highest levels in Silicon Valley while platforming prominent people linked to scientific racism, the Guardian reveals. But because of alleged financial ties between the non-profit that owns the building โ€“ Lightcone Infrastructure (Lightcone) โ€“ and jailed crypto mogul Sam Bankman-Fried, the administrators of FTX, Bankman-Fried's failed crypto exchange, are demanding the return of almost 5m that new court filings allege were used to bankroll the purchase of the property. During the last year, Lightcone and its director, Oliver Habryka, have made the 20m Lighthaven Campus available for conferences and workshops associated with the "longtermism", "rationalism" and "effective altruism" (EA) communities, all of which often see empowering the tech sector, its elites and its beliefs as crucial to human survival in the far future. At these events, movement influencers rub shoulders with startup founders and tech-funded San Francisco politicians โ€“ as well as people linked to eugenics and scientific racism. Since acquiring the Lighthaven property โ€“ formerly the Rose Garden Inn โ€“ in late 2022, Lightcone has transformed it into a walled, surveilled compound without attracting much notice outside the subculture it exists to promote.


Reading, writing and โ€ฆ disinformation: should schoolchildren be taught media literacy like maths?

The Guardian

Beneath an old Queenslander on the south side of the Brisbane River, beside a garage with a hand-painted sign that reads "recording" and above a computer in a cluttered spare room, is a Post-it note. The home โ€“ "not unlike Bluey's" โ€“ belongs to Bryce Corbett and doubles as an unofficial headquarters of the children's news podcast he founded and co-presents, Squiz Kids. Daily episodes tackle a headline story โ€“ like South Australia's proposal to ban children from social media โ€“ covered to inform, but not frighten, kids. The coating: a bit of fun science, pop culture and, of course, animal stories โ€“ the alligator that came to school, the world's funniest crab joke. Corbett's chat, too, is professional yet upbeat.


On Giant's Shoulders: Effortless Weak to Strong by Dynamic Logits Fusion

arXiv.org Artificial Intelligence

Efficient fine-tuning of large language models for task-specific applications is imperative, yet the vast number of parameters in these models makes their training increasingly challenging. Despite numerous proposals for effective methods, a substantial memory overhead remains for gradient computations during updates. \thm{Can we fine-tune a series of task-specific small models and transfer their knowledge directly to a much larger model without additional training?} In this paper, we explore weak-to-strong specialization using logit arithmetic, facilitating a direct answer to this question. Existing weak-to-strong methods often employ a static knowledge transfer ratio and a single small model for transferring complex knowledge, which leads to suboptimal performance. % To address this, To surmount these limitations, we propose a dynamic logit fusion approach that works with a series of task-specific small models, each specialized in a different task. This method adaptively allocates weights among these models at each decoding step, learning the weights through Kullback-Leibler divergence constrained optimization problems. We conduct extensive experiments across various benchmarks in both single-task and multi-task settings, achieving leading results. By transferring expertise from the 7B model to the 13B model, our method closes the performance gap by 96.4\% in single-task scenarios and by 86.3\% in multi-task scenarios compared to full fine-tuning of the 13B model. Notably, we achieve surpassing performance on unseen tasks. Moreover, we further demonstrate that our method can effortlessly integrate in-context learning for single tasks and task arithmetic for multi-task scenarios. (Our implementation is available in https://github.com/Facico/Dynamic-Logit-Fusion.)


