untangling text data mining
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Untangling Text Data Mining. Marti Hearst UC Berkeley SIMS ACL’99 Plenary Talk June 23, 1999. Outline. Untangling several different fields DM, CL, IA, TDM TDM examples TDM as Exploratory Data Analysis New Problems for Computational Linguistics Our current efforts. - PowerPoint PPT PresentationTRANSCRIPT
Untangling Text Data Mining
Marti Hearst UC Berkeley SIMS
ACL’99 Plenary TalkJune 23, 1999
Outline Untangling several different fields
– DM, CL, IA, TDM TDM examples TDM as Exploratory Data Analysis
– New Problems for Computational Linguistics– Our current efforts
Classifying Application Types
Patterns Non- NovelNuggets
NovelNuggets
Non- textualdata Standard data
miningDatabasequeries ?
Textual dataComputational
linguisticsI nformation
retrievalReal text
data mining
What is Data Mining? (Fayyad & Uthurusamy 96, Fayyad 97)
Fitting models to or determining patterns from very large datasets.
A “regime” which enables people to interact effectively with massive data stores.
Deriving new information from data.
Why Data Mining? Because the data is there. Because
– larger disks– faster cpus– high-powered visualization – networked information
are becoming widely available.
The Knowledge Discovery from Data Process (KDD)
KDD: The non-trivial process of identifying valid, novel, potentially useful, and ultimately understandable patterns in data. (Fayyad, Shapiro, & Smyth, CACM 96)
Note: data mining is just one step in the process
DM Touchstone Applications(CACM 39 (11) Special Issue)
Finding patterns across data sets:– Reports on changes in retail sales
» to improve sales– Patterns of sizes of TV audiences
» for marketing– Patterns in NBA play
» to alter, and so improve, performance – Deviations in standard phone calling
behavior » to detect fraud» for marketing
What is Data Mining?Potential point of confusion:
– The extracting ore from rock metaphor does not really apply to the practice of data mining
– If it did, then standard database queries would fit under the rubric of data mining
– In practice, DM refers to:» finding patterns across large datasets» discovering heretofore unknown information
What is Text Data Mining? Many peoples’ first thought:
– Make it easier to find things on the Web.– But this is information retrieval!
Needles in HaystacksThe emphasis in IR is in finding documents that already contain answers to questions.
Information RetrievalA restricted form of Information Access
The system has available only pre-existing, “canned” text passages.
Its response is limited to selecting from these passages and presenting them to the user.
It must select, say, 10 or 20 passages out of millions.
What is Text Data Mining? The metaphor of extracting ore from
rock:– Does make sense for extracting
documents of interest from a huge pile.
– But does not reflect notions of DM in practice:»finding patterns across large collections»discovering heretofore unknown
information
Real Text DM
What would finding a pattern across a large text collection really look like?
From: “The Internet Diary of the man who cracked the Bible Code” Brendan McKay, Yahoo Internet Life, www.zdnet.com/yil (William Gates, agitator, leader)
Bill Gates + MS-DOS in the Bible!
From: “The Internet Diary of the man who cracked the Bible Code”Brendan McKay, Yahoo Internet Life, www.zdnet.com/yil
Real Text DM The point:
– Discovering heretofore unknown information is not what we usually do with text.
– (If it weren’t known, it could not have been written by someone!)
However:– There is a field whose goal is to learn
about patterns in text for their own sake ...
Computational Linguistics! Goal: automated language understanding
– this isn’t possible– instead, go for subgoals, e.g.,
»word sense disambiguation»phrase recognition»semantic associations
Common current approach:– statistical analyses over very large text
collections
Why CL Isn’t TDM A linguist finds it interesting that
“cloying” co-occurs significantly with “Jar Jar Binks” ...
… But this doesn’t really answer a question relevant to the world outside the text itself.
Why CL Isn’t TDM We need to use the text indirectly
to answer questions about the world
Direct:– Analyze patent text; determine which word
patterns indicate various subject categories. Indirect:
– Analyze patent text; find out whether private or public funding leads to more inventions.
Why CL Isn’t TDM Direct:
– Cluster newswire text; determine which terms are predominant
Indirect:– Analyze newswire text; gather evidence
about which countries/alliances are dominating which financial sectors
Nuggets vs. Patterns TDM: we want to discover new information
… … As opposed to discovering which
statistical patterns characterize occurrence of known information.
Example: WSD– not TDM: computing statistics over a corpus to
determine what patterns characterize Sense S.– TDM: discovering the meaning of a new sense
of a word.