Understanding Performance of Long-Document Ranking Models through Comprehensive Evaluation and Leaderboarding

arXiv.org Artificial Intelligence

We evaluated 20+ Transformer models for ranking of long documents (including recent LongP models trained with FlashAttention) and compared them with a simple FirstP baseline, which applies the same model to the truncated input (at most 512 tokens). We used MS MARCO Documents v1 as a primary training set and evaluated both the zero-shot transferred and fine-tuned models. On MS MARCO, TREC DLs, and Robust04 no long-document model outperformed FirstP by more than 5% in NDCG and MRR (when averaged over all test sets). We conjectured this was not due to models' inability to process long context, but due to a positional bias of relevant passages, whose distribution was skewed towards the beginning of documents. We found direct evidence of this bias in some test sets, which motivated us to create MS MARCO FarRelevant (based on MS MARCO Passages) where the relevant passages were not present among the first 512 tokens. Unlike standard collections where we saw both little benefit from incorporating longer contexts and limited variability in model performance (within a few %), experiments on MS MARCO FarRelevant uncovered dramatic differences among models. The FirstP models performed roughly at the random-baseline level in both zero-shot and fine-tuning scenarios. Simple aggregation models including MaxP and PARADE Attention had good zero-shot accuracy, but benefited little from fine-tuning. Most other models had poor zero-shot performance (sometimes at a random baseline level), but outstripped MaxP by as much as 13-28% after fine-tuning. Thus, the positional bias not only diminishes benefits of processing longer document contexts, but also leads to model overfitting to positional bias and performing poorly in a zero-shot setting when the distribution of relevant passages changes substantially. We make our software and data available.


Breaking Boundaries: Investigating the Effects of Model Editing on Cross-linguistic Performance

arXiv.org Artificial Intelligence

The integration of pretrained language models (PLMs) like BERT and GPT has revolutionized NLP, particularly for English, but it has also created linguistic imbalances. This paper strategically identifies the need for linguistic equity by examining several knowledge editing techniques in multilingual contexts. We evaluate the performance of models such as Mistral, TowerInstruct, OpenHathi, Tamil-Llama, and Kan-Llama across languages including English, German, French, Italian, Spanish, Hindi, Tamil, and Kannada. Our research identifies significant discrepancies in normal and merged models concerning cross-lingual consistency. We employ strategies like 'each language for itself' (ELFI) and 'each language for others' (ELFO) to stress-test these models. Our findings demonstrate the potential for LLMs to overcome linguistic barriers, laying the groundwork for future research in achieving linguistic inclusivity in AI technologies.


Video-MME: The First-Ever Comprehensive Evaluation Benchmark of Multi-modal LLMs in Video Analysis

arXiv.org Artificial Intelligence

In the quest for artificial general intelligence, Multi-modal Large Language Models (MLLMs) have emerged as a focal point in recent advancements. However, the predominant focus remains on developing their capabilities in static image understanding. The potential of MLLMs in processing sequential visual data is still insufficiently explored, highlighting the absence of a comprehensive, high-quality assessment of their performance. In this paper, we introduce Video-MME, the first-ever full-spectrum, Multi-Modal Evaluation benchmark of MLLMs in Video analysis. Our work distinguishes from existing benchmarks through four key features: 1) Diversity in video types, spanning 6 primary visual domains with 30 subfields to ensure broad scenario generalizability; 2) Duration in temporal dimension, encompassing both short-, medium-, and long-term videos, ranging from 11 seconds to 1 hour, for robust contextual dynamics; 3) Breadth in data modalities, integrating multi-modal inputs besides video frames, including subtitles and audios, to unveil the all-round capabilities of MLLMs; 4) Quality in annotations, utilizing rigorous manual labeling by expert annotators to facilitate precise and reliable model assessment. 900 videos with a total of 254 hours are manually selected and annotated by repeatedly viewing all the video content, resulting in 2,700 question-answer pairs. With Video-MME, we extensively evaluate various state-of-the-art MLLMs, including GPT-4 series and Gemini 1.5 Pro, as well as open-source image models like InternVL-Chat-V1.5 and video models like LLaVA-NeXT-Video. Our experiments reveal that Gemini 1.5 Pro is the best-performing commercial model, significantly outperforming the open-source models. Our dataset along with these findings underscores the need for further improvements in handling longer sequences and multi-modal data. Project Page: https://video-mme.github.io