Nuggets vs. Patterns Nugget: a new, heretofore unknown item
of information. Pattern: distributions or rules that
characterize the occurrence (or non-occurrence) of a known item of information.
Application of rules can create nuggets in some circumstances.
Example: Lexicon Augmentation Application of a lexico-syntactic pattern:
NP0 such as NP1, {NP2 …, (and | or) NPi }i >= 1, implies thatforall NPi, i>=1, hyponym(NPi, NP0)
Extracts out a new hypernym:– “Agar is a substance prepared from a
mixture of red algae, such as Gelidium, for laboratory or industrial use.”
– implies hyponym(“Gelidium”, “red algae”) However, this fact was already known to
the author of the text.
The Quandry How do we use text to both
– Find new information not known to the author of the text
– Find information that is not about the text itself
Idea: Exploratory Data Analysis
Use large text collections to gather evidence to support (or refute) hypotheses– Not known to author: links across
many texts– Not self-referential: work within the
domain of discourse
Example: Etiology Given
– medical titles and abstracts– a problem (incurable rare disease)– some medical expertise
find causal links among titles– symptoms– drugs– results
Swanson Example (1991) Problem: Migraine headaches (M)
– stress associated with M– stress leads to loss of magnesium– calcium channel blockers prevent some M– magnesium is a natural calcium channel blocker– spreading cortical depression (SCD) implicated in
M– high levels of magnesium inhibit SCD– M patients have high platelet aggregability– magnesium can suppress platelet aggregability
All extracted from medical journal titles
How to Automate This? Idea: mixed-initiative interaction
– User applies tools to help explore the hypothesis space
– System runs suites of algorithms to help explore the space, suggest directions
Our Proposed Approach Three main parts
– UI for building/using strategies– Backend for interfacing with various
databases and translating different formats
– Content analysis/machine learning for figuring out good hypotheses/throwing out bad ones
How to find functions of genes? Important problem in molecular biology
– Have the genetic sequence– Don’t know what it does– But …
» Know which genes it coexpresses with» Some of these have known function
– So … Infer function based on function of co-expressed genes
» This is new work by Michael Walker and others at Incyte Pharmaceuticals
Make use of the literature Look up what is known about the other
genes. Different articles in different collections Look for commonalities
– Similar topics indicated by Subject Descriptors
– Similar words in titles and abstractsadenocarcinoma, neoplasm, prostate, prostatic
neoplasms, tumor markers, antibodies ...
Developing Strategies Different strategies seem needed for
different situations– First: see what is known about Kallikrein.– 7341 documents. Too many– AND the result with “disease” category
» If result is non-empty, this might be an interesting gene
– Now get 803 documents– AND the result with PSA
» Get 11 documents. Better!
Developing Strategies Look for commalities among these
documents– Manual scan through ~100 category
labels– Would have been better if
»Automatically organized» Intersections of “important” categories
scanned for first
Try a new tack Researcher uses knowledge of field to
realize these are related to prostate cancer and diagnostic tests
New tack: intersect search on all three known genes– Hope they all talk about diagnostics and
prostate cancer– Fortunately, 7 documents returned– Bingo! A relation to regulation of this
cancer
Formulate a Hypothesis Hypothesis: mystery gene has to do
with regulation of expression of genes leading to prostate cancer
New tack: do some lab tests– See if mystery gene is similar in
molecular structure to the others– If so, it might do some of the same
things they do
Strategies again In hindsight, combining all three
genes was a good strategy.– Store this for later
Might not have worked– Need a suite of strategies– Build them up via experience and a
good UI
The System Doing the same query with slightly different
values each time is time-consuming and tedious
Same goes for cutting and pasting results– IR systems don’t support varying queries
like this very well.– Each situation is a bit different
Some automatic processing is needed in the background to eliminate/suggest hypotheses
The UI part Need support for building strategies Mixed-initiative system
– Trade off between user-initiated hypotheses exploration and system-initiated suggestions
Information visualization– Another way to show lots of choices
Candidate Associations
Current Retrieval Results
Suggested Strategies
Summary The future: analyzing what the text
is about– We don’t know how; text is tough!– Idea: bring the user into the loop.– Build up piecewise evidence to
support hypotheses– Make use of partial domain models.
The Truth is Out There!
Summary Text Data Mining:
– Extracting heretofore undiscovered information from large text collections
Information Access TDM– IA: locating already known information that
is currently of interest Finding patterns across text is already
done in CL– Tells us about the behavior of language– Helps build very useful tools!